gebhart/patrepeval huggingface dataset:
Computer translation of IUPAC systematic organic chemical nomenclature. 2. Development of a formal grammar (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComputer translation of IUPAC systematic organic chemical nomenclature. 2. Development of a formal grammarD. I. Cooke-Fox, G. H. Kirby, and J. D. RaynerCite this: J. Chem. Inf. Comput. Sci. 1989, 29, 2, 106–112Publication Date (Print):May 1, 1989Publication History Published online1 May 2002Published inissue 1 May 1989https://pubs.acs.org/doi/10.1021/ci00062a010https://doi.org/10.1021/ci00062a010research-articleACS PublicationsRequest reuse permissionsArticle Views158Altmetric-Citations13LEARN 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 optionsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Peptide-oligourea hybrids analogue of GLP-1 with improved action in vivo (2019)

Peptides have gained so much attention in the last decade that they are now part of the main strategies, with small molecules and biologics, for developing new medicines. Despite substantial progress, the successful development of peptides as drugs still requires a number of limitations to be addressed, including short in vivo half-lives and poor membrane permeability. Here, we describe the use of oligourea foldamers as tool to improve the pharmaceutical properties of GLP-1, a 31 amino acid peptide hormone involved in metabolism and glycemic control. Our strategy consists in replacing four consecutive amino acids of GLP-1 by three consecutive ureido residues by capitalizing on the structural resemblance of oligourea and α-peptide helices. The efficacy of the approach is demonstrated with three GLP-1-oligourea hybrids showing prolonged activity in vivo. Our findings should enable the use of oligoureas in other peptides to improve their pharmaceutical properties and may provide new therapeutic applications.
A negative feedback loop of transcription factors that controls stem cell pluripotency and self‐renewal (2006)

Embryonic stem (ES) cells possess the ability to renew themselves while maintaining the capacity to differentiate into virtually all cell types of the body. Current evidence suggests that ES cells maintain their pluripotent state by expressing a battery of transcription factors including Oct4 and Nanog. However, little is known about how ES cells maintain the expression of these pluripotent factors in ES cells. Here we present evidence that Oct4, Nanog, and FoxD3 form a negative feedback loop to maintain their expression in pluripotent ES cells. First, Oct4 maintains Nanog activity by directly activating its promoter at sub-steady-state concentration but repressing it at or above steady-state levels. On the other hand, FoxD3 behaves as a positive activator of Nanog to counter the repressive effect of Oct4. The expression of Oct4 is activated by FoxD3 and Nanog but repressed by Oct4 itself, thus, exerting an important negative feedback loop to limit its own activity. Indeed, overexpression of either FoxD3 or Nanog in ES cells failed to increase the concentration of Oct4 beyond the steady-state concentration, whereas knocking down either FoxD3 or Nanog reduces the expression of Oct4 in ES cells. Finally, overexpression of Oct4 or Nanog failed to compensate the loss of Nanog or Oct4, respectively, suggesting that both are required for ES self-renewal and pluripotency. Our results suggest the FoxD3-Nanog-Oct4 loop anchors an interdependent network of transcription factors that regulate stem cell pluripotency.
Typing and subtyping of influenza viruses in clinical samples by PCR (1995)

Type A and B influenza viruses can cause a wide spectrum of illness, and these viruses are responsible for considerable mortality and morbidity. Rapid typing of isolates is desirable when amantadine treatment or prophylaxis of contacts of type A influenza virus carriers is considered, but the available rapid techniques lack sensitivity and standard diagnostic methods require expansion of virus in tissue culture or embryonated hens' eggs. We developed a series of oligonucleotide primers able to detect, type, and subtype type A influenza viruses in a single reverse transcription-PCR. RNA was isolated from clinical specimens, and cDNA was generated with random primers. PCR was carried out with a mixture of primers specific for influenza viruses of types B, A/H1 and A/H3, and subtyping of the neuraminidase was carried out on the same cDNA template under identical conditions. Amplified products were detected by ethidium bromide staining of amplified products after agarose gel electrophoresis. When it was used to test 98 clinical specimens, this method was comparable to standard culture techniques in the detection, typing, and subtyping of influenza viruses.
Discovery of (2E)-3-{2-Butyl-1-[2-(diethylamino)ethyl]-1H-benzimidazol-5-yl}-N-hydroxyacrylamide (SB939), an Orally Active Histone Deacetylase Inhibitor with a Superior Preclinical Profile (2011)

A series of 3-(1,2-disubstituted-1H-benzimidazol-5-yl)-N-hydroxyacrylamides (1) were designed and synthesized as HDAC inhibitors. Extensive SARs have been established for in vitro potency (HDAC1 enzyme and COLO 205 cellular IC(50)), liver microsomal stability (t(1/2)), cytochrome P450 inhibitory (3A4 IC(50)), and clogP, among others. These parameters were fine-tuned by carefully adjusting the substituents at positions 1 and 2 of the benzimidazole ring. After comprehensive in vitro and in vivo profiling of the selected compounds, SB939 (3) was identified as a preclinical development candidate. 3 is a potent pan-HDAC inhibitor with excellent druglike properties, is highly efficacious in in vivo tumor models (HCT-116, PC-3, A2780, MV4-11, Ramos), and has high and dose-proportional oral exposures and very good ADME, safety, and pharmaceutical properties. When orally dosed to tumor-bearing mice, 3 is enriched in tumor tissue which may contribute to its potent antitumor activity and prolonged duration of action. 3 is currently being tested in phase I and phase II clinical trials.
Synthesis of a Series of Substituted Phenylpropiolic Acids (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of a Series of Substituted Phenylpropiolic AcidsMelvin S. Newman and Stewart H. MerrillCite this: J. Am. Chem. Soc. 1955, 77, 21, 5549–5551Publication Date (Print):November 1, 1955Publication History Published online1 May 2002Published inissue 1 November 1955https://pubs.acs.org/doi/10.1021/ja01626a033https://doi.org/10.1021/ja01626a033research-articleACS PublicationsRequest reuse permissionsArticle Views700Altmetric-Citations18LEARN 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
Wireless thermal micro-ablation of skin for transdermal drug delivery (2005)

This paper presents design, fabrication, and experimental results of a wireless induction heating system for generating micron-scale pores in the skin by thermal micro-ablation to dramatically increase skin permeability to drugs, while maintaining the patient-friendliness of conventional transdermal patches. The micro-heating element arrays have been fabricated using electrodeposition of nickel on a SU8 patterned structure. The heating element arrays have been characterized by applying wireless AC magnetic excitation using a coil, and applied to an in-vitro skin ablation experiment. The experiment has confirmed that fabricated micro-heating elements are able to generate heat sufficient to induce localized micro-ablation in human skin.
Indicating Resolver Support of DNSSEC (2001)

In order to deploy DNSSEC (Domain Name System Security Extensions) operationally, DNSSEC aware servers should only perform automatic inclusion of DNSSEC RRs when there is an explicit indication that the resolver can understand those RRs. This document proposes the use of a bit in the EDNS0 header to provide that explicit indication and describes the necessary protocol changes to implement that notification.
A Mutation in the SDHC Gene of Complex II Increases Oxidative Stress, Resulting in Apoptosis and Tumorigenesis (2005)

Intracellular oxidative stress from mitochondria is thought to be important in carcinogenesis and tumorigenesis, but direct experimental proof is limited. In this study, a transgenic mouse cell line (SDHC E69) with a mutated SDHC gene (a subunit of complex II in the electron transport chain) was constructed to test this question. The SDHC E69 cells overproduced superoxide anion (O(2)(-)) from mitochondria, had elevated cytoplasmic carbonyl proteins and 8-OH-deoxyguanine in their DNA as well as significantly higher mutation frequencies than wild type. There were many apoptotic cells in this cell line, as predicted by the observed increase in caspase 3 activity, decrease in mitochondrial membrane potential, and structural changes in their mitochondria. In addition, some cells that escaped from apoptosis underwent transformation, as evidenced by the fact that SDHC E69 cells caused benign tumors when injected under the epithelium of nude mice. These results underscore the notion that mitochondrially generated oxidative stress can contribute to nuclear DNA damage, mutagenesis, and ultimately, tumorigenesis.
Aliphatic amino azides as key building blocks for efficient polyamine syntheses (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAliphatic amino azides as key building blocks for efficient polyamine synthesesBertrand Carboni, Aziza Benalil, and Michel VaultierCite this: J. Org. Chem. 1993, 58, 14, 3736–3741Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/jo00066a028https://doi.org/10.1021/jo00066a028research-articleACS PublicationsRequest reuse permissionsArticle Views3626Altmetric-Citations103LEARN 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
Hypothalamic localization of the feeding effect of agouti-related peptide and alpha-melanocyte-stimulating hormone. (2000)

The melanocortin-4 receptor (MC4R) in the hypothalamus is thought to be important in physiological regulation of food intake. We investigated which hypothalamic areas known to express MC4R are involved in the regulation of feeding by using alpha-melanocyte-stimulating hormone (alpha-MSH), an endogenous MC4R agonist, and agouti-related peptide (Agrp), an endogenous MC4R antagonist. Cannulae were inserted into the rat hypothalamic paraventricular (PVN), arcuate (Arc), dorsomedial (DMN), and ventromedial (VMN) nuclei; the medial preoptic (MPO), anterior hypothalamic (AHA), and lateral hypothalamic (LHA) areas; and the extrahypothalamic central nucleus of the amygdala (CeA). Agrp (83-132) (0.1 nmol) and [Nle4, D-Phe7]alpha(-MSH (NDP-MSH) (0.1 nmol), a stable alpha-MSH analog, were administered to fed and fasted rats, respectively. The PVN, DMN, and MPO were the areas with the greatest response to Agrp and NDP-MSH. At 8 h postinjection, Agrp increased feeding in the PVN by 218 +/- 23% (P < 0.005), in the DMN by 268 +/- 42% (P < 0.005), and in the MPO by 236 +/- 31% (P < 0.01) compared with a saline control group for each nucleus. NDP-MSH decreased food intake in the PVN by 52 +/- 6% (P < 0.005), in the DMN by 44 +/- 6% (P < 0.0001), and in the MPO by 55 +/- 6% (P < 0.0001) at 1 h postinjection. Injection into the AHA and CeA resulted in smaller alterations in food intake. No changes in feeding were seen after the administration of Agrp into the Arc, LHA, or VMN, but NDP-MSH suppressed food intake in the Arc and LHA. This study indicates that the hypothalamic nuclei expressing MC4R vary in their sensitivity to Agrp and alpha-MSH with regard to their effect on feeding.
A Clinical Score to Predict Acute Renal Failure after Cardiac Surgery (2004)

The risk of mortality associated with acute renal failure (ARF) after open-heart surgery continues to be distressingly high. Accurate prediction of ARF provides an opportunity to develop strategies for early diagnosis and treatment. The aim of this study was to develop a clinical score to predict postoperative ARF by incorporating the effect of all of its major risk factors. A total of 33,217 patients underwent open-heart surgery at the Cleveland Clinic Foundation (1993 to 2002). The primary outcome was ARF that required dialysis. The scoring model was developed in a randomly selected test set (n = 15,838) and was validated on the remaining patients. Its predictive accuracy was compared by area under the receiver operating characteristic curve. The score ranges between 0 and 17 points. The ARF frequency at each score level in the validation set fell within the 95% confidence intervals (CI) of the corresponding frequency in the test set. Four risk categories of increasing severity (scores 0 to 2, 3 to 5, 6 to 8, and 9 to 13) were formed arbitrarily. The frequency of ARF across these categories in the test set ranged between 0.5 and 22.1%. The score was also valid in predicting ARF across all risk categories. The area under the receiver operating characteristic curve for the score in the test set was 0.81 (95% CI 0.78 to 0.83) and was similar to that in the validation set (0.82; 95% CI 0.80 to 0.85; P = 0.39). In conclusion, a score is valid and accurate in predicting ARF after open-heart surgery; along with increasing its clinical utility, the score can help in planning future clinical trials of ARF.
Tables of the Speed of Sound in Water (1959)

An equation and tables for the speed of sound in water are reprinted from a recent paper published in The Journal of Research of the National Bureau of Standards.
Structure-based Calculation of the Equilibrium Folding Pathway of Proteins. Correlation with Hydrogen Exchange Protection Factors (1996)

A new statistical thermodynamic formalism has been developed in order to describe the equilibrium folding pathway of proteins. The resulting formalism allows calculation of the probabilities that individual amino acid residues will be in a native or native-like conformation for any given degree of folding of the protein molecule. The residue probabilities are defined by the probability distribution of conformational states and can be used to calculate experimental quantities like native-state, hydrogen exchange protection factors. A combinatorial algorithm aimed at generating a large ensemble of conformational states (10(4) to 10(6)) using the native structure as a template has been developed. The Gibbs energy and corresponding probability of each conformational state is estimated by using a previously developed structural parametrization of the energetics. The approach has been applied to five different proteins: hen egg-white lysozyme, equine lysozyme, bovine pancreatic trypsin inhibitor, staphylococcal nuclease and turkey ovomucoid third domain. The validity of the approach has been tested by comparing predicted and experimental hydrogen exchange protection factors. It is shown that for the above proteins 76%, 73%, 74%, 78% and 81% of all observed protection factors are predicted correctly. Furthermore, on average, the magnitude of the predicted protection factors, expressed as apparent free energies per residue deviate less than 1 kcal/mol from those obtained experimentally. These results represent the first attempt at predicting both the location and magnitude of hydrogen exchange protection factors from the high-resolution structure of a protein. The good agreement between experimental and predicted values has permitted a close examination of the nature of the equilibrium folding intermediates existing under conditions of maximal stability of the native state.
Synthesis and Anti-HIV Activity of some Novel Chain-Extended Phosphoramidate Derivatives of d4T (Stavudine): Esterase Hydrolysis as a Rapid Predictive Test for Antiviral Potency (1998)

Novel chain-extended nucleoside phosphoramidates of the anti-human immunodeficiency virus (HIV) drug d4T (stavudine) have been prepared as possible membrane-permeable prodrugs of the bio-active free 5'-monophosphates. Phosphorochloridate chemistry gave the target compounds in moderate to high yields, and all materials were fully characterized by spectroscopic and analytical methods. The compounds are related to the previously reported phenyl methoxyalaninyl derivative of d4T, which was shown to be a potent and selective inhibitor of HIV. In this study the amino acid nitrogen and ester moieties were separated by methylene spacers of between two and six carbon atoms. In vitro evaluation of these compounds indicated an almost complete lack of anti-HIV activity, the compounds being several orders of magnitude less potent than the corresponding alpha-amino acid derivatives. The reasons for the virtual lack of anti-HIV activity appear to involve poor enzyme-mediated hydrolysis.
Tissue Pressure Measurements as a Determinant for the Need of Fasciotomy (1975)

An experimental and clinical tehcnique of measuring tissue pressures within closed compartments demonstrates a normal tissue pressure is approximately zero mmHg, and increased markedly in compartmental syndromes. There is inadequate perfusion and relative ischemia when the tissue pressure within a closed compartment rises to within 10-30 mm Hg of the patient's diastolic blood pressure. Fasciotomy is usually indicated, therefore, when the tissue pressure rises to 40-45 mm Hg in a patient with a diastolic blood pressure of 70 mm Hg and any of the signs or symptoms of a compartmental syndrome. There is no effective tissue perfusion within a closed compartment when the tissue pressure equals or exceeds the patient's diastolic blood pressure. A fasciotomy is definitely indicated in this circumstance, although distal pulses may be present. The measurement of tissue pressure aids in the early diagnosis and appropriate treatment of compartmental syndromes.
A Biochemical Correlate of the Critical Period for Synaptic Modification in the Visual Cortex (1989)

Stimulation of phosphoinositide hydrolysis by excitatory amino acids was studied in synaptoneurosomes of kitten striate cortex at several postnatal ages. Ibotenate and glutamate stimulated phosphoinositide turnover during the second and third postnatal months; N-methyl-D-aspartate and DL-alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) were without effect. The developmental profile of ibotenate-stimulated phosphoinositide turnover parallels the postnatal changes in cortical susceptibility to visual deprivation. The transient increase in ibotenate-stimulated phosphoinositide turnover does not occur in visual cortex of kittens reared in complete darkness.
Primary Structure of a Human Small Nuclear Ribonucleoprotein Polypeptide as Deduced by cDNA Analysis (1989)

Anti-Sm is an antibody specificity often associated with the autoimmune disease systemic lupus erythematosus. The polypeptides Sm-B'/B (estimated molecular mass 27 and 26 kDa, respectively) are primary targets of Sm antibodies. Sm-B'/B are part of the core polypeptides of small ribonucleoprotein particles (snRNP) involved in pre-mRNA splicing. Sm-B'/B share the same amino-terminal sequence as we determined by microsequence analyses of the purified polypeptides. Oligonucleotide probes based on that sequence were used to isolate seven clones from a human lymphoblastoid cDNA library in lambda gt10. The clones contained a single coding region for a protein of approximately 25 kDa. The predicted amino-terminal sequence was identical to that of the isolated Sm-B'/B polypeptides. In vitro translation experiments produced a protein immunoreactive with human polyclonal anti-Sm antibodies. The isolation of only one unique cDNA sequence suggests that Sm-B'/B may be post-translational variants encoded by a single message. The specific structural features which distinguish Sm-B' from Sm-B have yet to be determined. Northern blot analysis confirmed the diverse tissue and species distribution expected for these immunologically conserved polypeptides. The Sm-B'/B primary sequence is rich in proline (20%) and glycine (15%) residues. The prolines are concentrated in the carboxyl-terminal half of the protein and display a repetitive unit that is shared with other snRNP and nucleic acid binding proteins. Analysis of these arrays suggests an eight residue proline-rich consensus sequence with potential as either an RNA binding domain, or as a site of protein/protein interaction.
Derivation and Properties of Recombinant Fab Antibodies to Coplanar Polychlorinated Biphenyls (2000)

Recombinant Fab antibodies (rFabs) specific for coplanar polychlorinated biphenyls (PCBs) were derived from a hybridoma cell line (Chiu et al. Anal. Chem. 1995, 67, 3829-3839). Immunoglobulin V(H)-C(H1) and V(L)-C(L) sequences from S2B1 messenger RNA were amplified by PCR and cloned into the M13 phagemid vector pComb3H. Phage displaying rFab were enriched by panning on a PCB hapten conjugate and expressed as soluble rFabs in Escherichia coli XL-1 Blue. Two rFab clones competitively bound PCBs 77 and 126 with half-maximal inhibition (I(50)) of 10-13 ppb in indirect and direct enzyme immunoassays (EIAs), with selectivity nearly identical to that of whole S2B1 IgG and its Fab fragments prepared by papain digestion. These results, and comparison of N-terminal amino acid sequences of MAb S2B1 and the rFab, indicated that rFab S2B1 is a functional copy of the MAb. The rFab S2B1 sequences have 75-89% sequence identity with antibodies that bind nitrophenyl haptens and are being used to construct a three-dimensional computational model of the PCB binding site.