gebhart/patrepeval huggingface dataset:
Protease Footprinting Analysis of Ternary Complex Formation by Human TFIIA (1997)

Transcription factor (TF) IIA performs two important regulatory functions during RNA polymerase II transcription: it is required for efficient binding of TFIID to a core promoter and it mediates the effects of upstream activators, both through direct interaction with the TATA box binding protein (TBP). To begin studying how TFIIA mediates these effects, we used a highly sensitive protease footprinting methodology to identify surfaces of human TFIIA participating in TFIIA x TBP x TATA ternary complex formation. Chymotrypsin and proteinase K cleavage patterns of TFIIA bearing a 32P-end-labeled gamma subunit revealed that amino acids 59-73 were protected from cleavage both in the context of an immobilized ternary complex and in a binary complex with TBP alone. In contrast, amino acids 341-367 in the beta portion of a 32P-labeled alpha-beta subunit were protected in the ternary but not in the binary complex, implying that those residues interact with promoter DNA. The regions of human TFIIA identified by protease footprinting are homologous to and encompass the yeast TFIIA residues that contact TBP and DNA in the recently solved crystal structure of the yeast ternary complex. The conservation of the regions and residues mediating complex formation implies that yeast and human TFIIA employ the same mechanism to stabilize the binding of TFIID to a core promoter.
Redox behavior of novel nickel and palladium complexes supported by trianionic non-innocent ligand containing β-diketiminate and phenol groups (2015)

A new type of nickel and palladium complexes with non-innocent β-diketiminate ligand having redox active phenol groups, 2,4-di-tert-butyl-6-(((1E,2E)-3-((3,5-di-tert-butyl-2-hydroxyphenyl)amino)-2-nitroallylidene)amino)phenol ( L H 3 , fully protonated form) have been developed, and the structure, physical properties, and reactivity of their one-electron and two-electron oxidized complexes, [M II (L •2- )] and [M II (L - )] + ( M = Ni II or Pd II ) have been examined in detail. The two-electron oxidized forms of both complexes, [M II (L - )] + , exhibited hydrogen atom abstraction ability from 1,4-cyclohexadiene (CHD) comparable to its copper analog [ Cu II ( L - )] + (Dalton Trans. 2013; 42: 2438-2444). The one-electron oxidized form of palladium complex, [ Pd II ( L •2- )], was also found to oxidize CHD, whereas the nickel analog, [ Ni II ( L •2- )], exhibited photo-induced oxidation ability of CHD.
Derzeitiger Stand der Therapie der BPD extrem unreifer Frühgeborener (ELWB) mit systemischen postnatalen Steroiden in Deutschland (2009)

Hintergrund: Wegen Auswirkungen auf die Hirnentwicklung sollen postnatale Steroide zur Behandlung der BPD nur noch bei Lebensgefahr eingesetzt werden. Spätfolgen können abhängig sein von der Art des verwendeten Steroids.
Aperture efficiency improvement of folded reflectarray using rectangle and split‐ring combined element (2018)

In this Letter, the aperture efficiency of a folded reflectarray is improved using a proposed element. This element is designed with a simple structure using a rectangle and split‐ring combined structure to obtain a more accurate reflection phase for the folded reflectarray than that of a conventional element in the millimetre wave frequency. Thus, a high aperture efficiency of 55.04% is obtained at 77 GHz. The element design concept and procedure are presented in detail.
Abstract 105: The nitroso-redox-induced SR Ca 2 + leak is temperature-sensitive: Role of Nitric Oxide Synthase 1 (2013)

Sarcomeric reticulum (SR) Ca 2+ leak contributes to an impaired Ca 2+ cycling and contractile dysfunction of the heart. Leak is thought to be regulated by post-translational modifications of RyR2 associated with nitroso-redox (NO/redox) imbalance. Ca 2+ cycling is affected by both NO signaling and temperature. We hypothesized that NO/redox balance modulates SR Ca 2+ leak in a temperature–dependent manner. We used tetracaine to investigate SR Ca 2+ leak in cardiomyocytes (CMs) using a model of NO/redox imbalance (NOS1 −/− mice) or WT mice. Reactive oxygen species (ROS) were measured by H 2 DCF. The expression of NOS isoforms was assessed by real time PCR. Experiments were carried out at 23°C - 37°C. The SR Ca 2+ leak increased as the temperature decreased from 34°C to 23°C in WT CMs whereas, in NOS1 −/− CMs, the leak suddenly increased when the temperature surpassed 30°C (Fig. A). SR Ca 2+ content in NOS1 −/− CMs was reduced at 37°C compared to 23°C (42.7 mol/L vs. 115.6 mol/L, respectively; p =0.001), whereas it was unaffected in WT CMs. Differences in Ca 2+ leak between WT and NOS1 −/− were magnified according the SR Ca 2+ load increased. Contrarily to WT, there was a trend to rise in ROS production at temperatures over 30°C in NOS1 −/− CMs (Fig. B). There was a linear association between ROS and leak in both strains. The NOS isoforms were unaffected by temperature in WT. Our observations show that Ca 2+ leak increases when the temperature drops below 34°C; however, in the absence of NOS1 activity, the leak rises at temperatures greater than 30°C, and is associated with more ROS production. These results suggest that Ca 2+ leak from the SR is regulated by a temperature-dependent balance between NO and ROS.
Fluorouracil exacerbates alpha-crystallin B chain—mediated cell migration in triple-negative breast cancer cell lines (2023)

Among triple-negative breast cancer (TNBC) subtypes, the basal-like 2 (BL2) subtype shows the lowest survival rate and the highest risk of metastasis after treatment with chemotherapy. Research has shown that αB-crystallin (CRYAB) is more highly expressed in the basal-like subtypes than in the other subtypes and is associated with brain metastasis in TNBC patients. We therefore hypothesized that αB-crystallin is associated with increased cell motility in the BL2 subtype after treatment with chemotherapy. Here, we evaluated the effect of fluorouracil (5-FU), a typical chemotherapy for the treatment of TNBC, on cell motility by utilizing a cell line with high αB-crystallin expression (HCC1806). A wound healing assay revealed that 5-FU significantly increased cell motility in HCC1806 cells, but not in MDA-MB-231 cells, which have low αB-crystallin expression. Also, cell motility was not increased by 5-FU treatment in HCC1806 cells harboring stealth siRNA targeting CRYAB. In addition, the cell motility of MDA-MB-231 cells overexpressing αB-crystallin was significantly higher than that of MDA-MB-231 cells harboring a control vector. Thus, 5-FU increased cell motility in cell lines with high, but not low, αB-crystallin expression. These results suggest that 5-FU-induced cell migration is mediated by αB-crystallin in the BL2 subtype of TNBC.
Penetrating Trauma to the Male External Genitalia (1998)

No AccessJournal of UrologyUrological Survey: Abstracts: Penis, Urethra, Trauma and Fistulas1 Dec 1998Penetrating Trauma to the Male External Genitalia K.J. Cline, J.A. Mata, D.D. Venable, and J.A. Eastham K.J. ClineK.J. Cline More articles by this author , J.A. MataJ.A. Mata More articles by this author , D.D. VenableD.D. Venable More articles by this author , and J.A. EasthamJ.A. Eastham More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(01)62358-9AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Penetrating Trauma to the Male External Genitalia." The Journal of Urology, 160(6 Part 1), p. 2313 Department of Urology, Louisiana State University Medical Center, Shreveport, Louisiana© 1998 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 160Issue 6 Part 1December 1998Page: 2313 Advertisement Copyright & Permissions© 1998 by American Urological Association, Inc.MetricsAuthor Information K.J. Cline More articles by this author J.A. Mata More articles by this author D.D. Venable More articles by this author J.A. Eastham More articles by this author Expand All Advertisement PDF downloadLoading ...
Data from Pathology of Breast and Ovarian Cancers among <i>BRCA1</i> and <i>BRCA2</i> Mutation Carriers: Results from the Consortium of Investigators of Modifiers of <i>BRCA1</i>/<i>2</i> (CIMBA) (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Previously, small studies have found that &lt;i&gt;BRCA1&lt;/i&gt; and &lt;i&gt;BRCA2&lt;/i&gt; breast tumors differ in their pathology. Analysis of larger datasets of mutation carriers should allow further tumor characterization.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; We used data from 4,325 &lt;i&gt;BRCA1&lt;/i&gt; and 2,568 &lt;i&gt;BRCA2&lt;/i&gt; mutation carriers to analyze the pathology of invasive breast, ovarian, and contralateral breast cancers.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; There was strong evidence that the proportion of estrogen receptor (ER)-negative breast tumors decreased with age at diagnosis among &lt;i&gt;BRCA1&lt;/i&gt; (&lt;i&gt;P-&lt;/i&gt;trend = 1.2 × 10&lt;sup&gt;−5&lt;/sup&gt;), but increased with age at diagnosis among &lt;i&gt;BRCA2&lt;/i&gt;, carriers (&lt;i&gt;P-&lt;/i&gt;trend = 6.8 × 10&lt;sup&gt;−6&lt;/sup&gt;). The proportion of triple-negative tumors decreased with age at diagnosis in &lt;i&gt;BRCA1&lt;/i&gt; carriers but increased with age at diagnosis of &lt;i&gt;BRCA2&lt;/i&gt; carriers. In both &lt;i&gt;BRCA1&lt;/i&gt; and &lt;i&gt;BRCA2&lt;/i&gt; carriers, ER-negative tumors were of higher histologic grade than ER-positive tumors (grade 3 vs. grade 1; &lt;i&gt;P&lt;/i&gt; = 1.2 × 10&lt;sup&gt;−13&lt;/sup&gt; for &lt;i&gt;BRCA1&lt;/i&gt; and &lt;i&gt;P&lt;/i&gt; = 0.001 for &lt;i&gt;BRCA2&lt;/i&gt;). ER and progesterone receptor (PR) expression were independently associated with mutation carrier status [ER-positive odds ratio (OR) for &lt;i&gt;BRCA2&lt;/i&gt; = 9.4, 95% CI: 7.0–12.6 and PR-positive OR = 1.7, 95% CI: 1.3–2.3, under joint analysis]. Lobular tumors were more likely to be &lt;i&gt;BRCA2-&lt;/i&gt;related (OR for &lt;i&gt;BRCA2&lt;/i&gt; = 3.3, 95% CI: 2.4–4.4; &lt;i&gt;P&lt;/i&gt; = 4.4 × 10&lt;sup&gt;−14&lt;/sup&gt;), and medullary tumors &lt;i&gt;BRCA1&lt;/i&gt;-related (OR for &lt;i&gt;BRCA2&lt;/i&gt; = 0.25, 95% CI: 0.18–0.35; &lt;i&gt;P&lt;/i&gt; = 2.3 × 10&lt;sup&gt;−15&lt;/sup&gt;). ER-status of the first breast cancer was predictive of ER-status of asynchronous contralateral breast cancer (&lt;i&gt;P&lt;/i&gt; = 0.0004 for &lt;i&gt;BRCA1&lt;/i&gt;; &lt;i&gt;P&lt;/i&gt; = 0.002 for &lt;i&gt;BRCA2&lt;/i&gt;). There were no significant differences in ovarian cancer morphology between &lt;i&gt;BRCA1&lt;/i&gt; and &lt;i&gt;BRCA2&lt;/i&gt; carriers (serous: 67%; mucinous: 1%; endometrioid: 12%; clear-cell: 2%).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions/Impact:&lt;/b&gt; Pathologic characteristics of &lt;i&gt;BRCA1&lt;/i&gt; and &lt;i&gt;BRCA2&lt;/i&gt; tumors may be useful for improving risk-prediction algorithms and informing clinical strategies for screening and prophylaxis. &lt;i&gt;Cancer Epidemiol Biomarkers Prev; 21(1); 134–47. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Performance of widely tunable Yb:YAG microchip lasers (2000)

We developed a tunable intracavity frequency-doubled Yb:YAG microchip laser and applied this tunable green laser to wavelength-multiplexed holographic memory. The tunable Yb:YAG green laser output a maximum power of 520 mW and a tuning range of 22.4 nm with single frequency. Moreover, we improved tuning range of fundamental oscillation and maximum tuning range of 84.5 nm (λ =1024.1~1108.6 nm) was obtained. Additionally, we investigate edge-pumped YbrYAG microchip lasers to achieve high power and brightness laser performances.
Can Program Synthesis be Used to Learn Merge Conflict Resolutions? An Empirical Analysis (2021)

Forking structure is widespread in the open-source repositories and that causes a significant number of merge conflicts. In this paper, we study the problem of textual merge conflicts from the perspective of Microsoft Edge, a large, highly collaborative fork off the main Chromium branch with significant merge conflicts. Broadly, this study is divided into two sections. First, we empirically evaluate textual merge conflicts in Microsoft Edge and classify them based on the type of files, location of conflicts in a file, and the size of conflicts. We found that ~28% of the merge conflicts are 1-2 line changes, and many resolutions have frequent patterns. Second, driven by these findings, we explore Program Synthesis (for the first time) to learn patterns and resolve structural merge conflicts. We propose a novel domain-specific language (DSL) that captures many of the repetitive merge conflict resolution patterns and learn resolution strategies as programs in this DSL from example resolutions. We found that the learned strategies can resolve 11.4% of the conflicts (~41% of 1-2 line changes) that arise in the C++ files with 93.2% accuracy.
Morfessor and Hutmegs : Unsupervised Morpheme Segmentation for Highly-Inflecting and Compounding Languages (2005)

In this work, we announce the Morfessor 1.0 software package, which is a program that takes as input a corpus of raw text and produces a segmentation of the word forms observed in the text. The segmentation obtained often resembles a linguistic morpheme segmentation. In addition, we briefly describe the Hutmegs package, also publicly available for research purposes. Hutmegs contains semi-automatically produced correct, or gold-standard, morpheme segmentations for a large number of Finnish and English word forms. One easy way for the reader to familiarize himself with our work is to test the demonstration program on our Internet site. The demo shows how Morfessor segments words that the user types in.
Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics (2019)

CRISPR-Cas9 is the state-of-the-art technology for editing and manipulating nucleic acids. However, the occurrence of off-target mutations can limit its applicability. Here, all-atom enhanced molecular dynamics (MD) simulations-using Gaussian accelerated MD (GaMD)-are used to decipher the mechanism of off-target binding at the molecular level. GaMD reveals that base pair mismatches in the target DNA at distal sites with respect to the protospacer adjacent motif (PAM) can induce an extended opening of the RNA:DNA heteroduplex, which leads to newly formed interactions between the unwound DNA and the L2 loop of the catalytic HNH domain. These conserved interactions constitute a "lock" effectively decreasing the conformational freedom of the HNH domain and hampering its activation for cleavage. Remarkably, depending on their positions at PAM distal sites, DNA mismatches responsible for off-target cleavages are unable to "lock" the HNH domain, thereby leading to the unselective cleavage of DNA sequences. In consistency with the available experimental data, the ability to "lock" the catalytic HNH domain in an inactive "conformational checkpoint" is shown to be a key determinant in the onset of off-target effects. This mechanistic rationale contributes in clarifying a long lasting open issue in the CRISPR-Cas9 function and poses the foundation for designing novel and more specific Cas9 variants, which could be obtained by magnifying the "locking" interactions between HNH and the target DNA in the presence of any incorrect off-target sequence, thus preventing undesired cleavages.
Surgical approach to piles at risk of severe postoperative pain: tricks and tips. (2017)

Hemorrhoidectomy, LigaSure, Painless procedure.
Optimization of bright, highly flexible, and humidity insensitive porphyrin-based oxygen-sensing materials (2021)

Optimal oxygen-sensing materials have been developed with high brightness, fast response, humidity insensitivity, high photostability, and flexibility, which can serve as good resources for oxygen-sensing devices in medical applications.
Cu(II) carboxylate arene C─H functionalization: Tuning for nonradical pathways (2022)

We report carbon-hydrogen acetoxylation of nondirected arenes benzene and toluene, as well as related functionalization with pivalate and 2-ethylhexanoate ester groups, using simple copper(II) [Cu(II)] salts with over 80% yield. By changing the ratio of benzene and Cu(II) salts, 2.4% conversion of benzene can be reached. Combined experimental and computational studies results indicate that the arene carbon-hydrogen functionalization likely occurs by a nonradical Cu(II)-mediated organometallic pathway. The Cu(II) salts used in the reaction can be isolated, recycled, and reused with little change in reactivity. In addition, the Cu(II) salts can be regenerated in situ using oxygen and, after the removal of the generated water, the arene carbon-hydrogen acetoxylation and related esterification reactions can be continued, which leads to a process that enables recycling of Cu(II).
Maduropeptin, a complex of new macromolecular antitumor antibiotics. (1991)

Maduropeptin, a complex of new macromolecular antitumor antibiotics, is a metabolite of Actinomadura madurae H710-49. The active components maduropeptins A1, A2 and B are acidic chromopeptides with MW of around 22,500 and composed of 14 types of amino acids and an unstable chromophore. The antibiotics are active in vitro against Gram-positive bacteria and highly cytotoxic to tumor cells. They produced significant prolongation of survival time of mice implanted with P388 leukemia and B16 melanoma.
Supplementary Table 2 from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression (2023)

Supplementary Table 2 from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression
Optical transparency of SiO 2 glass in vacuum ultraviolet region and defect formation by F 2 laser (2001)

Vacuum ultraviolet (vuv) absorption edge and defect formation by F<SUB>2</SUB> excimer laser irradiation in synthetic SiO<SUB>2</SUB> glasses, which have no detectable amount of point defects, were found to be controlled by the physical disorder of the network structure. The vuv edge shifts to a long wavelength side with increasing the fraction of 3- or 4-membered ring structures that are composed of strained Si- O-Si bonds. The defect formation by F<SUB>2</SUB> laser irradiation occurs via one-photon absorption processes and the primarily created defects are a pair of E' center and non-bridging oxygen hole center. The ratio of saturated defect concentrations created by the irradiation is close to that of the fraction of 3- or 4-membered ring structures in the network structure. The present results demonstrate that physical disorder primarily controls the transparency in the vuv regime and damage sensitivity to F<SUB>2</SUB> laser pulse.
Rydberg states of DABCO.cntdot.Krn clusters (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRydberg states of DABCO.cntdot.Krn clustersD. Bahatt, U. Even, and A. GedankenCite this: J. Phys. Chem. 1993, 97, 28, 7189–7193Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/j100130a011https://doi.org/10.1021/j100130a011research-articleACS PublicationsRequest reuse permissionsArticle Views43Altmetric-Citations4LEARN 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 Other access options Get e-Alerts
Properdin binding to complement activating surfaces depends on initial C3b deposition (2017)

Two functions have been assigned to properdin; stabilization of the alternative convertase, C3bBb, is well accepted, whereas the role of properdin as pattern recognition molecule is controversial. The presence of nonphysiological aggregates in purified properdin preparations and experimental models that do not allow discrimination between the initial binding of properdin and binding secondary to C3b deposition is a critical factor contributing to this controversy. In previous work, by inhibiting C3, we showed that properdin binding to zymosan and Escherichia coli is not a primary event, but rather is solely dependent on initial C3 deposition. In the present study, we found that properdin in human serum bound dose-dependently to solid-phase myeloperoxidase. This binding was dependent on C3 activation, as demonstrated by the lack of binding in human serum with the C3-inhibitor compstatin Cp40, in C3-depleted human serum, or when purified properdin is applied in buffer. Similarly, binding of properdin to the surface of human umbilical vein endothelial cells or Neisseria meningitidis after incubation with human serum was completely C3-dependent, as detected by flow cytometry. Properdin, which lacks the structural homology shared by other complement pattern recognition molecules and has its major function in stabilizing the C3bBb convertase, was found to bind both exogenous and endogenous molecular patterns in a completely C3-dependent manner. We therefore challenge the view of properdin as a pattern recognition molecule, and argue that the experimental conditions used to test this hypothesis should be carefully considered, with emphasis on controlling initial C3 activation under physiological conditions.
Adaptive neural network identifiers for effective control of turbogenerators in a multimachine power system (2002)

This paper provides a novel method for nonlinear identification of multiple turbogenerators in a five-machine 12-bus power system using continually online trained (COT) artificial neural networks (ANNs). Each turbogenerator in the power system is equipped with all adaptive ANN identifier, which is able to identify/model its particular turbogenerator and rest of the network to which it is connected from moment to moment, based on only local measurements. Each adaptive ANN turbogenerator can be used in the design of a nonlinear controller for each turbogenerator in a multimachine power system. Simulation results for the adaptive ANN identifiers are presented.
Validity and Sensitivity to Change of Patient-Reported Pain and Disability Measures for Elbow Pathologies (2013)

The PREE, the pASES-e, and the DASH have acceptable validity and sensitivity to change. The pASES-e function subscale is the least sensitive to change and is less correlated to other measures.