gebhart/patrepeval huggingface dataset:
DNA bases beyond Watson and Crick (2014)

I am going to discuss the latest results related to the function and distribution of the new nucleobases 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), 5-carboxycytosine (caC) and 5-hydroxymethyluracil. These nucleobases seem to play an important role in epigenetic reprogramming of stem cells and some of these bases are also detected at relatively high levels in brain tissues. I will present new synthetic routes that enable preparation of these compounds and of the corresponding phosphoramidites using modern metal organic chemistry. Finally I will discuss how chemistry leads to new insights into the biology of stem cell development processes. In particular mass spectroscopy in combination with the availability of isotopically labeled material allows investigation of the distribution of these novel bases in various tissues and during stem cell development. The recently discovered base formylcytosine for example, is present at relatively high levels in stem cells and its distribution varies during development in a wave like fashion. I am going to describe the distribution of carboxylcytosine in somatic tissues and in stem cells and will provide new quantitative data derived from a detailed mass spectrometric analysis. In order to elucidate the function of the nucleobases we devised a new isotope tracing experiment that enables us to unravel the biochemistry of the bases with high precision and accuracy. I will discuss the synthesis of double [N]-labeled hmC, fC and caC and the preparation of DNA containing these isotopologes. The DNA strands are subsequently added to stem cell nuclear extracts and the formation of the novel nucleobases is followed by high sensitive mass spectrometry.
Tracheotomy in the Preschool Population: Indications and Outcomes (2007)

Tracheotomy procedures in the preschool population remain uncommon; however, nearly half of those studied were performed as a direct result of otherwise preventable trauma.
Autonomic Query Parallelization using Non-dedicated Computers: An Evaluation of Adaptivity Options (2006)

Writing parallel programs that can take advantage of non-dedicated processors is much more difficult than writing such programs for networks of dedicated processors. In a non-dedicated environment such programs must use autonomic techniques to respond to the unpredictable load fluctuations that characterize the computational model. In the area of adaptive query processing (AQP), several techniques have been proposed for dynamically redistributing processor assignments throughout a computation to take account of varying resource capabilities, but we know of no previous study that compares their performance. This paper presents an simulation based evaluation of these autonomic parallelization techniques in a uniform environment and compares on how well they improve the scaleability of the computation. The existing strategies are compared with a new approach inspired by work on distributed hash tables. The evaluation identifies situations in which each strategy may be used effectively and it should be avoided.
Copper-Catalyzed sp<sup>3</sup> C–H Amination (2012)

Among the transition metals, copper-based catalyst systems enable the widest range of N-containing reagents in C–H amination to allow for the direct incorporation of versatile N-based functionalities via ubiquitous C–H bonds. In addition to nitrene-based approaches involving sulfonyliminoiodinanes (PhI═NSO2R), diverse non-nitrene protocols have been developed that allow for the direct use of organic amides, nitrosoarenes, and hydroxylamines, strained heterocycles such as oxaziridines, acetonitrile, secondary sulfonylamines, and even alkylamines and arylamines. Synthetic, mechanistic, and theoretical studies reveal discrete copper nitrenes [Cu]═NR and copper amides [Cu]–NHR to be key reactive intermediates in C–H amination. Copper-catalyzed sp3 C–H amination is reviewed, connecting catalytic reactivity patterns with likely copper intermediates wherever possible, with the goal to stimulate the further development of C–H functionalization reactions with copper which possess significant sustainability advantages over other contemporary approaches involving noble metals.
Targeting Diabetes with a Novel Small Molecule Activator of Sarco/endoplasmic Reticulum Ca2+‐ATPase (SERCA) (2013)

Diabetes represents an enormous burden due to the risk of complications and impact on mortality and morbidity. Endoplasmic reticulum (ER) stress has been shown to be a causative factor in diabetic pathophysiology. A major cause of ER stress is disturbed calcium homeostasis caused by dysfunctional Sarco/ER Ca2+‐ATPase (SERCA). Using novel screening methodology, we have developed a series of novel, drug‐like small molecules that activate SERCA and rescue various cell lines from ER stress‐induced cell death. Among our SERCA allosteric agonists, CDN1163 (CDN) significantly reduced the plasma levels of glucose and triglyceride in obese diabetic mice. Interestingly, the obese mice maintained a lower glucose level, identical to lean mice, for over 6 weeks after CDN has been administered. CDN also decreased hepatic steatosis and the expression of genes involved in gluconeogenesis and lipogenesis, and attenuated ER stress via PERK and IRE1a pathways independent of change in the expression of chaperones. Furthermore, CDN improved mitochondrial function through increased mitochondrial biogenesis and oxidative phosphorylation, upregulated the expression of antioxidant enzymes and attenuated ER stress‐induced apoptosis. Taken together, our data demonstrate that developing drug therapy that directly activates endogenous SERCA may constitute a novel therapeutic potential to treat diabetes. (NIH HL097357 )
Disease type-associated increases of the plasma levels and ligand expression for natural alpha- or beta-galactoside-binding immunoglobulin G subfractions in patients with lung cancer (1997)

The presence of natural carbohydrate-binding antibodies may play a role in host defence against malignant cells in addition to elicitation of an immune response by artificial carbohydrate antigens. Human serum contains immunoglobulin G(2) (IgG) fractions with selectivity to alpha- and to beta-galactosides, respectively, irrespective of the type of blood group of the donor. To determine whether these naturally occurring subfractions may have any relevance for tumor disease control, their binding to malignant cells was ascertained by cytofluorimetric assays in vitro with a number of human tumor cell lines of different histogenetic origin. The affinity of cell binding was comparable to that of binding to lactosylated or melibiosylated neoglycoconjugates as model ligands in solid-phase assays and K-D values were found to be in the range of 5-300 nM. Cross-reactivity of the anomer-selective subfractions to the other type of ligand was observed to be rather low. When the IgG contents of plasma samples of patients with diverse types of lung cancer were assessed, the concentrations of both galactoside-binding immunoglobulin G subfractions were significantly increased in association with presence of small cell lung carcinoma and of metastatic lesions to the lung without any marked change in the overall IgG plasma level. Such an apparently general enhancement was seen for patients with adenocarcinoma and included both subfractions with no impact on their percentage in the total IEC content. When detergent extracts of tumor and tumor-free specimens of the same patient were analyzed with the affinity purified antibody subfractions to comparatively determine ligand presentation, increases in sugar-inhibitable binding were especially noted for the tumor tissue of small cell lung carcinomas and apparently tumor-free samples of cases with lung metastasis. Material from other types of lung cancer revealed no significant indication for disease-related alterations with the exception of carcinoids. These data demonstrate that plasma levels and ligand expression for two types of natural galactoside-binding immunoglobulin G fractions can show nonuniform responses in patients within the class of lung cancer. They encourage to deliberately monitor these parameters of the natural carbohydrate-directed antibody fractions in cancer patients with various types of disease to clarify the clinical significance of respective malignancy-associated changes.
A mixed integer nonlinear programming model for retrofitting heat-exchanger networks (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA mixed integer nonlinear programming model for retrofitting heat-exchanger networksAmy R. Ciric and Christodoulos A. FloudasCite this: Ind. Eng. Chem. Res. 1990, 29, 2, 239–251Publication Date (Print):February 1, 1990Publication History Published online1 May 2002Published inissue 1 February 1990https://pubs.acs.org/doi/10.1021/ie00098a014https://doi.org/10.1021/ie00098a014research-articleACS PublicationsRequest reuse permissionsArticle Views523Altmetric-Citations63LEARN 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-Alertsclose Get e-Alerts
Observation of prolonged power transients in a reconfigurable all optical network (2002)

We observe power transients lasting several seconds in a reconfigurable network including cascaded channel power equalizers and chains of fiber amplifiers in a 1898 km fiber link. Gain clamping of the fiber amplifiers proves effective in suppressing the power transients.
Mechanical Breakdown of Soap-Base Greases. (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanical Breakdown of Soap-Base Greases.R. J. Moore and A. M. CravathCite this: Ind. Eng. Chem. 1951, 43, 12, 2892–2897Publication Date (Print):December 1, 1951Publication History Published online1 May 2002Published inissue 1 December 1951https://pubs.acs.org/doi/10.1021/ie50504a064https://doi.org/10.1021/ie50504a064research-articleACS PublicationsRequest reuse permissionsArticle Views109Altmetric-Citations15LEARN 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
Relationship of P-glycoprotein and carcinoembryonic antigen expression in human colon carcinoma to local invasion, dna ploidy, and disease relapse (1994)

The results indicate that diffuse P-gp immunostaining is present in the majority of Stage B2 human colon cancers and therefore may be an important contributor to their intrinsic drug resistance. The association between a high level of P-gp expression and disease relapse suggests that P-gp can be of prognostic value in Stage B2 colon cancers.
Cholestatic Hepatitis as a Main Manifestation of Mycoplasma pneumoniae Infection (1995)

Arav-Boger, Ravit; Assia, Ayala; Spirer, Zvi; Bujanover, Yoram; Reif, Shimon Author Information
Ring Rearrangement Metathesis of Substituted 2‐Aminonorbornenes. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Assessment of station cable condition using wireless telemetry and diagnostic tests (2002)

Following the premature in-service failure of a 15 kV, XLPE insulated cable in a hydraulic generating station, a program was devised to: determine the root cause of failure; assess the condition of the remaining cables in the station; and ensure that the field modifications proposed to rectify the problem were effective. The underlying mechanism driving the failure was found to be overheating of the cable sheath as a result of the inadvertent formation of ground loops in the cable support structure, and hence circulating currents. Physicochemical tests of cable sections recovered from the failed circuit showed that the cable had experienced temperatures in excess of 115 /spl deg/C. Electrical diagnostic testing of the affected cable circuits indicated that the majority of the cable length was unaffected by the overheating. However, the portion of the cable within the switchgear cubicle may have undergone some ageing as evidenced by higher dielectric loss values. On-line temperature measurements, including those on the current-carrying components using wireless telemetry, confirmed that one of the sources of the high temperatures was the ground structure in the cubicle.
Chemical defense against predators and bacterial fouling in the Mediterranean sponges Axinella polypoides and A. verrucosa  (2010)

The diverse natural products found within sponges mediate many of their ecological interactions, including predator feeding deterrence and defense against fouling. Pyrrole-imidazole compounds, often involved in such ecological interactions, are exclusively found in marine sponges, mainly from the genera Axinella and Agelas. Employing field and laboratory assays, we studied the chemical defense of 2 co-occurring Mediterranean sponges, Axinella polypoides and A. verrucosa, collected from the Gulf of Naples, Italy, against microbial fouling, as well as their feeding deterrence against the generalist shrimp Palaemon elegans. These assays revealed no activity in the extracts of A. polypoides, while the n-butanol part of the A. verrucosa extract showed activity in all assays at natural concentrations. This fraction of the extract contains the bromopyrrole hymenidin, and our assays revealed antibacterial and feeding deterrence activity for this pure compound. 1 H nuclear magnetic resonance quantification confirmed the presence of hymenidin and debromo-carteramine A, another previously isolated antibacterial compound, at ecologically relevant concentrations in the n-butanol part of the A. verrucosa extract. Our results indicate different antimicrobial and feeding deterrence defense strategies in the 2 examined sympatric sponge species, and multiple defensive roles of hymenidin in the defense of A. verrucosa, similar to those of other bromopyrroles isolated from taxonomically related Caribbean sponges.
Isoflavones As Potentiators of Antibacterial Activity (2003)

Isoflavones isolated from Lupinus argenteus were found to potentiate the antibacterial activity of alpha-linolenic acid, also found in the same plant. The isoflavones also potentiated the activity of the natural plant antibiotic berberine and the synthetic fluoroquinoline antibiotic norfloxacin. The isoflavones increased the uptake of berberine into Staphylococcus aureus cells, indicating that they may be inhibiting a multidrug resistance pump (MDR). Thus, L. argenteus contains a weak antibacterial and also MDR pump inhibitors, which increase its potency.
Regulation of Tissue Factor Signaling by Tissue Factor Pathway Inhibitor. (2004)

Abstract Tissue factor initiates the coagulation cascade as well as cellular signaling through the activation of cell surface protease activated receptors (PARs), relevant to inflammation, tumor metastasis and angiogenesis. Tissue factor pathway inhibitor-1 (TFPI-1) is the major regulator of TF initiated coagulation, but recombinant TFPI-1 (rTFPI-1) has shown limited efficacy on sepsis-associated inflammatory responses and mortality. In TNF-stimulated human umbilical vein endothelial cells (HUVECs), we demonstrate with specific blocking antibodies that endogenous TFPI effectively controls TF procoagulant activity as well as TF-dependent signaling through PAR1 and PAR2. The effect of rTFPI-1 on coagulation and signaling was tested in TF-transfected CHO-cells or in HUVECs transduced with TF to overcome the inhibitory threshold of endogenous TFPI-1. Under conditions that specifically measure signaling of the ternary TF-VIIa-Xa complex, 2.5–5 nM rTFPI-1 inhibited TF-dependent Xa generation by >80% but the signaling of the ternary complex through PAR1 at these concentrations of rTFPI-1 was only marginally inhibited. Moreover, studies with proteoglycan-deficient CHO cells provided genetic evidence that PG binding facilitates the inhibitory activities of rTFPI-1 on coagulation and signaling. In HUVECs that co-expressed PAR2 with TF, three different signaling responses of the ternary TF-VIIa-Xa complex were inhibited by ~ 50% at 1.2–2.5 nM rTFPI-1, but the inhibitory potency of rTFPI-1 to block Xa generation was consistently higher relative to its effect on signaling. These data demonstrate that coagulation initiation phase signaling can occur in the absence of the activation of coagulation. The results also establish that endogenously expressed TFPI-1, known to be entirely GPI-anchored in endothelial cells, is a potent, negative regulator of ternary complex-mediated PAR signaling. The efficacy of rTPFI-1 appears to be influenced by the presence of PAR2, further emphasizing the close reciprocal signaling linkage of PAR2 and TF demonstrated in angiogenesis and cellular signaling targeting the TF cytoplasmic domain by phosphorylation.
Room-Temperature Ammonia Gas Sensing Using Mixed-Valent CuCo<sub>2</sub>O<sub>4</sub> Nanoplatelets: Performance Enhancement through Stoichiometry Control (2018)

We report the sensing properties of an interesting ternary oxide CuCo<sub>2</sub>O<sub>4</sub> (CCO) which comprises two earth-abundant transition elements, both capable of supporting multiple valence states. We have used a synthesis protocol, which renders unique nanoplatelet-type morphology but with a degree of biphasic character (CuO as a secondary phase in addition to the defect-spinel Cu<sub>1-<i>x</i></sub> Co<sub>2</sub>O<sub>4</sub>). This sample constitution can be controlled through the use of cation off-stoichiometry, and the same also influence the sensing response significantly. In particular, a Co 10 at. % excess CCO (CCO-Co(10)) case exhibits a good response (∼7.9% at 400 ppm) for NH<sub>3</sub> gas with a complete recovery at room temperature (23 °C, ±1 °C) in 57% RH. The material performance was investigated for other gases such as H<sub>2</sub>S, NO<sub>2</sub>, and CO. A good response is observed for H<sub>2</sub>S and NO<sub>2</sub> gases but without a recovery; however, for CO, a poor response is noted. Herein, we discuss the specific results for ammonia sensing for the CCO-Co(10) case in detail via the use of different characterizations and outline the difference between the cases of the single-phase defect-stabilized material versus nonpercolating biphasic material.
BEAM PLASMA AMPLIFIERS (1961)

Recent experiments on electron beam-plasma interactions were performed using a thermally generated cesium plasma. The experimental results obtained are in excellent agreement with the theoretical predictions. These experiments show that the possibilities of using this inter action for the amplification of microwaves may, in the future, provide significant advantages over the existing devices now available. There is a possibility of obtaining high efficiencies at high-power levels. Because no circuit is used, and because it may be possible to couple to the beam in radically new ways, millimeter wavelength amplifiers and cillators based on beam-plasma interaction look devices aie discussed. (auth)
Reconstitution of nativelike nuclear acceptor sites of the avian oviduct progesterone receptor: evidence for involvement of specific chromatin proteins and specific DNA sequences (1984)

A specific fraction of avian oviduct chromosomal proteins can be reannealed to pure avian DNA to reconstitute nativelike specific nuclear binding sites (acceptor sites) for the oviduct progesterone receptor (PR). These specific nuclear binding sites represent the difference between the binding to the reconstituted NAP and that to pure DNA. The specific fraction of chromatin protein which contains the acceptor activity, fraction CP-3, is very tightly bound to hen DNA in a complex termed nucleoacidic protein (NAP). Removal of the CP-3 fraction from NAP results in a loss of specific PR binding sites. Resins containing chromatin adsorbed to hydroxylapatite are used as a rapid method to isolate the CP-3 fraction. Reconstitution of the CP-3 fraction to DNA by the described method involving a regressing gradient of 6-0 M guanidine hydrochloride (Gdn-HCl) results in a reconstituted NAP which displays specific PR binding sites identical with those in native (undissociated) NAP and whole chromatin. Optimal conditions and potential problems for reconstituting these nucleoproteins are described. Only partially purified receptor preparations were used in these cell-free binding analyses since they have been shown to bind with similar properties and patterns as the nuclear binding in vivo. Therefore, the binding of PR to the reconstituted NAPs was demonstrated to be receptor dependent, saturable, and of high affinity. Further, the pattern of binding to the reconstituted sites mimics those which are observed in vivo. Thus, nonfunctional receptors that cannot translocate and bind to the nuclear acceptor sites in vivo also failed to bind to the acceptor sites on the reconstituted NAPs generated by the acceptor proteins. In contrast, the binding to pure DNA does not reflect these receptor differences in receptor bindings. Specific binding of PR to reconstituted NAP can be reversed by again removing the protein fraction. Moreover, the specific binding can be destroyed by proteases and protected by protease inhibitors, indicating that acceptor activity is proteinaceous in nature. The reconstitution of the activity is both a concentration-dependent and time-dependent process. During the reconstitution, acceptor activity appears to reconstitute on the DNA when the Gdn-HCl concentration reaches 2.0 M. By use of the reconstitution method as an assay for acceptor activity, the activity in the CP-3 fraction was shown by molecular sieve chromatography to elute in a relatively broad molecular weight range between 13 000 and 25 000. The activity also focuses in isoelectric focusing resins with apparent pI's of 5.2 and 6.4.(ABSTRACT TRUNCATED AT 400 WORDS)