gebhart/patrepeval huggingface dataset:
Comparisons between small ribosomal RNA and theoretical minimal RNA ring secondary structures confirm phylogenetic and structural accretion histories (2020)

Ribosomal RNAs are complex structures that presumably evolved by tRNA accretions. Statistical properties of tRNA secondary structures correlate with genetic code integration orders of their cognate amino acids. Ribosomal RNA secondary structures resemble those of tRNAs with recent cognates. Hence, rRNAs presumably evolved from ancestral tRNAs. Here, analyses compare secondary structure subcomponents of small ribosomal RNA subunits with secondary structures of theoretical minimal RNA rings, presumed proto-tRNAs. Two independent methods determined different accretion orders of rRNA structural subelements: (a) classical comparative homology and phylogenetic reconstruction, and (b) a structural hypothesis assuming an inverted onion ring growth where the three-dimensional ribosome's core is most ancient and peripheral elements most recent. Comparisons between (a) and (b) accretions orders with RNA ring secondary structure scales show that recent rRNA subelements are: 1. more like RNA rings with recent cognates, indicating ongoing coevolution between tRNA and rRNA secondary structures; 2. less similar to theoretical minimal RNA rings with ancient cognates. Our method fits (a) and (b) in all examined organisms, more with (a) than (b). Results stress the need to integrate independent methods. Theoretical minimal RNA rings are potential evolutionary references for any sequence-based evolutionary analyses, independent of the focal data from that study.
Delay Fault Testing of Core-Based Systems-on-a-Chip (2003)

Existing approaches for modular manufacturing testing of core-based systems-on-a- chip (SOCs) do not provide an), explicit mechanism for high quality two-pattern tests required-for performance validation through delay fault testing. This paper proposes a new approach for broadside delay fault testing of core-based SOCs, by adapting the existing solutions for automatic test pattern generation and design for test support, test access mechanism division and test scheduling.
Curing partially brominated poly(isobutylene-co-4-methylstyrene) elastomers with phenolic resins: Mechanistic investigation (2001)

The crosslinking of partially brominated poly(isobutylene-co-4-methylstyrene) elastomer 1 by phenolic resin crosslinkers was investigated. The curing was modeled using small molecule analogs of the elastomer and the phenolic resin. In order to mimic the conditions that prevail within the highly aliphatic rubber, the study was carried out in isooctane using catalysts such as coated ZnO that are compatible with such low polar media. In situ NMR analysis was used to probe the reaction between the molecular analogs. p-Isopropyl benzyl bromide was used as the elastomer analog and hydroxymethyl phenols were used as the resin analogs. Isotopic labeling allowed for independent yet simultaneous monitoring of the reactivity of the elastomer and resin analogs. The resin analog reacted with the elastomer analog via an electrophilic aromatic substitution, leading to the formation of a dibenzyl type ether and benzyl-phenyl type ethers as reaction intermediates. At lower temperatures the elastomer analog reacted with itself in a competing “self-cure” process that may be suppressed by increasing the homogeneity of the reaction mixture or by increasing the temperature of the reaction. The applicability of the mechanism was confirmed by successful model cure experiments involving a low molecular weight sample of elastomer 1 and the phenolic resin analog. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 80: 680–685, 2001
Benefits of catch-up in vaccination against human papillomavirus in medium- and low-income countries (2013)

Human papillomavirus (HPV) vaccination of a birth cohort of girls in the 9-13 age range is recommended as a priority, but decreases in HPV vaccine cost may make catch-up of a few additional cohorts more attractive not only in high-income countries. We assessed the reduction in HPV16 and 18 infections that could be achieved in a medium- (Poland) and a low-income (Guinea) country by adding one-time catch-up of 12- to 19-year-old girls to the vaccination of 11-year-old girls. According to our ad hoc adapted dynamic model of HPV infection transmission, the addition of catch-up was estimated to bring forward the 50% reduction of HPV16/18 prevalence due to vaccination in women ≤35 by as much as 5 years. Catch-up of 12- to 15-year olds reduced the cumulative probability of HPV16/18 infections by age 35 in the relevant cohorts by about 30% in both countries. Catch-up of 16- to 19-year-old girls added little. Regardless of the chosen catch-up strategy, 16 to 20% of HPV16/18 prevention from vaccination was attributable to herd immunity. Assuming a sufficiently low vaccine cost, the addition of a catch-up round is, therefore, worth considering in medium/low-income countries to extend vaccine benefits to less young adolescent girls whose future access to cervical screening is uncertain.
Break Characteristic Modelling for Debris Generation Following a Design Basis Loss of Coolant Accident (2004)

An important safety concern regarding long-term recirculation cooling following a loss of coolant accident (LOCA) is the transport of debris materials to interceptors (i.e. trash racks, debris screens, suction strainers) inside containment and the potential for debris accumulation to result in adverse blockage effects. Debris resulting from a LOCA, together with pre-existing debris, could block the emergency core cooling system (ECCS) debris interceptors and result in degradation or loss of recirculation flow margin. Potential debris sources can be divided into three categories: (1) debris that is generated by the LOCA and is transported by blowdown forces (e.g. insulation, paint); (2) debris that is generated or transported by washdown; and (3) other debris that existed before a LOCA (dust, sand, etc.). Each debris source is separately evaluated to estimate the quantity and other ...
Cathepsin S inhibitors: 2004 – 2010 (2011)

Although > 40 patent applications have appeared between 2004 and 2010, the decrease in applications focusing on cathepsin S over the past 2 - 3 years may reflect a renewed interest in other cathepsins, especially cathepsin K, for which a small molecule inhibitor is currently in Phase III clinical trials.
Supplementary Figure Legends 1-6 from The Somatostatin Analogue Octreotide Confers Sensitivity to Rapamycin Treatment on Pituitary Tumor Cells (2023)

Supplementary Figure Legends 1-6 from The Somatostatin Analogue Octreotide Confers Sensitivity to Rapamycin Treatment on Pituitary Tumor Cells
Degradation potentials of dissolved organic carbon (DOC) from thawed permafrost peat (2017)

Global warming can substantially affect the export of dissolved organic carbon (DOC) from peat-permafrost to aquatic systems. The direct degradability of such peat-derived DOC, however, is poorly constrained because previous permafrost thaw studies have mainly addressed mineral soil catchments or DOC pools that have already been processed in surface waters. We incubated peat cores from a palsa mire to compare an active layer and an experimentally thawed permafrost layer with regard to DOC composition and degradation potentials of pore water DOC. Our results show that DOC from the thawed permafrost layer had high initial degradation potentials compared with DOC from the active layer. In fact, the DOC that showed the highest bio- and photo-degradability, respectively, originated in the thawed permafrost layer. Our study sheds new light on the DOC composition of peat-permafrost directly upon thaw and suggests that past estimates of carbon-dioxide emissions from thawed peat permafrost may be biased as they have overlooked the initial mineralization potential of the exported DOC.
Evidence for a Continuous Transition between Thiaphosphetane and Betaine-Type Structures in the Thio-Wittig Reaction (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTEvidence for a Continuous Transition between Thiaphosphetane and Betaine-Type Structures in the Thio-Wittig ReactionCarsten Puke, Gerhard Erker, Nicola C. Aust, Ernst-Ulrich Würthwein, and Roland FröhlichView Author Information Organisch-Chemisches Institut der Universität Münster, Corrensstrasse 40 D-48149 Münster, Germany Cite this: J. Am. Chem. Soc. 1998, 120, 19, 4863–4864Publication Date (Web):May 5, 1998Publication History Received23 June 1997Published online5 May 1998Published inissue 1 May 1998https://pubs.acs.org/doi/10.1021/ja9720669https://doi.org/10.1021/ja9720669rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views369Altmetric-Citations52LEARN 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 optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Chemical calculations,Chemical structure,Molecular structure,Organic reactions,Solvents Get e-Alerts
CLINICAL AND FUNCTIONAL RESULTS OF CATARACT SURGERY EMPLOYING A COMBINATION OF ND-YAG (1.44ΜM) AND HE-NE (0.63ΜM) LASER RADIATION FOR CRYSTALLINE LENS FRAGMENTATION (2015)

Purpose. To investigate and compare the results of clinical application of microinvasive laser cataract extraction (mLCE) based on combined impact of endodissector (Nd-YAG laser 1.44μm) and bio-stimulator (low-power He-Ne laser 0.63μm) with a basic laser cataract extraction technique (LCE) and microinvasive ultrasound phacoemulsification (mPE).Material and methods. Senile cataract extraction with implantation of elastic IOLs into capsular bag was performed in 3 groups of patients: mLCE was performed in 148 eyes, LCE – in 176 eyes and mPE – in 204 eyes.Results. As a whole, surgery and postoperative period coursed with no complications and with minimal reactivity. When compared mLCE with LCE there were reduced energy power, reduced volume of irrigation, less induced astigmatism, better corneal thickness and endothelial cell count loss. When compared mLCE with mPE, the number of eyes with corneal edema was 2 times less, along with reduced transient hypertension and corneal endothelial cell count loss.Conclusion. The developed mLCE technology using two kinds of laser radiations, has several significant clinical advantages providing better safety and efficacy of senile cataract surgical treatment.
An Efficient Two‐Step Preparation of α‐, β‐, γ‐ or δ‐Amino Acids from 2‐Pyrazinones, 2‐Hydroxypyrimidines or 2‐Pyridones Respectively (2018)

A practical and efficient two‐step procedure is reported for the preparation of a variety of α‐, β‐, γ‐ and δ‐amino acids from 2‐pyridone, 2‐pyrazinone or 2‐hydroxypyrimidine and derivatives. The procedure is amenable to scale‐up and in most cases no chromatographic purification of the product is required. This approach is useful, especially in the synthesis of amino acids or deuterated amino acids that are not obtained by other methods.
Internal Lysine Palmitoylation in Adenylate Cyclase Toxin from Bordetella pertussis (1994)

A number of bacterial protein toxins, including adenylate cyclase (AC) toxin from Bordetella pertussis, require the product of an accessory gene in order to express their biological activities. In this study, mass spectrometry was used to demonstrate that activated, wild-type AC toxin was modified by amide-linked palmitoylation on the epsilon-amino group of lysine 983. This modification was absent from a mutant in which the accessory gene had been disrupted. A synthetic palmitoylated peptide corresponding to the tryptic fragment (glutamine 972 to arginine 984) that contained the acylation blocked AC toxin-induced accumulation of adenosine 3',5'-monophosphate, whereas the non-acylated peptide had no effect.
Chiral P-Heterocycles: Efficient Method for the Resolution of 3-Methyl-3-phospholene 1-Oxides (2008)

The enantiomers of 1-aryl-, 1-alkyl- and 1-alkoxy-3-methyl-3-phospholene 1-oxides were separated in good yields and in high enantiomeric excesses (up to > 99% ee) by resolution via formation of diastereomeric complexes with (–)-(4R,5R)-4,5-bis(diphenylhydroxymethyl)-2,2-dimethyldioxolane (TADDOL) or (–)-(2R,3R)-α,α,α′,α′-tetraphenyl-1,4-dioxaspiro[4.5]decan-2,3-dimethanol.
Cross-Network Embedding for Multi-Network Alignment (2019)

Recently, data mining through analyzing the complex structure and diverse relationships on multi-network has attracted much attention in both academia and industry. One crucial prerequisite for this kind of multi-network mining is to map the nodes across different networks, i.e., so-called network alignment. In this paper, we propose a cross-network embedding method CrossMNA for multi-network alignment problem through investigating structural information only. Unlike previous methods focusing on pair-wise learning and holding the topology consistent assumption, our proposed CrossMNA considers the multi-network scenarios which involve at least two types of networks with diverse network structures. CrossMNA leverages the cross-network information to refine two types of node embedding vectors, i.e., inter-vector for network alignment and intra-vector for other downstream network analysis tasks. Finally, we verify the effectiveness and efficiency of our proposed method using several real-world datasets. The extensive experiments show that our CrossMNA can significantly outperform the existing baseline methods on multi-network alignment task, and also achieve better performance for link prediction task with less memory usage.
Exploring the Potential Antidepressant Mechanisms of TNFα Antagonists (2019)

Human and animal studies suggest an intriguing relationship between the immune system and the development of depression. Some peripherally produced cytokines, such as TNF-α, can cross the blood brain barrier and result in activation of brain microglia which produces additional TNF-α and fosters a cascade of events including decreases in markers of synaptic plasticity and increases in neurodegenerative events. This is exemplified by preclinical studies, which show that peripheral administration of pro-inflammatory cytokines can elicit depression-like behavior. Importantly, this depression-like behavior can be ameliorated by anti-cytokine therapies. Work in our laboratory suggests that TNF-α is particularly important for the development of a depressive phenotype and that TNF-α antagonists might have promise as novel antidepressant drugs. Future research should examine rates of inflammation at baseline in depressed patients and whether anti-inflammatory agents could be included as part of the treatment regimen for depressive disorders.
Nanodiamond vacuum field emission device with gate modulated triode characteristics (2013)

A three-electrode nanodiamond vacuum field emission (VFE) device with gate modulated triode characteristics is developed by integrating nanodiamond emitter with self-aligned silicon gate and anode, employing a mold transfer technique in conjunction with chemical vapor deposition of nanodiamond. Triode behavior showing emission current modulation with high current density at low operating voltages is achieved. A systematic analysis based on modified Fowler-Nordheim theory is used to analyze gate modulated VFE characteristics, confirming the triode field emission mechanism and operating principle. The realization of an efficient VFE microtriode has achieved the fundamental step for further development of vacuum integrated microelectronics.
Capillary Zone Electrophoresis (1983)

Zone electrophoresis in open tubular capillaries is a useful approach to high-resolution separations of charged substances. Efficient heat transfer from small diameter capillaries permits application of unusually high voltages, which promote more effective separations and increase the speed of analyses. A sample injection technique and on-line zone detection create an instrumental format for zone electrophoresis. The basic theory, system parameters, and preliminary results are described.
Overcoming Hypoxia-Mediated Tumor Progression: Combinatorial Approaches Targeting pH Regulation, Angiogenesis and Immune Dysfunction (2016)

Hypoxia is an important contributor to the heterogeneity of the microenvironment of solid tumors and is a significant environmental stressor that drives adaptations which are essential for the survival and metastatic capabilities of tumor cells. Critical adaptive mechanisms include altered metabolism, pH regulation, epithelial-mesenchymal transition, angiogenesis, migration/invasion, diminished response to immune cells and resistance to chemotherapy and radiation therapy. In particular, pH regulation by hypoxic tumor cells, through the modulation of cell surface molecules such as extracellular carbonic anhydrases (CAIX and CAXII) and monocarboxylate transporters (MCT-1 and MCT-4) functions to increase cancer cell survival and enhance cell invasion while also contributing to immune evasion. Indeed, CAIX is a vital regulator of hypoxia mediated tumor progression, and targeted inhibition of its function results in reduced tumor growth, metastasis, and cancer stem cell function. However, the integrated contributions of the repertoire of hypoxia-induced effectors of pH regulation for tumor survival and invasion remain to be fully explored and exploited as therapeutic avenues. For example, the clinical use of anti-angiogenic agents has identified a conundrum whereby this treatment increases hypoxia and cancer stem cell components of tumors, and accelerates metastasis. Furthermore, hypoxia results in the infiltration of myeloid-derived suppressor cells (MDSCs), regulatory T cells (Treg) and Tumor Associated Macrophages (TAMs), and also stimulates the expression of PD-L1 on tumor cells, which collectively suppress T-cell mediated tumor cell killing. Therefore, combinatorial targeting of angiogenesis, the immune system and pH regulation in the context of hypoxia may lead to more effective strategies for curbing tumor progression and therapeutic resistance, thereby increasing therapeutic efficacy and leading to more effective strategies for the treatment of patients with aggressive cancer.
Rapid expansion method (REM) for time‐stepping in reverse time migration (RTM) (2009)

We show that the wave equation solution using a conventional finite‐difference scheme, derived commonly by the Taylor series approach, can be derived directly from the rapid expansion method (REM). After some mathematical manipulation we consider an analytical approximation for the Bessel function where we assume that the time step is sufficiently small. From this derivation we find that if we consider only the first two Chebyshev polynomials terms in the rapid expansion method we can obtain the second order time finite‐difference scheme that is frequently used in more conventional finite‐difference implementations. We then show that if we use more terms from the REM we can obtain a more accurate time integration of the wave field. Consequently, we have demonstrated that the REM is more accurate than the usual finite‐difference schemes and it provides a wave equation solution which allows us to march in large time steps without numerical dispersion and is numerically stable. We illustrate the method with post and pre stack migration results.
Modification of epithelial permeability by cationic polypeptides (1993)

It has been demonstrated that protamine sulfate (PS; a cationic polypeptide composed of 70% arginine) increases the apical membrane conductance of the mammalian urinary bladder. In this report, synthetic cationic polypeptides (CpP; e.g., polyarginine) were used to determine whether the response of the bladder to PS was due to its cationic nature (i.e., its arginine content). We demonstrate that CpP induce a large increase in the cation and anion conductance of the apical membrane of the rabbit urinary bladder epithelium. The modulation of the membrane conductance by CpP is dependent upon a number of parameters. 1) The magnitude of the conductance change was voltage dependent. 2) An increase in the total charge per molecule increased the rate of conductance change. 3) An increase in the charge density (ratio of charged amino acids to total amino acids) increased the rate of change of conductance. 4) La3+ inhibited the ability of CpP to alter the membrane conductance. 5) The rate of reversal of the CpP-induced conductance was dependent upon the total charge per molecule as well as the charge density. 6) The level of self-inhibition (ability of solution CpP to inhibit the CpP-induced membrane conductance) was inversely correlated with the charge density and was also concentration dependent, with less inhibition occurring at low mucosal CpP concentrations. These data are consistent with a model developed to describe the effect of PS on the conductive properties of the urinary bladder epithelium.
Blue-Green Laser Technology (2010)

Advancements in solid-state laser-technology including diode-pumping and availability of high-quality laser materials has enabled a variety of previously unattainable applications. We will review recent developments in solid-state lasers operating in the bluegreen-region of the spectrum. Article not available.
Synthesis and thermodynamic study of transition metal ion (Mn2+, Co2+, Cu2+, and Zn2+) exchanged zeolites A and Y (2016)

Transition metal cations (Mn(2+), Co(2+), Cu(2+), and Zn(2+)) containing zeolites A and Y were synthesized by ion exchange and their thermochemistry was investigated by differential scanning calorimetry and high temperature oxide melt solution calorimetry. The enthalpies of formation from oxides for Mn, Co, Cu, and Zn zeolites A range from 14.0 ± 1.3 to 67.6 ± 5.5 kJ mol(-1) and those for Mn, Co, Cu, and Zn zeolites Y range from 8.0 ± 2.0 to 32.6 ± 1.8 kJ mol(-1). All these zeolites are thus metastable with respect to oxide components and to other dense phases. The formation enthalpies of Mn and Zn exchanged zeolites A and Y are less endothermic than those of corresponding Co and Cu exchanged A and Y. These energetics are consistent with metal oxygen bond lengths and related to crystal field effects of transition metal ions. Similar thermodynamic trends have been seen in transition metal containing spinel, olivine and pyroxene materials. The enthalpies of exchange of transition metals in zeolites A and Y with sodium in aqueous solution are calculated and suggest that these zeolites could be reasonably effective sorbents for heavy metal waste.