gebhart/patrepeval huggingface dataset:
DNA synthesis from unbalanced nucleotide pools causes limited DNA damage that triggers ATR-CHK1-dependent p53 activation (2008)

p53-dependent G(1) and G(2) cell cycle checkpoints are activated in response DNA damage that help to maintain genomic stability. p53 also helps to protect cells from damage that occurs during S phase, for example, when the cells are starved for DNA precursors or irradiated with a low dose of UV. p53 is activated in normal cells starved for pyrimidine nucleotides by treatment with N-(phosphonacetyl)-l-aspartate (PALA). The treated cells progress through a first S phase with kinetics similar to those of untreated cells. However, the DNA of the treated cells begins to become damaged rapidly, within 12 h, as revealed by a comet assay, which detects broken DNA, and by staining for phosphorylated histone H2AX, which accumulates at sites of DNA damage. Because the cells survive, the damage must be reversible, suggesting single-strand breaks or gaps as the most likely possibility. The transiently damaged DNA stimulates activation of ATR and CHK1, which in turn catalyze the phosphorylation and accumulation of p53. Although PALA-induced DNA damage occurs only in dividing cells, the p53 that is activated is only competent to transcribe genes such as p21 and macrophage inhibitory cytokine 1 (whose products regulate G(2) and G(1) or S phase checkpoints, respectively) after the cells have exited the S phase during which damage occurs. We propose that p53 is activated by stimulation of mismatch repair in response to the misincorporation of deoxynucleotides into newly synthesized DNA, long before the lack of pyrimidine nucleoside triphosphates causes the rate of DNA synthesis to slow appreciably.
Identification and expression of mammalian long‐chain PUFA elongation enzymes (2002)

In mammalian cells, Sprecher has proposed that the synthesis of long-chain PUFA from the 20-carbon substrates involves two consecutive elongation steps, a delta6-desaturation step followed by retroconversion (Sprecher, H., Biochim. Biophys. Acta 1486, 219-231, 2000). We searched the database using the translated sequence of human elongase ELOVL5, whose encoded enzyme elongates monounsaturated and polyunsaturated FA, as a query to identify the enzyme(s) involved in elongation of very long chain PUFA. The database search led to the isolation of two cDNA clones from human and mouse. These clones displayed deduced amino acid sequences that had 56.4 and 58% identity, respectively, to that of ELOVL5. The open reading frame of the human clone (ELOVL2) encodes a 296-amino acid peptide, whereas the mouse clone (Elovl2) encodes a 292-amino acid peptide. Expression of these open reading frames in baker's yeast, Saccharomyces cerevisiae, demonstrated that the encoded proteins were involved in the elongation of both 20- and 22-carbon long-chain PUFA, as determined by the conversion of 20:4n-6 to 22:4n-6, 22:4n-6 to 24:4n-6, 20:5n-3 to 22:5n-3, and 22:5n-3 to 24:5n-3. The elongation activity of the mouse Elovl2 was further demonstrated in the transformed mouse L cells incubated with long-chain (C20- and C22-carbon) n-6 and n-3 PUFA substrates by the significant increase in the levels of 24:4n-6 and 24:5n-3, respectively. This report demonstrates the isolation and identification of two mammalian genes that encode very long chain PUFA specific elongation enzymes in the Sprecher pathway for DHA synthesis.
Target-seeking antifibrotic compound enhances wound healing and suppresses scar formation in mice (2010)

Permanent scars form upon healing of tissue injuries such as those caused by ischemia (myocardial infarction, stroke), trauma, surgery, and inflammation. Current options in reducing scar formation are limited to local intervention. We have designed a systemically administered, target-seeking biotherapeutic for scar prevention. It consists of a vascular targeting peptide that specifically recognizes angiogenic blood vessels and extravasates into sites of injury, fused with a therapeutic molecule, decorin. Decorin prevents tissue fibrosis and promotes tissue regeneration by inhibiting TGF-β activity and by other regulatory activities. The decorin-targeting peptide fusion protein had substantially increased neutralizing activity against TGF-β1 in vitro compared with untargeted decorin. In vivo, the fusion protein selectively accumulated in wounds, and promoted wound healing and suppressed scar formation at doses where nontargeted decorin was inactive. These results show that selective targeting yields a tissue-healing and scar-reducing compound with enhanced specificity and potency. This approach may help make reducing scar formation by systemic drug delivery a feasible option for surgery and for the treatment of pathological processes in which scar formation is a problem.
Silicon molecular beam epitaxy (1985)

Many works are now conducted in the worldwide scale on silicon molecular beam epitaxy (Si MBE) including homoepitaxy, doping, heteroepitaxy such as silicon/insulator, silicon/other semiconductor, and silicon/metal (silicide), and poly-Si deposition. As for device applications, work is now moving from conventional discrete devices to integrated circuits and structures unique to Si MBE. In this paper, various aspects of Si MBE are reviewed.
Significance of blood vessel leakiness in cancer. (2002)

Despite major advances in the field of tumor angiogenesis, relatively little attention has been paid to the permeability of blood vessels in tumors. The leakiness of tumor vessels is well documented in experimental tumor models and in human cancer, but the mechanism is poorly understood, as are the implications to the rate of cancer growth, predisposition to metastasis, and delivery of macromolecular therapeutics to tumor cells. Sixteen experts in the fields of cancer biology and vascular biology gathered at the William Guy Forbeck "Focus on the Future" Conference to discuss this topic. The meeting was the first of its kind focused on the significance of blood vessel leakiness in tumors. The participants discussed the cellular basis of tumor vessel leakiness, endothelial barrier function of blood vessels, monitoring tumor vessel leakiness, mediators of endothelial leakiness, consequences of tumor vessel leakiness, genomic analysis of vascular targets, targeting drugs to tumor vessels, and therapeutic manipulation of tumor vessels. The group concluded that a more complete understanding of the basic biology of tumor vessels will be necessary to fully appreciate the consequences of vessel leakiness in cancer. New research tools such as intravital measurements of tumor blood flow and vessel leakiness, in vivo phage display, magnetic resonance imaging, and use of selective angiogenesis inhibitors will contribute to this understanding.
Outbreaks of human infection caused by pyogenic streptococci of Lancefield groups C and G (1989)

Within a collection of 749 strains of group C streptococci (Streptococcus equisimilis) and 2348 of group G, isolated over a period of 6 years, there were clusters from 63 probable outbreaks of infection. These occurred in burns and maternity units, hospital wards, outpatient clinics, army camps and religious communities. Overall, it was possible to identify T-protein antigens in 88% of the group C strains and in 82% of group G. Serotyping by the identification of T-protein antigens was a useful method for the subdivision of these strains.
Association of the tyrosine kinase LCK with phospholipase C-gamma 1 after stimulation of the T cell antigen receptor. (1992)

Stimulation of the T cell antigen receptor (TCR) activates a protein tyrosine kinase and leads to the tyrosine phosphorylation of phosphoinositide-specific phospholipase C-gamma 1 (PLC gamma 1). The molecular interactions involved in this phosphorylation are not known. After stimulation of the TCR on Jurkat T cells, tyrosine-phosphorylated proteins of 36, 38, 58, and 63 kD coprecipitate with PLC gamma 1. An identical pattern of proteins precipitate with TrpE fusion proteins that contain the Src homology (SH) 2 domains of PLC gamma 1, indicating that these regions of PLC gamma 1 are responsible for binding. TCR stimulation leads to an association between the SH2 domains of PLC gamma 1 and a protein tyrosine kinase, which, by peptide mapping, is identical to p56lck. These studies establish that p56lck associates with PLC gamma 1 as a result of TCR stimulation of Jurkat cells, suggesting that p56lck plays a central role in coupling the TCR to the activation of PLC gamma 1.
Serotypes of beta-hemolytic Treponema hyodysenteriae (1979)

Cultures form 13 isolates of pathogenic, beta-hemolytic Treponema hyodysenteriae from 11 geographically separate outbreaks and 2 experimentally induced cases of swine dysentery were lyophilized and extracted with hot phenol-water. The resulting water phases were examined serologically with antisera produced in rabbits against whole-cell bacterins of the 13 isolates for evidence of antigenic classes within the species. Water-phase antigens gave precipitin reactions with homologous antisera. Results from cross-testing of each water phase with each antiserum showed four serologically distinct groups among the isolants examined. Based on precipitin reactions in agarose gel, four serotypes of pathogenic, beta-hemolytic T. hyodysenteriae are proposed.
The hydrolysis of lysophospholipids and nucleotides by autotaxin (NPP2) involves a single catalytic site (2003)

Autotaxin (NPP2) is a tumor cell motility-stimulating factor that displays both a nucleotide pyrophosphatase/phosphodiesterase activity and a recently described lysophospholipase D activity. The hydrolysis of nucleotides is a metal-assisted reaction that occurs via a nucleotidylated threonine in the catalytic site. We show here that the catalytic site threonine and the metal-coordinating residues are also essential for the hydrolysis of lysophospholipids. In comparing the substrate specificity of NPP2 and the closely related NPP1 and NPP3, we found that only NPP2 displayed a lysophospholipase D activity, whereas NPP1 and NPP3 had a much higher nucleotide pyrophosphatase activity.
Landmark-based user location inference in social media (2013)

Location profiles of user accounts in social media can be utilized for various applications, such as disaster warnings and location-aware recommendations. In this paper, we propose a scheme to infer users' home locations in social media. A large portion of existing studies assume that connected users (i.e., friends) in social graphs are located in close proximity. Although this assumption holds for some fraction of connected pairs, sometimes connected pairs live far from each other. To address this issue, we introduce a novel concept of landmarks, which are defined as users with a lot of friends who live in a small region. Landmarks have desirable features to infer users' home locations such as providing strong clues and allowing the locations of numerous users to be inferred using a small number of landmarks. Based on this concept, we propose a landmark mixture model (LMM) to infer users' location. The experimental results using a large-scale Twitter dataset show that our method improves the accuracy of the state-of-the-art method by about 27%.
A high‐fat diet leads to the progression of non‐alcoholic fatty liver disease in obese rats (2004)

Fatty livers of obese fa/fa rats are vulnerable to injury when challenged by insults such as endotoxin, ischemia-reperfusion or acute ethanol treatment. The objective of this study was to evaluate whether a high-fat diet can act as a "second hit" and cause progression to liver injury in obese fa/fa rats compared with lean Fa/? rats. Accordingly, obese fa/fa rats and their lean littermates were fed a diet low in fat (12% of total calories) or a diet with 60% calories as lard for 8 weeks. Hyperglycemia and steatohepatitis occurred in the fa/fa rats fed the high-fat diet. This was accompanied by liver injury as assessed by alanine aminotransferase, hematoxilin and eosin staining, increased TNFalpha and stellate cell-derived TGFbeta, collagen deposition, and up-regulation of alpha-smooth muscle actin. Active MMP13 decreased in fa/fa rats independently of the diet, and TIMP1 expression increased with the high-fat diet, especially in fa/fa rats. Although UCP2 expression was higher in fa/fa rats regardless of the diet, minor changes in ATP levels were observed. Oxidative stress occurred in the fa/fa rats fed the high-fat diet as lipid peroxidation and protein carbonyls were elevated, while glutathione and antioxidant enzymes were very low. Expression and activity of cytochrome P450 2E1 and xanthine oxidase activity were down-regulated in fa/fa compared with Fa/? rats, and no effect was seen by the high-fat diet. However, NADPH oxidase activity increased 2.5-fold in fa/fa rats fed with the high-fat diet. In summary, a high-fat diet induces liver injury in fa/fa rats leading to periportal fibrosis. A role for oxidative stress is suggested via increased NADPH oxidase activity, lipid peroxidation, protein carbonyl formation, and low antioxidant defense.
Synthesis of 6,7-dialkoxy-2-arylmethylidene-2,3- dihydrobenzo[4,5]imidazo[2,1-b][1,3]thiazol-3-ones exhibiting anti-inflammatory activity. (2000)

New 6,7-dialkoxy-2-arylmethylidene-2,3- dihydrobenzo[4,5]imidazo[2,1-b][1,3]thiazol-3-ones (3a-h, 4b, c, e, g) were synthesized from 2-(5,6-dialkoxy-1H-benzo[d]imidazol-2-ylsulfanyl)acetic acids (1, 2) and corresponding aromatic aldehydes in acetic anhydride. The compounds 3e, f and 4b, g were also synthesized from corresponding aromatic aldehydes and 6,7-dialkoxy-2,3-dihydrobenzo[4,5]imidazo[2,1-b][1,3]thiazol -3-ones (5, 6) obtained by the cyclization of the acids 1 and 2 in acetic anhydride. The synthesized compounds 3a-h and 4b, c, e, g exhibit anti-inflammatory activity.
Wavelet transform domain filters: a spatially selective noise filtration technique (1994)

Wavelet transforms are multiresolution decompositions that can be used to analyze signals and images. They describe a signal by the power at each scale and position. Edges can be located very effectively in the wavelet transform domain. A spatially selective noise filtration technique based on the direct spatial correlation of the wavelet transform at several adjacent scales is introduced. A high correlation is used to infer that there is a significant feature at the position that should be passed through the filter. The authors have tested the technique on simulated signals, phantom images, and real MR images. It is found that the technique can reduce noise contents in signals and images by more than 80% while maintaining at least 80% of the value of the gradient at most edges. The authors did not observe any Gibbs' ringing or significant resolution loss on the filtered images. Artifacts that arose from the filtration are very small and local. The noise filtration technique is quite robust. There are many possible extensions of the technique. The authors see its applications in spatially dependent noise filtration, edge detection and enhancement, image restoration, and motion artifact removal. They have compared the performance of the technique to that of the Weiner filter and found it to be superior.
Radiolabeled Anti-CD20 Monoclonal Antibodies for the Treatment of B-Cell Lymphoma (2002)

Article Tools REVIEW ARTICLE Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.2002.02.126 Journal of Clinical Oncology - published online before print September 21, 2016 PMID: 12177115 Radiolabeled Anti-CD20 Monoclonal Antibodies for the Treatment of B-Cell Lymphoma Robert O. DillmanxRobert O. DillmanSearch for articles by this author Show More From the Hoag Cancer Center, Newport Beach, CA. https://doi.org/10.1200/JCO.2002.02.126 First Page Full Text PDF Figures and Tables © 2002 by American Society of Clinical Oncology
<p>Identification of a Novel MPRIP-ROS1 Fusion and Clinical Efficacy of Crizotinib in an Advanced Lung Adenocarcinoma Patient: A Case Report</p> (2020)

The study identified a novel MPRIP-ROS1 fusion that was sensitive to crizotinib, which provided a new driver of lung adenocarcinoma and potential therapeutic target for crizotinib. It also expanded NSCLC treatment of ROS1 rearrangement and highlighted the importance of genetic testing for precise treatment decision-making.
Global Gene Expression Profiling Reveals Widespread yet Distinctive Translational Responses to Different Eukaryotic Translation Initiation Factor 2B-Targeting Stress Pathways (2005)

Global inhibition of protein synthesis is a hallmark of many cellular stress conditions. Even though specific mRNAs defy this (e.g., yeast GCN4 and mammalian ATF4), the extent and variation of such resistance remain uncertain. In this study, we have identified yeast mRNAs that are translationally maintained following either amino acid depletion or fusel alcohol addition. Both stresses inhibit eukaryotic translation initiation factor 2B, but via different mechanisms. Using microarray analysis of polysome and monosome mRNA pools, we demonstrate that these stress conditions elicit widespread yet distinct translational reprogramming, identifying a fundamental role for translational control in the adaptation to environmental stress. These studies also highlight the complex interplay that exists between different stages in the gene expression pathway to allow specific preordained programs of proteome remodeling. For example, many ribosome biogenesis genes are coregulated at the transcriptional and translational levels following amino acid starvation. The transcriptional regulation of these genes has recently been connected to the regulation of cellular proliferation, and on the basis of our results, the translational control of these mRNAs should be factored into this equation.
A hybrid surface/image-based approach to facilitate ultrasound/CT registration (2011)

Registration of intra-operative ultrasound with preoperative CT is highly desirable as a navigational aid for surgeons and interventional radiologists. Image-based solutions generally achieve poor results due to substantially different image appearance of ultrasound and CT. A method is presented that uses surface information and tracked ultrasound to improve registration results. Tracked ultrasound is combined with surface and image-based registration techniques to register ultrasound to CT. Surface data is acquired using an optically tracked range sensor, for example time-of-flight camera. Range data is registered to CT using robust point-set registration; this registration provides an approximate transformation from tracker to CT coordinates. The ultrasound probe is also optically tracked. The probe position and surface-based registration provide a first estimate for the position of the ultrasound image in CT coordinates. This estimate is subsequently refined by a final image-based registration stage. Initial tests using Coherent Point Drift algorithm for registering surface data to CT show favorable results. Tests using both simulated and real time-of-flight range data have good convergence over a wide initial translation and rotation misalignment domain. Preliminary testing using time-of-flight surface data suggests that surface to CT registration may be useful as an initial guess enabling later more precise (but less robust) image based methods for registering ultrasound images to CT. We believe this method will enable image-based algorithms to robustly converge to an optimal registration solution.
Utility of Approximate Entropy From Overnight Pulse Oximetry Data in the Diagnosis of the Obstructive Sleep Apnea Syndrome (2006)

Approximate entropy (ApEn) is a family of statistics introduced as a quantification of regularity in time series without any a priori knowledge about the system generating them. The aim of this preliminary study was to assess whether a time series analysis of arterial oxygen saturation (SaO2) signals from overnight pulse oximetry by means of ApEn could yield essential information on the diagnosis of obstructive sleep apnea (OSA) syndrome. We analyzed SaO2 signals from 187 subjects: 111 with a positive diagnosis of OSA and 76 with a negative diagnosis of OSA. We divided our data in a training set (44 patients with OSA Positive and 30 patients with OSA Negative) and a test set (67 patients with OSA Positive and 46 patients with OSA Negative). The training set was used for algorithm development and optimum threshold selection. Results showed that recurrence of apnea events in patients with OSA determined a significant increase in ApEn values. This method was assessed prospectively using the test dataset, where we obtained 82.09% sensitivity and 86.96% specificity. We conclude that ApEn analysis of SaO2 from pulse oximetric recording could be useful in the study of OSA.
Electron transport and visible light absorption in a plasmonic photocatalyst based on strontium niobate (2017)

Semiconductor compounds are widely used for photocatalytic hydrogen production applications, where photogenerated electron-hole pairs are exploited to induce catalysis. Recently, powders of a metallic oxide (Sr<sub>1-x</sub>NbO<sub>3</sub>, 0.03<x<0.20) were reported to show competitive photocatalytic efficiencies under visible light, which was attributed to interband absorption. This discovery expanded the range of materials available for optimized performance as photocatalysts. Here we study epitaxial thin films of SrNbO<sub>3+δ</sub> and find that their bandgaps are ∼4.1 eV. Surprisingly, the carrier density of the conducting phase exceeds 10<sup>22</sup> cm<sup>-3</sup> and the carrier mobility is only 2.47 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup>. Contrary to earlier reports, the visible light absorption at 1.8 eV (∼688 nm) is due to the plasmon resonance, arising from the large carrier density. We propose that the hot electron and hole carriers excited via Landau damping (during the plasmon decay) are responsible for the photocatalytic property of this material under visible light irradiation.
Manipulation of a Nuclear NAD+ Salvage Pathway Delays Aging without Altering Steady-state NAD+ Levels (2002)

Yeast deprived of nutrients exhibit a marked life span extension that requires the activity of the NAD(+)-dependent histone deacetylase, Sir2p. Here we show that increased dosage of NPT1, encoding a nicotinate phosphoribosyltransferase critical for the NAD(+) salvage pathway, increases Sir2-dependent silencing, stabilizes the rDNA locus, and extends yeast replicative life span by up to 60%. Both NPT1 and SIR2 provide resistance against heat shock, demonstrating that these genes act in a more general manner to promote cell survival. We show that Npt1 and a previously uncharacterized salvage pathway enzyme, Nma2, are both concentrated in the nucleus, indicating that a significant amount of NAD(+) is regenerated in this organelle. Additional copies of the salvage pathway genes, PNC1, NMA1, and NMA2, increase telomeric and rDNA silencing, implying that multiple steps affect the rate of the pathway. Although SIR2-dependent processes are enhanced by additional NPT1, steady-state NAD(+) levels and NAD(+)/NADH ratios remain unaltered. This finding suggests that yeast life span extension may be facilitated by an increase in the availability of NAD(+) to Sir2, although not through a simple increase in steady-state levels. We propose a model in which increased flux through the NAD(+) salvage pathway is responsible for the Sir2-dependent extension of life span.