gebhart/patrepeval huggingface dataset:
A XML-Based Approach to Integrating Heterogeneous Yeast Genome Data. (2004)

Abstract. While there are an increasing number of genomes (including the human genome) whose sequences have been fully or nearly completed, the budding yeast Saccharomyces cerevisiae was the first fully sequenced eukaryotic genome. Given its ease of genetic manipulation and the fact that many of its genes are strikingly similar to human genes, the yeast genome has been studied extensively through a wide range of biological experiments (e.g., microarray experiments). As a result, a large variety of types of yeast genome data have been generated and made accessible through many resources (e.g., SGD, MIPS, and YPD). While these resources serve many specific needs of individual researchers, we can reap more benefits by integrating these disparate datasets to facilitate larger-context data mining. However, such integrated analysis is hampered by the heterogeneous formats that are used for data distribution. With the increasing use of eXtensible Mark Language (XML) in the bioinformatics domain, we demonstrate how to use XML to standardize the exchange of a variety of types of yeast data between different resources. In particular, we propose a standard XML format called “Yeast Hub XML ” (YHX). This format consists of: i) metadata and ii) data. While the former describes the resource and data structure, the latter is used to represent the data. In addition, we apply various XML-related technologies including XPath and XSLT to query, integrate, and transform multiple XML datasets. We have implemented a prototype yeast hub server that allows sharing, querying, and integration of different types and formats of yeast genome data that are located in disparate sources. 1.
Real‐Time Digital Signal Processing (2006)

Preface. Chapter 1. Introduction to Real-Time Digital Signal Processing. Chapter 2. Introduction to TMS320C55x Digital Signal Processor. Chapter 3. DSP Fundamentals and Implementation Considerations. Chapter 4. Design and Implementation of FIR Filters. Chapter 5. Design and Implementation of IIR Filters. Chapter 6. Frequency Analysis and Fast Fourier Transform. Chapter 7. Adaptive Filtering. Chapter 8. Digital Signal Generators. Chapter 9. Dual-Tone Multi-Frequency Detection. Chapter 10. Adaptive Echo Cancellation. Chapter 11. Speech Coding Techniques. Chapter 12. Speech Enhancement Techniques. Chapter 13. Audio Signal Processing. Chapter 14. Channel Coding Techniques. Chapter 15. Introduction to Digital Image Processing. Appendix A: Some Useful Formulas and Definitions. A.1 Trigonometric Identities. A.2 Geometric Series. A.3 Complex Variables. A.4 Units of Power. References. Appendix B: Software Organization and List of Experiments. Index.
<p>Supraspinatus muscle location changes after arthroscopic rotator cuff repair: a potential source of preoperatively predicting tear patterns</p> (2019)

Level IV (case series).
Supplementary Figure 3 from Activation of the <i>NOTCH</i> Pathway in Head and Neck Cancer (2023)

&lt;p&gt;PDF file - 108K, Validation of JAG1, JAG2, NOTCH1 and PSEN1 overexpression in TCGA HNSCC cohort. A, Overexpression of JAG1, JAG2 and NOTCH1 in tumors in comparison to that in normal tissues in the TCGA HNSCC cohort. B, Overexpression of JAG1 and PSEN1 in the tumors with increased copy number gains in comparison to that in the normal tissues as well as to that in the tumors without copy number gains in the TCGA HNSCC cohort. N, normal mucosa; T, HNSCC tumors; -, without JAG1 or PSEN1 copy number gain; +, with JAG1 or PSEN1 copy number gain. Dots, relative expression levels in different tissue samples. Boxes represent the interquartile range (25th-75th percentile) and horizontal lines inside the boxes indicate median. Whiskers indicate the minimum and maximum values. P value was calculated by using t test.&lt;/p&gt;
Benzyne cycloaddition onto carbon nanohorns (2013)

A facile approach for the covalent functionalization of carbon nanohorns (CNHs) based on the benzyne cycloaddition reaction is presented. The benzynes were in situ generated from either anthranilic acid by decomposition of the internal benzenediazonium-2-carboxylate or from 2-(trimethylsilyl)-phenyl triflate by fluoride ion attack at the silicon atom followed by displacement of the trimethylsilyl group under mild conditions. Moreover, the functionalization reaction was tested and performed under conventional conditions as well as under microwave irradiation. Modified CNHs possessing fused rings onto their graphitic skeleton were fully characterized by means of complementary spectroscopic techniques, thermogravimetric analysis, electron microscopy and light scattering. Moreover, Sonogashira coupling with propargyl alcohol followed by condensation with thioctic acid, to the iodo-modified CNHs obtained from the cycloaddition reaction of 2-amino-5-iodobenzoic acid with CNHs, resulted in the preparation of a new CNH-based material in which endocyclic disulfides are extended from the fused rings onto CNHs. The latter moieties were used to immobilize gold nanoparticles, furnishing the CNH-Au(nano) hybrid material, in which the former were identified with the aid of UV-Vis and EDX spectroscopy.
Dynamic Chromatin Localization of Sirt6 Shapes Stress- and Aging-Related Transcriptional Networks (2011)

The sirtuin Sirt6 is a NAD-dependent histone deacetylase that is implicated in gene regulation and lifespan control. Sirt6 can interact with the stress-responsive transcription factor NF-κB and regulate some NF-κB target genes, but the full scope of Sirt6 target genes as well as dynamics of Sirt6 occupancy on chromatin are not known. Here we map Sirt6 occupancy on mouse promoters genome-wide and show that Sirt6 occupancy is highly dynamic in response to TNF-α. More than half of Sirt6 target genes are only revealed upon stress-signaling. The majority of genes bound by NF-κB subunit RelA recruit Sirt6, and dynamic Sirt6 relocalization is largely driven in a RelA-dependent manner. Integrative analysis with global gene expression patterns in wild-type, Sirt6-/-, and double Sirt6-/- RelA-/- cells reveals the epistatic relationships between Sirt6 and RelA in shaping diverse temporal patterns of gene expression. Genes under the direct joint control of Sirt6 and RelA include several with prominent roles in cell senescence and organismal aging. These data suggest dynamic chromatin relocalization of Sirt6 as a key output of NF-κB signaling in stress response and aging.
Dasatinib (SPRYCEL®) in Children and Adolescents with Relapsed or Refractory Leukemia: Preliminary Results of the CA180018 Phase I/II Study. (2006)

Abstract Leukemia is the most common type of cancer in pediatric patients (pts). Treatment options for Philadelphia-chromosome positive (Ph+) acute lymphoblastic leukemia (ALL) and chronic myeloid leukemia (CML) include: risk-adapted chemotherapy, imatinib (im) and stem cell transplant (SCT). Relapsed leukemia has few therapeutic options. Dasatinib (SPRYCEL®, formerly BMS-354825) is a novel, oral, multi-targeted kinase inhibitor of BCR-ABL, KIT, and SRC kinases that was recently granted approval for adults with CML, and Ph+ ALL with resistance or intolerance to prior therapy. CA180018 is the first trial evaluating dasatinib in pediatric patients pts and Ph+ and in Ph- leukemias. CA180018 is a phase I/II dose-finding study of dasatinib in pts aged 1–20 with CML or relapsed Ph+ ALL resistant or intolerant to im, or Ph- ALL or AML in ≥2nd relapse performed in collaboration with 12 centers (6 countries) from the ITCC Consortium. Preliminary data are available on the first 15 pts treated from March-July 2006 (2 chronic phase (CP) CML, 7 Ph+ ALL, 1 accelerated phase (AP) CML, 3 Ph- ALL, and 2 Ph- AML) at a starting dose of 60 mg/m2 daily (course = 3 weeks). Intra-patient dose escalation was allowed for lack of initial response, and a 3+3 design for maximum tolerated dose (MTD) determination. Hematologic, cytogenetic, and molecular responses, as well as plasma and cerebrospinal fluid (CSF) pharmacokinetic (PK) analysis and BCR-ABL mutational analysis are ongoing. Median age was 11 yrs (range 4–17), median time from diagnosis of leukemia was 19.5 months (range 1.4–89.9). Prior therapy included chemotherapy, im, and stem cell transplant. Median duration on study is 0.69 month (range 0.03–3.45). Intra-patient dose escalation to 80 or 100 mg/m2 occurred in 7 pts. Six pts remain on study. There have been 7 responders: 4 complete hematologic responses (CHR): 1 CP CML, 1 AP CML, 2 Ph+ ALL; 5 cytogenetic responses (CyR): 2 Ph+ ALL complete CyR (CCyR), 1 AP CML CCyR, 1 CP CML partial CyR (PCyR), 1 Ph+ ALL minor CyR who never achieved a CHR, and then progressed; and 2 Ph+ ALL pts with CNS disease who cleared the CSF of leukemic blasts with single agent dasatinib. Preliminary PK in 7 pts showed rapid absorption with a median Tmax of 1.0 h, and mean terminal phase half-life (SD) of 2.7 (1.1) h. There is one dose-limiting toxicity (DLT): grade 4 anaphylactic shock which occurred 5 hours after the first dose. Dasatinib has otherwise been well tolerated up to 100 mg/m2 with toxicities including grade 3/4 thrombocytopenia, and sepsis. Nine pts are off study: 8 for progressive disease (2 Ph+ ALL pts with a resistant T315I BCR-ABL mutation), and 1 DLT. These preliminary results provide evidence supporting the safety and efficacy of dasatinib in pediatric pts with relapsed or refractory leukemia. An updated analysis including further enrollment, safety data, PK, cytogenetic and molecular responses, and mutational analyses will be presented.
Development of MIM/Ta2O5capacitor process for 0.10‐µm DRAM (2004)

Abstract As the fabrication dimension becomes smaller, it becomes increasingly difficult to ensure storage capacitance for DRAM. For this reason, a capacitor process using high‐permittivity insulating films is strongly desired. In the research reported here, an MIM/tantalum pentoxide capacitor process is developed with ruthenium as an electrode material. The ruthenium CVD technique, the use of amorphous tantalum nitride as anti‐oxide barrier metal, and a contamination elimination process using periodic acid have been developed. By packaging as 0.13‐µm DRAM, capacitance performance equivalent to silica film is realized with a film thickness of 0.8 nm. The process is considered to be applicable to 0.10‐µm DRAM. © 2004 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 87(2): 26–36, 2004; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecjb.10111
Amino Acid Residues Contributing to the Substrate Specificity of the Influenza A Virus Neuraminidase (1999)

Influenza A viruses possess two glycoprotein spikes on the virion surface: hemagglutinin (HA), which binds to oligosaccharides containing terminal sialic acid, and neuraminidase (NA), which removes terminal sialic acid from oligosaccharides. Hence, the interplay between these receptor-binding and receptor-destroying functions assumes major importance in viral replication. In contrast to the well-characterized role of HA in host range restriction of influenza viruses, there is only limited information on the role of NA substrate specificity in viral replication among different animal species. We therefore investigated the substrate specificities of NA for linkages between N-acetyl sialic acid and galactose (NeuAcalpha2-3Gal and NeuAcalpha2-6Gal) and for different molecular species of sialic acids (N-acetyl and N-glycolyl sialic acids) in influenza A viruses isolated from human, avian, and pig hosts. Substrate specificity assays showed that all viruses had similar specificities for NeuAcalpha2-3Gal, while the activities for NeuAcalpha2-6Gal ranged from marginal, as represented by avian and early N2 human viruses, to high (although only one-third the activity for NeuAcalpha2-3Gal), as represented by swine and more recent N2 human viruses. Using site-specific mutagenesis, we identified in the earliest human virus with a detectable increase in NeuAcalpha2-6Gal specificity a change at position 275 (from isoleucine to valine) that enhanced the specificity for this substrate. Valine at position 275 was maintained in all later human viruses as well as swine viruses. A similar examination of N-glycolylneuraminic acid (NeuGc) specificity showed that avian viruses and most human viruses had low to moderate activity for this substrate, with the exception of most human viruses isolated between 1967 and 1969, whose NeuGc specificity was as high as that of swine viruses. The amino acid at position 431 was found to determine the level of NeuGc specificity of NA: lysine conferred high NeuGc specificity, while proline, glutamine, and glutamic acid were associated with lower NeuGc specificity. Both residues 275 and 431 lie close to the enzymatic active site but are not directly involved in the reaction mechanism. This finding suggests that the adaptation of NA to different substrates occurs by a mechanism of amino acid substitutions that subtly alter the conformation of NA in and around the active site to facilitate the binding of different species of sialic acid.
Solvent Dependence of the 2-Naphthyl(carbomethoxy)carbene Singlet−Triplet Energy Gap (2002)

The solvent dependence of the 2-naphthyl(carbomethoxy)carbene (2) singlet-triplet energy gap has been examined by time-resolved infrared (TRIR) and computational methods. The ground state of 2 changes from the triplet state in hexane to the singlet state in acetonitrile. Preferential stabilization of the singlet carbene is the result of its increased dipole moment in polar solvents. Variable-temperature TRIR experiments provide measurements of the enthalpic and entropic differences between (1)2 and (3)2 and suggest that solvent and geometry effects on the entropy of singlet and triplet carbenes can offset differences arising from spin multiplicity. B3LYP calculations using the polarizable continuum solvation model (PCM) reproduce the general trends in enthalpic differences seen experimentally.
Enucleation of renal cell carcinoma with ablation of the tumour base (2008)

The present series and other available clinical data suggest that enucleation with cavity ablation is an oncologically sound approach that is simple, versatile and obviates the need for renal ischaemia.
Salmonella typhimuriumA1-R Exquisitely Targets and Arrests a Matrix-producing Triple-negative Breast Carcinoma in a PDOX Model (2021)

S. typhimurium A1-R has future clinical potential for triple-negative MPBC patients.
Bismuth‐Catalyzed Growth of SnS2 Nanotubes and Their Stability (2009)

Nanotubes of tin disulfide were fabricated from SnS2 nanoflakes by the vapor–liquid–solid process using bismuth nanodroplets as a catalyst. The SnS2 reagent in the gas phase preferentially adsorbs onto the bismuth particles; upon cooling, nucleation and growth of SnS2 nanotubes occurs (see HRTEM image). Annealing the nanotubes results in the formation of SnS2/SnS superlattices. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
ChemInform Abstract: Carbon‐Carbon Bond‐Forming Reaction Through a η5‐ Pentadienylchromium Complex. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
EPR Spectroscopy of Iron- and Nickel-Doped [ZnAl]-Layered Double Hydroxides: Modeling Active Sites in Heterogeneous Water Oxidation Catalysts (2019)

Iron-doped nickel layered double hydroxides (LDHs) are among the most active heterogeneous water oxidation catalysts. Due to interspin interactions, however, the high density of magnetic centers results in line-broadening in magnetic resonance spectra. As a result, gaining atomic-level insight into the catalytic mechanism via electron paramagnetic resonance (EPR) is not generally possible. To circumvent spin-spin broadening, iron and nickel atoms were doped into nonmagnetic [ZnAl]-LDH materials and the coordination environments of the isolated Fe(III) and Ni(II) sites were characterized. Multifrequency EPR spectroscopy identified two distinct Fe(III) sites (<i>S</i> = 5/2) in [Fe:ZnAl]-LDH. Changes in zero field splitting (ZFS) were induced by dehydration of the material, revealing that one of the Fe(III) sites was solvent-exposed (i.e., at an edge, corner, or defect site). These solvent-exposed sites featured an axial ZFS of 0.21 cm<sup>-1</sup> when hydrated. The ZFS increased dramatically upon dehydration (to -1.5 cm<sup>-1</sup>), owing to lower symmetry and a decrease in the coordination number of iron. The ZFS of the other ("inert") Fe(III) site maintained an axial ZFS of 0.19-0.20 cm<sup>-1</sup> under both hydrated and dehydrated conditions. We observed a similar effect in [Ni:ZnAl]-LDH materials; notably, Ni(II) (<i>S</i> = 1) atoms displayed a single, small ZFS (±0.30 cm<sup>-1</sup>) in hydrated material, whereas two distinct Ni(II) ZFS values (±0.30 and ±1.1 cm<sup>-1</sup>) were observed in the dehydrated samples. Although the magnetically dilute materials were not active catalysts, the identification of model sites in which the coordination environments of iron and nickel were particularly labile (e.g., by simple vacuum drying) is an important step toward identifying sites in which the coordination number may drop spontaneously in water, a probable mechanism of water oxidation in functional materials.
A Linguistic Approach to Categorical Color Assignment for Data Visualization (2015)

When data categories have strong color associations, it is useful to use these semantically meaningful concept-color associations in data visualizations. In this paper, we explore how linguistic information about the terms defining the data can be used to generate semantically meaningful colors. To do this effectively, we need first to establish that a term has a strong semantic color association, then discover which color or colors express it. Using co-occurrence measures of color name frequencies from Google n-grams, we define a measure for colorability that describes how strongly associated a given term is to any of a set of basic color terms. We then show how this colorability score can be used with additional semantic analysis to rank and retrieve a representative color from Google Images. Alternatively, we use symbolic relationships defined by WordNet to select identity colors for categories such as countries or brands. To create visually distinct color palettes, we use k-means clustering to create visually distinct sets, iteratively reassigning terms with multiple basic color associations as needed. This can be additionally constrained to use colors only in a predefined palette.
Effect of Aluminium on High-Energy Ball Milling and Spark Plasma Sintering of Silicon Nitride (2005)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Equilibrative nucleoside transporter 1 (ENT1) regulates postischemic blood flow during acute kidney injury in mice (2012)

A complex biologic network regulates kidney perfusion under physiologic conditions. This system is profoundly perturbed following renal ischemia, a leading cause of acute kidney injury (AKI) - a life-threatening condition that frequently complicates the care of hospitalized patients. Therapeutic approaches to prevent and treat AKI are extremely limited. Better understanding of the molecular pathways promoting postischemic reflow could provide new candidate targets for AKI therapeutics. Due to its role in adapting tissues to hypoxia, we hypothesized that extracellular adenosine has a regulatory function in the postischemic control of renal perfusion. Consistent with the notion that equilibrative nucleoside transporters (ENTs) terminate adenosine signaling, we observed that pharmacologic ENT inhibition in mice elevated renal adenosine levels and dampened AKI. Deletion of the ENTs resulted in selective protection in Ent1-/- mice. Comprehensive examination of adenosine receptor-knockout mice exposed to AKI demonstrated that renal protection by ENT inhibitors involves the A2B adenosine receptor. Indeed, crosstalk between renal Ent1 and Adora2b expressed on vascular endothelia effectively prevented a postischemic no-reflow phenomenon. These studies identify ENT1 and adenosine receptors as key to the process of reestablishing renal perfusion following ischemic AKI. If translatable from mice to humans, these data have important therapeutic implications.
Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation (2012)

We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.