gebhart/patrepeval huggingface dataset:
A proton-NMR study of the DNA binding characteristics of thioformyldistamycin, an amide isosteric lexitropsin (1992)

The interaction of thioformyldistamycin, an amide isostere of the naturally occurring antibiotic distamycin A, with a self-complementary decadeoxynucleotide duplex, d(CGCAATTGCG)2, has been examined using a variety of high-field 1H-NMR techniques. The ligand exhibits two forms in solution arising from geometric isomerism due to restricted rotation around the thioformamide bond. Only the thermodynamically more stable Z-form is shown to bind to the oligonucleotide along its minor groove at the central 5'-AATT segment with the end groups of the ligand extending into the flanking GC regions but without any close contact at the amidinium terminus. Cross-peaks involving characteristic intra- and interresidue proton connectivities in the 2D experiments (COSY and NOESY) were employed to assign individual resonances of both strands in the asymmetric DNA-drug complex. The solution structure of the complex was constructed by molecular mechanics calculations based upon initial estimates of drug-DNA NOE contacts and further refined through energy minimization. These results complement previous structural studies on distamycin and other lexitropsins with oligonucleotides. The exchange of the ligand between two equivalent binding sites on the DNA sequence was estimated to occur at 40 s-1 with a free energy of activation of 16.5 kcal.mol-1 at 321-326 K. There was no evidence of formation of a 2:1 drug-oligomer complex, in contrast to the case of the natural product, which is attributed to steric demands of the larger sulfur atom.
Aromatic Fluorine Compounds. VII. Replacement of Aromatic -Cl and -NO2 Groups by -F1,2 (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAromatic Fluorine Compounds. VII. Replacement of Aromatic -Cl and -NO2 Groups by -F1,2G. C. Finger and C. W. KruseCite this: J. Am. Chem. Soc. 1956, 78, 23, 6034–6037Publication Date (Print):December 1, 1956Publication History Published online1 May 2002Published inissue 1 December 1956https://pubs.acs.org/doi/10.1021/ja01604a022https://doi.org/10.1021/ja01604a022research-articleACS PublicationsRequest reuse permissionsArticle Views2664Altmetric-Citations159LEARN 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
Incorporation of an Active Site Inhibitor in Factor VIIa Alters the Affinity for Tissue Factor (1997)

Recent studies showed that the administration of active site-inhibited factor VIIa blocked factor VIIa/tissue factor-induced fibrin and thrombus formation in ex vivo and in vivo model systems. These studies suggest that inactivated factor VIIa competes efficiently with plasma factor VII(a) for a limited number of tissue factor sites. In the present study, we compared the interactions of factor VIIa and active site-inhibited factor VIIa with tissue factor. Competition studies of factor VIIa and active site-inhibited factor VIIa in a factor X activation assay showed that the affinity of the latter for relipidated tissue factor was 5-fold higher than that of factor VIIa. Radioligand binding studies with a human bladder carcinoma cell line (J82) and surface plasmon resonance studies using soluble tissue factor demonstrated a faster association and a slower dissociation for the active site-inhibited factor VIIa. Studies of equilibrium binding to cell surface tissue factor showed that the affinity of active site-inhibited VIIa was 5-fold higher than that of factor VIIa to non-functional tissue factor sites, whereas both inactivated factor VIIa and factor VIIa bound to functional tissue factor sites with the same high affinity. Comparison of the CD spectra of factor VIIa and active site-inactivated factor VIIa revealed structural differences in the protease domain. The potential physiological implications of these findings are discussed.
Empirical comparison of algorithms for network community detection (2010)

Detecting clusters or communities in large real-world graphs such as large social or information networks is a problem of considerable interest. In practice, one typically chooses an objective function that captures the intuition of a network cluster as set of nodes with better internal connectivity than external connectivity, and then one applies approximation algorithms or heuristics to extract sets of nodes that are related to the objective function and that look like good communities for the application of interest.In this paper, we explore a range of network community detection methods in order to compare them and to understand their relative performance and the systematic biases in the clusters they identify. We evaluate several common objective functions that are used to formalize the notion of a network community, and we examine several different classes of approximation algorithms that aim to optimize such objective functions. In addition, rather than simply fixing an objective and asking for an approximation to the best cluster of any size, we consider a size-resolved version of the optimization problem. Considering community quality as a function of its size provides a much finer lens with which to examine community detection algorithms, since objective functions and approximation algorithms often have non-obvious size-dependent behavior.
Increased frequency of alloantigen-reactive helper T lymphocytes is associated with human cardiac allograft rejection. (1993)

Endomyocardial biopsy (EMB) is the standard method of monitoring heart transplant recipients for the development of allograft rejection. To date, noninvasive methods to detect cardiac allograft rejection have lacked adequate sensitivity and specificity for wide clinical application. In this study, limiting dilution analysis (LDA) was used to quantitate the number of donor alloantigen-reactive helper T lymphocytes (HTLs) in the peripheral blood of cardiac transplant recipients. Cadaveric donor splenocytes were cryopreserved, providing a source of donor alloantigenic stimulation for these assays. Peripheral blood mononuclear cells were harvested from cardiac transplant recipients before transplantation and at the time of EMB. LDA of donor-reactive HTLs was conducted simultaneously on all time points to minimize experimental variation, and these data were related to EMB scores. Frequencies of donor-reactive HTLs in pretransplant samples were highly variable, ranging from 1/1381 to < 1/200,000, and correlated poorly with the degree of HLA disparity. During episodes of moderate rejection, donor-specific HTL frequencies increased an average of 6 times their post-transplant baseline frequency. Additionally, 10-fold increases in HTL frequencies were seen preceding EMB-diagnosed rejection in several individuals. These data indicate that episodes of allograft rejection are associated with increases in the number of circulating donor-reactive HTL which are frequently detected before the development of histologically defined rejection. Thus, monitoring HTL frequencies may serve as a non-invasive method for detecting and predicting cardiac allograft rejection. Furthermore, this assay may provide a valuable means of assessing the in vivo efficacy of various immunosuppressive therapies.
Identification of new genes regulated by the marRAB operon in Escherichia coli (1995)

Random TnphoA and TnlacZ translational fusions were introduced into an Escherichia coli strain with a deletion of the multiple antibiotic resistance (mar) locus, complemented in trans by a temperature-sensitive plasmid bearing the mar locus with a constitutively expressed mar operon. Five gene fusions (two with lacZ and three with phoA) regulated by the mar operon were identified by increased or decreased marker enzyme activity following loss of the complementary plasmid at the restrictive temperature. Expression of LacZ from both lacZ fusions increased in the presence of the mar operon; expression from the three phoA fusions was represented by the mar operon. The lacZ fusions were mapped at 31.5 and 14 min on the Escherichia coli chromosome. One of the phoA fusions was located at 51.6 min while the two others mapped at 77 min. Cloning and sequencing of a portion of the fused genes showed all of them to be different. The phoA fusions at 77 min were located in a recently identified gene, slp, a lipoprotein of unknown function (D.M. Alexander and A. C. St. John, Mol. Microb. 11:1059-1071, 1994). The others showed no homology with any known genes of E. coli. The insertions caused small but reproducible changes in the antibiotic susceptibility profile. This approach has enabled the identification of new genes in E. coli which are regulated by the marRAB operon and involved in the Mar phenotype.
Nicotinic Treatment for Cognitive Dysfunction (2002)

Nicotinic medications may provide beneficial therapeutic treatment for cognitive dysfunction such as Alzheimer's disease, schizophrenia and attention deficit hyperactivity disorder (ADHD). For development of nicotinic treatments we are fortunate to have a well characterized lead compound, nicotine. Transdermal nicotine patches offer a way to deliver measured doses of nicotine in a considerably safer fashion than the more traditional means of administration, tobacco smoking. We have found that transdermal nicotine significantly improves attentional function in people with Alzheimer's disease, schizophrenia or ADHD as well as normal nonsmoking adults. To follow-up on this proof of principal that nicotinic treatment of cognitive dysfunction holds promise, it is important to use animal models to determine the critical neurobehavioral bases for nicotinic involvement in cognitive function so that more selective nicotinic analogues that improve cognitive function with fewer side effects can be developed. We have found with local infusion in rat studies that the hippocampus and amygdala are important substrates for nicotinic effects on working memory function. Both alpha7 and alpha4beta2 nicotinic receptors are involved in working memory. Nicotinic interactions with dopaminergic and glutaminergic systems are also important in the basis of cognitive function. Studies of the neural nicotinic mechanisms underlying cognitive function are key for opening avenues for development of safe and effective nicotinic treatments for cognitive dysfunction.
The development of the PAR Index (Peer Assessment Rating): reliability and validity (1992)

The PAR Index has been developed to provide a single summary score for all the occlusal anomalies which may be found in a malocclusion. The score provides an estimate of how far a case deviates from normal alignment and occlusion. The difference in scores between the pre- and post-treatment cases reflects the degree of improvement and, therefore, the success of treatment. Excellent reliability was exhibited within and between examiners (Intraclass Correlation Coefficient, R greater than 0.91). The components of the PAR Index have been weighted to reflect current British orthodontic opinion and is flexible in that the weightings could be changed to reflect future standards and standards currently being achieved in other countries. The PAR Index offers uniformity and standardization in assessing the outcome of orthodontic treatment.
Bubble size measurements using the nonlinear mixing of two frequencies (1984)

A double frequency method of measuring bubble size which has better spatial resolution than previous techniques, is described. Bubbles are insonified simultaneously by a swept, relatively low, ‘‘pumping’’ frequency near their resonance and a high ‘‘imaging’’ frequency. Theoretical expressions are derived for the sound scattered by a bubble under the influence of these two frequencies. Existence of sharp resonance behavior in the scattered sound at the sum frequency is shown both theoretically and experimentally.
Behavioral modeling of RF power amplifiers based on pruned volterra series (2004)

Behavioral modeling techniques provide a convenient and efficient means to predict system-level performance without the computational complexity of full circuit simulation or physics-level analysis of nonlinear systems, thereby significantly speeding up the analysis process. General Volterra series based models have been successfully applied for radio frequency (RF) power amplifier (PA) behavioral modeling, but their high complexity tends to limit their applications to "weakly" nonlinear systems. To model a PA with strong nonlinearities and long memory effects, for example, the general Volterra model involves a great number of coefficients. In this letter, we propose a new simplified Volterra series based model for RF power amplifiers by employing a "near-diagonality" pruning algorithm to remove the coefficients which are very small, or else not sensitive to the output error, therefore dramatically reducing the complexity of the behavioral model.
Thermally assisted flash annealing of silicon and germanium (1978)

The radiant energy from high-intensity xenon flash lamps can be used to anneal damage in semiconductors if the sample is moderately heated before and during the flash. The annealing takes place in air via the solid-phase epitaxy process in &amp;lt;50 μsec and does not alter doping profiles or result in loss of volatile species.
Visceral Adiposity, Not Abdominal Subcutaneous Fat Area, Is Associated With an Increase in Future Insulin Resistance in Japanese Americans (2008)

Greater visceral adiposity is associated with an increase in future insulin resistance.
Prediction of proton magnetic resonance shifts: The dependence on hydrogen charges obtained by iterative partial equalization of orbital electronegativity (1981)

Abstract Proton chemical shifts correlate linearly with charges on hydrogen obtained by a method for iterative partial equalization of orbital electronegativity. The compounds studied comprise a wide variety of classes of molecules; all points fall on a single correlation line, showing the general importance of electronic effects in proton chemical shifts and the physical significance of the atomic charges. On the other hand, as there is no general correlation between charges on carbon and on hydrogen atoms, proton chemical shifts cannot be used as probes for charge densities on carbon atoms. Deviations from the correlation line can be attributed to anisotropy effects and provide an estimate for their magnitude.
A Third-Generation Lentivirus Vector with a Conditional Packaging System (1998)

Vectors derived from human immunodeficiency virus (HIV) are highly efficient vehicles for in vivo gene delivery. However, their biosafety is of major concern. Here we exploit the complexity of the HIV genome to provide lentivirus vectors with novel biosafety features. In addition to the structural genes, HIV contains two regulatory genes, tat and rev, that are essential for HIV replication, and four accessory genes that encode critical virulence factors. We previously reported that the HIV type 1 accessory open reading frames are dispensable for efficient gene transduction by a lentivirus vector. We now demonstrate that the requirement for the tat gene can be offset by placing constitutive promoters upstream of the vector transcript. Vectors generated from constructs containing such a chimeric long terminal repeat (LTR) transduced neurons in vivo at very high efficiency, whether or not they were produced in the presence of Tat. When the rev gene was also deleted from the packaging construct, expression of gag and pol was strictly dependent on Rev complementation in trans. By the combined use of a separate nonoverlapping Rev expression plasmid and a 5' LTR chimeric transfer construct, we achieved optimal yields of vector of high transducing efficiency (up to 10(7) transducing units [TU]/ml and 10(4) TU/ng of p24). This third-generation lentivirus vector uses only a fractional set of HIV genes: gag, pol, and rev. Moreover, the HIV-derived constructs, and any recombinant between them, are contingent on upstream elements and trans complementation for expression and thus are nonfunctional outside of the vector producer cells. This split-genome, conditional packaging system is based on existing viral sequences and acts as a built-in device against the generation of productive recombinants. While the actual biosafety of the vector will ultimately be proven in vivo, the improved design presented here should facilitate testing of lentivirus vectors.
GCS-100, a novel galectin-3 antagonist, modulates MCL-1, NOXA, and cell cycle to induce myeloma cell death (2010)

GCS-100 is a galectin-3 antagonist with an acceptable human safety profile that has been demonstrated to have an antimyeloma effect in the context of bortezomib resistance. In the present study, the mechanisms of action of GCS-100 are elucidated in myeloma cell lines and primary tumor cells. GCS-100 induced inhibition of proliferation, accumulation of cells in sub-G(1) and G(1) phases, and apoptosis with activation of both caspase-8 and -9 pathways. Dose- and time-dependent decreases in MCL-1 and BCL-X(L) levels also occurred, accompanied by a rapid induction of NOXA protein, whereas BCL-2, BAX, BAK, BIM, BAD, BID, and PUMA remained unchanged. The cell-cycle inhibitor p21(Cip1) was up-regulated by GCS-100, whereas the procycling proteins CYCLIN E2, CYCLIN D2, and CDK6 were all reduced. Reduction in signal transduction was associated with lower levels of activated IkappaBalpha, IkappaB kinase, and AKT as well as lack of IkappaBalpha and AKT activation after appropriate cytokine stimulation (insulin-like growth factor-1, tumor necrosis factor-alpha). Primary myeloma cells showed a direct reduction in proliferation and viability. These data demonstrate that the novel therapeutic molecule, GCS-100, is a potent modifier of myeloma cell biology targeting apoptosis, cell cycle, and intracellular signaling and has potential for myeloma therapy.
Effective Preexposure Tuberculosis Vaccines Fail To Protect When They Are Given in an Immunotherapeutic Mode (2000)

Two vaccine formulations previously shown to induce protective immunity in mice and prevention of long-term necrosis in guinea pigs were tested as potential immunotherapeutic vaccines in mice earlier infected by aerosol with Mycobacterium tuberculosis. Neither vaccine had any effect on the course of the infection in the lungs, but both reduced the bacterial load in the spleen. Similarly, inoculation with Mycobacterium bovis BCG had no effect whatsoever and, if given more than once, appeared to induce an increasingly severe pyogranulomatous response in the lungs of these mice.
Catheter cleaning for re-use in intermittent catheterization: new light on an old problem. (1995)

Clean intermittent catheterization is a common method of urinary elimination for people with Spinal Cord Injuries. The methods of catheter cleaning for re-use, however, have not been validated with research studies. This study compared the effectiveness of Hydrogen Peroxide, vinegar, dishwashing detergent, and tap water alone to clean catheters contaminated with Pseudomonas aeruginosa and Escherichia coli. The effect of rinsing and drying before cleaning was also examined, as well as the effect of storage in paper or plastic bags after cleaning. Results indicated that rinsing and drying catheters immediately after use was the most effective at reducing bacteria to very near zero. Elements of a procedure are outlined, as well as plans for further development and testing of a rinse & dry procedure for catheter cleaning and re-use.
Shimmer: a spatial heterodyne spectrometer for remote sensing of Earth’ middle atmosphere (2002)

It is well known and demonstrated that interference spectroscopy offers capabilities to obtain passive remote optical sensing spectra of high precision and also achieves economies in size, cost, and ease of deployment compared with more conventional systems. We describe the development of a near-ultraviolet spatial heterodyne spectrometer designed for remote sensing of the global distribution of the hydroxyl radical OH in the Earth's middle atmosphere. The instrument, known as SHIMMER (Spatial Heterodyne Imager for Mesospheric Radicals), is expected to obtain its first OH measurement from space in early 2002 from the Space Shuttle.
Circulating erythropoietin and interleukin-6 concentrations increase in critically ill children with sepsis and septic shock (1996)

Plasma erythropoietin and IL-6 values are increased in critically ill children with sepsis or septic shock in comparison with controls. The data indicate that one or more plasma factors are responsible for stimulation of hypoxia-induced erythropoietin production in the Hep 3B cell line and suggest a possible role for IL-6 in the regulation of erythropoletin production in critically ill children with sepsis or septic shock.
Simultaneous combined interventional percutaneous left atrial auricle and atrial septal defect closure (2006)

A 79-year-old man presented with atrial fibrillation, cerebral embolic events and intracerebral bleeding under oral anticoagulation and a haemodynamically significant secundum atrial …
New Surfactant with SP-B and C Analogs Gives Survival Benefit after Inactivation in Preterm Lambs (2012)

For the first time a synthetic surfactant containing both surfactant protein B and C analogs showed significant benefit over animal derived surfactant in an in vivo model of surfactant inactivation in premature lambs.
Modulation of natural killer and lymphokine-activated killer cell cytotoxicity by lactoferrin (1992)

Natural killer (NK) and lymphokine-activated killer (LAK) cell cytotoxic functions can be strongly augmented by the iron-carrier protein lactoferrin (LF). LF significantly enhances NK and LAK activities when added at the beginning of NK or LAK cytotoxicity assays. LF is effective in augmenting cytotoxic activities at concentrations as low as 0.75 microgram/ml, and higher concentrations of LF induce greater augmentation of NK and LAK. Iron does not appear to be essential for LF to increase NK and LAK, as depleting iron from LF with the chelator deferoxamine does not affect the capacity of LF to increase cytotoxicity. LF is known to have RNase enzymatic activity, and LF enhancement of NK and LAK can be blocked by RNA. However, LFs from two different sources with over 100-fold difference in RNase activity are equally effective in enhancing NK and LAK. Furthermore, purified non-LF RNase does not modulate NK or LAK activity and DNA is as effective as RNA in blocking LF augmentation of NK or LAK cytotoxicity. Therefore, the RNase activity is unlikely to be responsible for LF enhancement of the cytotoxicities. Newborn infants are known to have low NK activity and NK and LAK cells have been implicated in host defense against microbial infections. Thus, maternal milk-derived LF may have a role in boosting antimicrobial immunity in the early stages of life. In adults, LF released from neutrophils may enhance NK and LAK functions in the inflammatory process induced by microbial infections.