gebhart/patrepeval huggingface dataset:
Impact of a CXCL12/CXCR4 Antagonist in Bleomycin (BLM) Induced Pulmonary Fibrosis and Carbon Tetrachloride (CCl4) Induced Hepatic Fibrosis in Mice (2016)

Modulation of chemokine CXCL12 and its receptor CXCR4 has been implicated in attenuation of bleomycin (BLM)-induced pulmonary fibrosis and carbon tetrachloride (CCl4)-induced hepatic injury. In pulmonary fibrosis, published reports suggest that collagen production in the injured lung is derived from fibrocytes recruited from the circulation in response to release of pulmonary CXCL12. Conversely, in hepatic fibrosis, resident hepatic stellate cells (HSC), the key cell type in progression of fibrosis, upregulate CXCR4 expression in response to activation. Further, CXCL12 induces HSC proliferation and subsequent production of collagen I. In the current study, we evaluated AMD070, an orally bioavailable inhibitor of CXCL12/CXCR4 in alleviating BLM-induced pulmonary and CCl4-induced hepatic fibrosis in mice. Similar to other CXCR4 antagonists, treatment with AMD070 significantly increased leukocyte mobilization. However, in these two models of fibrosis, AMD070 had a negligible impact on extracellular matrix deposition. Interestingly, our results indicated that CXCL12/CXCR4 signaling has a role in improving mortality associated with BLM induced pulmonary injury, likely through dampening an early inflammatory response and/or vascular leakage. Together, these findings indicate that the CXCL12-CXCR4 signaling axis is not an effective target for reducing fibrosis.
The effect of Lasik surgery on myopic anisometropes’ sensory eye dominance (2017)

Lasik is a common surgery for treating anisometropia. In this study, we asked a specific question: what's the effect of Lasik surgery on anisometropes' sensory eye dominance ? Fifteen myopic anisometropes (mean age: 23 ± 6.9 years old; 6 females) participated in our experiment. We quantitatively measured participants' sensory eye dominance before and after the Lasik surgery using a binocular phase combination paradigm. We found no significant change of sensory eye dominance within 16 weeks (measured between 8 to 96 days, for one or two repetitions) after the surgery (t(14) = -1.44, p = 0.17). A further following on eight patients showed that patients' two eyes were much more balanced at 16 weeks or more (measured one or two times between 112 to 408 days) after the surgery (t(7) = -3.79, p = 0.007). Our results suggest that the benefit of Lasik surgery on anisometropes' sensory eye dominance is not immediate, a long-term 'adaptation' period (16 weeks or more) is necessary to enable the surgery to be truly effective.
On Simulation of Simulink Models for Model-Based Design (2007)

To remain competitive and reduce cost, industry increasingly relies on computational models (Mosterman, 2004). Designing computational models and using numerical simulation is an alternative to building hardware prototypes for testing purposes. Computational modeling (Aberg and Gage, 2004; Breunese et al., 1995; Cellier et al., 1996; Culley and Wallace, 1994) has a number of advantages over traditional engineering methods, such as:• Computational models tend to be less expensive to produce and easier to modify. • The ease of modification enables answering “what-if” questions by facilitating rapid exploration ofdesign options, a task that is time consuming and expensive with physical prototypes. Additionally, some experiments require multiple simulations with different parameters which can be performed through Monte Carlo simulations. This is impossible with physical prototypes because these are prohibitively expensive.
N-terminal RASSF family (2011)

Epigenetic inactivation of tumor suppressor genes is a hallmark of cancer development. RASSF1A (Ras Association Domain Family 1 isoform A) tumor suppressor gene is one of the most frequently epigenetically inactivated genes in a wide range of adult and children's cancers and could be a useful molecular marker for cancer diagnosis and prognosis. RASSF1A has been shown to play a role in several biological pathways, including cell cycle control, apoptosis and microtubule dynamics. RASSF2, RASSF4, RASSF5 and RASSF6 are also epigenetically inactivated in cancer but have not been analysed in as wide a range of malignancies as RASSF1A. Recently four new members of the RASSF family were identified these are termed N-Terminal RASSF genes (RASSF7-RASSF10). Molecular and biological analysis of these newer members has just begun. This review highlights what we currently know in respects to structural, functional and molecular properties of the N-Terminal RASSFs.
Nanocomposite Nafion-Silica membranes for direct methanol fuel cells (2005)

Commercially available proton exchange membranes such as Nafion do not meet the requirements for high power density direct methanol fuel cells, partly due to their high methanol permeability. The aim of this work is to develop a new class of high-proton conductivity membranes, with thermal and mechanical stability similar to Nafion and reduced methanol permeability. Nanocomposite membranes were produced by the in-situ sol-gel synthesis of silicon dioxide particles in preformed Nafion membranes. Microstructural modification of Nafion membranes with silica nanoparticles was shown in this work to reduce methanol crossover from 7.48x10-6 cm2s^-1 for pure Nafion® to 2.86 x10-6 cm2s^-1 for nanocomposite nafion membranes (Methanol 50% (v/v) solution, 75 degrees C). Best results were achieved with a silica composition of 2.6% (w/w). We propose that silica inhibits the conduction of methanol through Nafion by blocking sites necessary for methanol diffusion through the polymer electrolyte membrane. Effects of surface chemistry, nanoparticle formation and interactions with Nafion matrix are further addressed.
Tuning the shape of nanoparticles to control their catalytic properties: selective hydrogenation of 1,3-butadiene on Pd/Al2O3 (2008)

Shape-controlled Pd nanoparticles supported on powder alumina are more efficient for selective butadiene hydrogenation to butene when they exhibit high fractions of (111) facets.
Preparation and Characterization of Inclusion Complexes of Biodegradable Amphiphilic Poly(ethylene oxide)−Poly[(R)-3-hydroxybutyrate]−Poly(ethylene oxide) Triblock Copolymers with Cyclodextrins (2003)

Inclusion complexes (ICs) of biodegradable amphiphilic poly(ethylene oxide)−poly[(R)-3-hydroxybutyrate]−poly(ethylene oxide) triblock copolymers with α-cyclodextrin (α-CD) or γ-cyclodextrin (γ-CD) were prepared from aqueous medium. The ICs were characterized by XRD, DSC, 13C CP/MAS NMR, 1H NMR, FTIR, and TGA. The results of XRD and 13C CP/MAS NMR indicated that the ICs formed channel structure, and the α-CD or γ-CD molecules in the ICs adopted a more symmetric conformation compared with their uncomplexed states. As to the triblock copolymers, while the poly(ethylene oxide) blocks were included in the channel structure, the poly[(R)-3-hydroxybutyrate] block was partially threaded by α-CD or γ-CD, which was confirmed by the results of XRD, DSC, 1H NMR, and FTIR. The formation of ICs led to an increase in the thermal stability of both cyclodextrins and the triblock copolymers.
Experimental Study of Confined Turbulent Vortical Flow in a Narrow Annulus (2014)

An experimental study was carried out to investigate the turbulent flow field of confined vortical flow in a narrow annulus. The test section consists of two concentric annuli that are separated by a tube with four equally spaced rectangular apertures. Water is passing from the inner annulus to the outer annulus and the main region of interest is near aforementioned rectangular holes. Flow velocity was measured using a stereoscopic particle image velocimetry (PIV) system. The small size of the outer annulus required development of multiple improvements to the PIV system. Stereoscopic calibration within the curved and narrow annulus required development of a calibration method that ensured accurate alignment of the laser sheet to provide an accurate polynomial mapping of the physical coordinates to the pixel location on the ICCD chips of the cameras. Macro lenses were used to provide the desired field of view. Test section dimensions required accurate vertical repositioning of the cameras and the laser within the measurement plane. This was implemented using a two-axis positioning system. Reflections within the outer annulus required development of a polyurethane based paint that reflected the laser light with a shifted wavelength. The paint survived high shear stresses and pressure gradients during testing. Three dimensional flow field was assembled based on measurements taken, providing insight into the behavior of the flow as it exits the aperture and mixes in the outer annulus. A vortex core was identified. The results of measurements are compared to CFD results and serve as a tool validating the CFD model. Both the CFD and the measured results predict similar trends in flow behavior, showing strong radial and tangential components of velocity at the plane coincident with the edge of the hole.
Supplementary Table S2 from Discovery of Candidate DNA Methylation Cancer Driver Genes (2023)

&lt;p&gt;MethSig DNAme drivers.&lt;/p&gt;
Post-treatment Mortality Among Patients With Tuberculosis: A Prospective Cohort Study of 10 964 Patients in Vietnam (2018)

Patients treated for tuberculosis had a markedly elevated risk of death, particularly in the post-treatment period. Interventions to reduce tuberculosis mortality must enhance the early detection of drug-resistance, improve treatment effectiveness, and address non-communicable diseases.
Bypass of a Nick by the Replisome of Bacteriophage T7 (2011)

DNA polymerase and DNA helicase are essential components of DNA replication. The helicase unwinds duplex DNA to provide single-stranded templates for DNA synthesis by the DNA polymerase. In bacteriophage T7, movement of either the DNA helicase or the DNA polymerase alone terminates upon encountering a nick in duplex DNA. Using a minicircular DNA, we show that the helicase · polymerase complex can bypass a nick, albeit at reduced efficiency of 7%, on the non-template strand to continue rolling circle DNA synthesis. A gap in the non-template strand cannot be bypassed. The efficiency of bypass synthesis depends on the DNA sequence downstream of the nick. A nick on the template strand cannot be bypassed. Addition of T7 single-stranded DNA-binding protein to the complex stimulates nick bypass 2-fold. We propose that the association of helicase with the polymerase prevents dissociation of the helicase upon encountering a nick, allowing the helicase to continue unwinding of the duplex downstream of the nick.
Supplementary Figure from Comprehensive Serum Proteome Profiling of Cytokine Release Syndrome and Immune Effector Cell–Associated Neurotoxicity Syndrome Patients with B-Cell ALL Receiving CAR T19 (2023)

Supplementary Figure from Comprehensive Serum Proteome Profiling of Cytokine Release Syndrome and Immune Effector Cell–Associated Neurotoxicity Syndrome Patients with B-Cell ALL Receiving CAR T19
Inactive matriptase-2 mutants found in IRIDA patients still repress hepcidin in a transfection assay despite having lost their serine protease activity (2012)

Mutations of the TMPRSS6 gene, which encodes Matriptase-2, are responsible for iron-refractory iron-deficiency anemia. Matriptase-2 is a transmembrane protease that downregulates hepcidin expression. We report one frameshift (p.Ala605ProfsX8) and four novel missense mutations (p.Glu114Lys, p.Leu235Pro, p.Tyr418Cys, p.Pro765Ala) found in IRIDA patients. These mutations lead to changes in both the catalytic and noncatalytic domains of Matriptase-2. Analyses of the mutant proteins revealed a reduction of autoactivating cleavage and the loss of N-Boc-Gln-Ala-Arg-p-nitroanilide hydrolysis. This resulted either from a direct modification of the active site or from the lack of the autocatalytic cleavage that transforms the zymogen into an active protease. In a previously described transfection assay measuring the ability of Matriptase-2 to repress the hepcidin gene (HAMP) promoter, all mutants retained some, if not all, of their transcriptional repression activity. This suggests that caution is called for in interpreting the repression assay in assessing the functional relevance of Matriptase-2 substitutions. We propose that Matriptase-2 activity should be measured directly in the cell medium of transfected cells using the chromogenic substrate. This simple test can be used to determine whether a sequence variation leading to an amino acid substitution is functionally relevant or not.
Publishing Translational Research of Nanomedicine in ACS Nano (2022)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTPublishing Translational Research of Nanomedicine in ACS NanoTony HuTony HuMore by Tony Huhttps://orcid.org/0000-0002-5166-4937, C. Jeffrey BrinkerC. Jeffrey BrinkerMore by C. Jeffrey Brinkerhttps://orcid.org/0000-0002-7145-9324, Warren C. W. ChanWarren C. W. ChanMore by Warren C. W. Chanhttps://orcid.org/0000-0001-5435-4785, Chunying ChenChunying ChenMore by Chunying Chenhttps://orcid.org/0000-0002-6027-0315, Xiaodong ChenXiaodong ChenMore by Xiaodong Chenhttps://orcid.org/0000-0002-3312-1664, Dean HoDean HoMore by Dean Ho, Kazunori KataokaKazunori KataokaMore by Kazunori Kataokahttps://orcid.org/0000-0002-8591-413X, Nicholas A. KotovNicholas A. KotovMore by Nicholas A. Kotovhttps://orcid.org/0000-0002-6864-5804, Luis M. Liz-MarzánLuis M. Liz-MarzánMore by Luis M. Liz-Marzánhttps://orcid.org/0000-0002-6647-1353, Andre E. NelAndre E. NelMore by Andre E. Nelhttps://orcid.org/0000-0002-5232-4686, Wolfgang J. ParakWolfgang J. ParakMore by Wolfgang J. Parakhttps://orcid.org/0000-0003-1672-6650, and Molly StevensMolly StevensMore by Molly Stevenshttps://orcid.org/0000-0002-7335-266XCite this: ACS Nano 2022, 16, 11, 17479–17481Publication Date (Web):November 22, 2022Publication History Published online22 November 2022Published inissue 22 November 2022https://pubs.acs.org/doi/10.1021/acsnano.2c10967https://doi.org/10.1021/acsnano.2c10967editorialACS PublicationsCopyright © 2022 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views4322Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (981 KB) Get e-AlertscloseSUBJECTS:Assays,Cancer,Diagnostic imaging,Nanomaterials,Nanotechnology Get e-Alerts
Nucleotide sequence and characteristics of the gene for l‐lactate dehydrogenase of Thermus caldophilus GK24 and the deduced amino‐acid sequence of the enzyme (1986)

The gene for L-lactate dehydrogenase (LDH) (EC 1.1.1.27) of Thermus caldophilus GK24 was cloned in Escherichia coli using synthetic oligonucleotides as hybridization probes. The nucleotide sequence of the cloned DNA was determined. The primary structure of the LDH was deduced from the nucleotide sequence. The deduced amino acid sequence agreed with the NH2-terminal and COOH-terminal sequences previously reported and the determined amino acid sequences of the peptides obtained from trypsin-digested T. caldophilus LDH. The LDH comprised 310 amino acid residues and its molecular mass was determined to be 32,808. On alignment of the whole amino acid sequences, the T. caldophilus LDH showed about 40% identity with the Bacillus stearothermophilus, Lactobacillus casei and dogfish muscle LDHs. The T. caldophilus LDH gene was expressed with the E. coli lac promoter in E. coli, which resulted in the production of the thermophilic LDH. The gene for the T. caldophilus LDH showed more than 40% identity with those for the human and mouse muscle LDHs on alignment of the whole nucleotide sequences. The G + C content of the coding region for the T. caldophilus LDH was 74.1%, which was higher than that of the chromosomal DNA (67.2%). The G + C contents in the first, second and third positions of the codons used were 77.7%, 48.1% and 95.5% respectively. The high G + C content in the third base caused extremely non-random codon usage in the LDH gene. About half (48.7%) the codons in the LDH gene started with G, and hence there were relatively high contents of Val, Ala, Glu and Gly in the LDH. The contents of Pro, Arg, Ala and Gly, which have high G + C contents in their codons, were also high. Rare codons with U or A as the third base were sometimes used to avoid the TCGA sequence, the recognition site for the restriction endonuclease, TaqI. Two TCGA sequences were found only in the sequence of CTCGAG (XhoI site) in the sequenced region of the T. caldophilus DNA. There were three segments with similar sequences in the two 5' non-coding regions, probably the promoter and ribosome-binding regions, of the genes for the T. caldophilus LDH and the Thermus thermophilus 3-isopropylmalate dehydrogenase.
Stimulation of the left ventricle through the coronary sinus with a newly developed ‘over the wire’ lead system — early experiences with lead handling and positioning (2001)

The new 'over the wire' lead and guiding catheter system allows uncomplicated access to the coronary sinus and the depth of the coronary vein tributaries. Left ventricular sensing and pacing thresholds are acceptable for chronic use in implanted cardiac rhythm management systems.
Open channel deterministic lateral displacement for particle and cell sorting (2017)

We present the use of capillary driven flow over patterned surfaces to achieve cheap and simple, but powerful separation of biologically relevant particle systems. The wide use of microfluidics is often hampered by the propensity for devices to clog due to the small channel sizes and the inability to access the interior of devices for cleaning. Often the devices can only be used for a limited duration and most frequently only once. In addition the cost and power requirements of flow control equipment limits the wider spread of the devices. We address these issues by presenting a simple particle- and cell-sorting scheme based on controlled fluid flow on a patterned surface. The open architecture makes it highly robust and easy to use. If clogging occurs it is straightforward to rinse the device and reuse it. Instead of external mechanical pumps, paper is used as a capillary pump. The different fractions are deposited in the paper and can subsequently be handled independently by simply cutting the paper for downstream processing and analyses. The sorting, based on deterministic lateral displacement, performs equivalently well in comparison with standard covered devices. We demonstrate successful separation of cancer cells and parasites from blood with good viability and with relevance for diagnostics and sample preparation. Sorting a mixture of soil and blood, we show the potential for forensic applications.
Prion protein preamyloid and amyloid deposits in Gerstmann-Sträussler-Scheinker disease, Indiana kindred. (1992)

Gerstmann-Sträussler-Scheinker disease (GSS) is a familial neurological disorder pathologically characterized by amyloid deposition in the cerebrum and cerebellum. In GSS, the amyloid is immunoreactive to antisera raised against the prion protein (PrP) 27-30, a proteinase K-resistant peptide of 27-30 kDa that is derived by limited proteolysis from an abnormal isoform of a neuronal sialoglycoprotein of 33-35 kDa designated PrPSc. Polyclonal antibodies raised against synthetic peptides homologous to residues 15-40 (P2), 90-102 (P1), and 220-232 (P3) of the amino acid sequence deduced from hamster PrP cDNA were used to investigate immunohistochemically the distribution of PrP and PrP fragments in the brains of two patients from the Indiana kindred of GSS. Two types of anti-PrP-immunoreactive deposits were found: (i) amyloid deposits, which were exclusively labeled by anti-P1 antiserum to residues 90-102 of PrP, and (ii) preamyloid deposits, which were labeled by all anti-PrP antisera but did not exhibit the tinctorial and optical properties of amyloid. The latter appeared as diffuse immunostaining of the neuropil that targeted to areas in which amyloid deposits were most abundant. They were partially resistant to proteinase K digestion and consisted ultrastructurally of amorphous, flaky, electron-dense material. These findings substantiate our previous observation that the major amyloid component in the GSS Indiana kindred is an internal fragment of PrP and indicate that full-length abnormal isoforms of PrP and/or large PrP fragments accumulate in brain regions most affected by amyloid deposition. These findings support the view that in the GSS Indiana kindred a stepwise degradation of PrP occurs in situ in the process of amyloid fibril formation.
Thioredoxin expression in primary T-cell acute lymphoblastic leukemia and its therapeutic implication. (2001)

Increased expression of intracellular thioredoxin has been implicated in the inhibition of apoptosis and in a decrease in the sensitivity of the malignancies to drug-induced apoptosis. In the present studies, we analyzed expression of thioredoxin in samples from 28 children with T-cell acute lymphoblastic leukemia and analyzed their sensitivity toward inhibition of thioredoxin expression. Thioredoxin was expressed in variable amounts. Higher expression was associated with higher WBC counts. Exogenously added thioredoxin stimulated proliferation of clonogenic cells among the T-cell acute lymphoblastic leukemia samples expressing relatively lower levels of intracellular thioredoxin, whereas there was no effect on the clonogenic cells expressing high levels of thioredoxin. In addition, there was differential sensitivity of the leukemia clonogenic cells toward 1-methylpropyl 2-imidazolyl disulfide, an inhibitor of thioredoxin expression, as compared with normal hematopoietic progenitors. This suggests the possibility of using this approach for treatment. Because overexpression of thioredoxin is associated with resistance to many anticancer drugs, the inhibition of thioredoxin expression may overcome this drug resistance and probably sensitize leukemia cells to other chemotherapeutic agents.