gebhart/patrepeval huggingface dataset:
BASIC MECHANISMS OF TRANSCRIPT ELONGATION AND ITS REGULATION (1997)

Ternary complexes of DNA-dependent RNA polymerase with its DNA template and nascent transcript are central intermediates in transcription. In recent years, several unusual biochemical reactions have been discovered that affect the progression of RNA polymerase in ternary complexes through various transcription units. These reactions can be signaled intrinsically, by nucleic acid sequences and the RNA polymerase, or extrinsically, by protein or other regulatory factors. These factors can affect any of these processes, including promoter proximal and promoter distal pausing in both prokaryotes and eukaryotes, and therefore play a central role in regulation of gene expression. In eukaryotic systems, at least two of these factors appear to be related to cellular transformation and human cancers. New models for the structure of ternary complexes, and for the mechanism by which they move along DNA, provide plausible explanations for novel biochemical reactions that have been observed. These models predict that RNA polymerase moves along DNA without the constant possibility of dissociation and consequent termination. A further prediction of these models is that the polymerase can move in a discontinuous or inchworm-like manner. Many direct predictions of these models have been confirmed. However, one feature of RNA chain elongation not predicted by the model is that the DNA sequence can determine whether the enzyme moves discontinuously or monotonically. In at least two cases, the encounter between the RNA polymerase and a DNA block to elongation appears to specifically induce a discontinuous mode of synthesis. These findings provide important new insights into the RNA chain elongation process and offer the prospect of understanding many significant biological regulatory systems at the molecular level.
Structural Basis of Chemokine Receptor Function—A Model for Binding Affinity and Ligand Selectivity (2006)

Chemokine receptors play fundamental roles in human physiology from embryogenesis to inflammatory response. The receptors belong to the G-protein coupled receptor class, and are activated by chemokine ligands with a range of specificities and affinities that result in a complicated network of interactions. The molecular basis for function is largely a black box, and can be directly attributed to the lack of structural information on the receptors. Studies to date indicate that function can be best described by a two-site model, that involves interactions between the receptor N-domain and ligand N-terminal loop residues (site-I), and between receptor extracellular loop and the ligand N-terminal residues (site-II). In this review, we describe how the two-site model could modulate binding affinity and ligand selectivity, and also highlight some of the unique chemokine receptor features, and their role in function.
Codes with locality for two erasures (2014)

In this paper, we study codes with locality that can recover from two erasures via a sequence of two local, parity-check computations. By a local parity-check computation, we mean recovery via a single parity-check equation associated with small Hamming weight. Earlier approaches considered recovery in parallel; the sequential approach allows us to potentially construct codes with improved minimum distance. These codes, which we refer to as locally 2-reconstructible codes, are a natural generalization along one direction, of codes with all-symbol locality introduced by Gopalan et al, in which recovery from a single erasure is considered. By studying the generalized Hamming weights of the dual code, we derive upper bounds on the minimum distance of locally 2-reconstructible codes and provide constructions for a family of codes based on Turán graphs, that are optimal with respect to this bound. The minimum distance bound derived here is universal in the sense that no code which permits all-symbol local recovery from 2 erasures can have larger minimum distance regardless of approach adopted. Our approach also leads to a new bound on the minimum distance of codes with all-symbol locality for the single-erasure case.
Effect of the character of autonomic response and the emotional and personality features of a human being on reactions of the vestibular system. (2000)

A moderate degree (R = 0.37-0.45) of correlation between the values of vestibular reactivity, autonomic response, and emotional and personality characteristics was revealed. A conclusion was made that the following features of the background functional organization of the vestibular system, autonomic and emotional and personality characteristics are space sickness predictors: (1) a high coefficient of enhancement of the vestibuloocular reflex (VOR) and its asymmetry with an excess of the physiological norm limits, (2) the presence of depressive manifestations, (3) the impulsive and autistic personality type, and (4) a relative sympathetic deficit and/or increased parasympathetic effects at rest and when engaged in activity. [Translated from Fiziologiya Cheloveka, vol. 25, no. 5, 1999 Sep-Oct, p. 57-63]
Effect of Neuropeptide Y (NPY) on Oral Ethanol Intake in Wistar, Alcohol-Preferring (P), and -Nonpreferring (NP) Rats (2001)

Background: Neuropeptide Y (NPY) deficient mice consume more ethanol than controls, whereas NPY over-expressing mice consume less ethanol than controls. Thus, ethanol drinking may be inversely associated with NPY activity. To determine whether exogenously administered NPY would alter ethanol intake, two experiments were conducted. Methods: A within-subject design was used with intracerebroventricular (ICV) administration of NPY or artificial cerebral spinal fluid (aCSF) into the lateral ventricles. Infusions were separated by 2 to 7 days. In experiment 1, male Wistar rats (n= 10) were tested for the effects of NPY on an intake of 5% sucrose or 8% (w/v) ethanol during daily 2-hr testing periods with food and water available at all other times. In experiment 2, male alcohol-preferring (P) and alcohol-nonpreferring (NP) rats (n= 8/line) were tested for the effects of NPY on 8% (w/v) ethanol intake. Results: In experiment 1, NPY (5, 10, 20 μg) significantly increased sucrose intake relative to aCSF baseline in Wistar rats, a finding consistent with previous observations of the orexigenic effects of the peptide. However, NPY (10 μg) did not alter ethanol intake in Wistar rats. In experiment 2, NPY (5 and 10 μg) significantly decreased ethanol intake in P rats, but not in NP rats. Conclusion: The reduction in ethanol intake seen with the P rats is consistent with the postulated negative relationship between NPY activity and ethanol intake. The lack of effect of NPY on ethanol intake in Wistar and NP rats may be related to the lower baseline levels of ethanol intake in these rats or to differential central nervous system basal NPY activity or sensitivity to the peptide.
Direct Evidence for a Role of the “Spot 14” Protein in the Regulation of Lipid Synthesis (1995)

"Spot 14" is a nuclear protein that is rapidly induced by thyroid hormone (T3) and dietary carbohydrate in liver. We used an antisense oligonucleotide to inhibit induction of spot 14 protein by T3 and glucose in primary cultures of rat hepatocytes to test the hypothesis that the protein could function in the regulation of lipid synthesis. Spot 14 protein was undetectable in hepatocytes maintained in 5.5 mM glucose without T3, and was induced within 4 h after addition of 27.5 mM glucose and 50 nM T3 to the culture medium, reaching a maximal level within 24 h. Accumulation of spot 14 protein was markedly inhibited in hepatocytes transfected with a spot 14 antisense oligonucleotide, but not in those treated with a control oligonucleotide. Transfection of the antisense, but not control, oligonucleotide also abrogated the increase in lipogenesis induced by T3 and glucose. Reduced triglyceride formation accounted for the diminished net lipid synthesis. In contrast to lipogenesis, glucose uptake was not significantly affected by the transfections. Antisense transfection inhibited the induction of both ATP-citrate lyase and fatty acid synthase immunoreactivities, as well as malic enzyme activity, indicating that the observed reduction in lipogenesis could be explained by diminished cellular content of lipogenic enzymes. Reduced malic enzyme activity in antisense-transfected hepatocytes was accompanied by lowered relative abundance of malic enzyme mRNA, suggesting that the antisense effects on lipogenic enzymes were mediated at the pretranslational level. The oligonucleotides did not significantly affect lipogenesis in a rat hepatoma cell line that does not express detectable spot 14 mRNA or protein. These data directly implicate the spot 14 protein in the transduction of hormonal and dietary signals for increased lipid metabolism in hepatocytes.
Bioelectrochemical Propulsion (2005)

A carbon fiber having a terminal glucose oxidizing microanode and an O2 reducing microcathode is propelled at the water-O2 interface. The electron current in the fiber is accompanied by a flux of hydrated protons that is so fast at the solution-air interface, where the viscous drag is small, that the fiber's velocity is 1 cm s-1.
Clinical decision support system: Risk level prediction of heart disease using weighted fuzzy rules (2011)

As people have interests in their health recently, development of medical domain application has been one of the most active research areas. One example of the medical domain application is the detection system for heart disease based on computer-aided diagnosis methods, where the data are obtained from some other sources and are evaluated based on computer-based applications. Earlier, the use of computer was to build a knowledge based clinical decision support system which uses knowledge from medical experts and transfers this knowledge into computer algorithms manually. This process is time consuming and really depends on medical experts’ opinions which may be subjective. To handle this problem, machine learning techniques have been developed to gain knowledge automatically from examples or raw data. Here, a weighted fuzzy rule-based clinical decision support system (CDSS) is presented for the diagnosis of heart disease, automatically obtaining knowledge from the patient’s clinical data. The proposed clinical decision support system for the risk prediction of heart patients consists of two phases: (1) automated approach for the generation of weighted fuzzy rules and (2) developing a fuzzy rule-based decision support system. In the first phase, we have used the mining technique, attribute selection and attribute weightage method to obtain the weighted fuzzy rules. Then, the fuzzy system is constructed in accordance with the weighted fuzzy rules and chosen attributes. Finally, the experimentation is carried out on the proposed system using the datasets obtained from the UCI repository and the performance of the system is compared with the neural network-based system utilizing accuracy, sensitivity and specificity.
Labeling of Monoclonal Antibodies with Diethylenetriaminepentaacetic Acid-Appended Radioiodinated Peptides Containingd-Amino Acids (1999)

The optimal use of radioiodinated internalizing monoclonal antibodies (mAbs) for radioimmunotherapy necessitates the development of practical methods for increasing the level of retention of 131I in the tumor. Lysosomally trapped ("residualizing") iodine radiolabels that have been previously designed are based mostly on carbohydrate-tyramine adducts, but these methods have drawbacks of low overall yields and/or high levels of mAb aggregation. We have developed a method using thiol-reactive diethylenetriaminepentaacetic acid (DTPA)-peptide adducts wherein the peptides are assembled with one or more D-amino acids, including D-tyrosine. Two such substrates, R-Gly-D-Tyr-D-Lys[1-(p-thiocarbonylaminobenzyl)DTPA], referred to as IMP-R1, and [R-D-Ala-D-Tyr-D-Tyr-D-Lys]2(CA-DTPA), referred to as IMP-R2, wherein R is 4-(N-maleimidomethyl)cyclohexane-1-carbonyl, were synthesized by preparing functional group-protected peptides on a solid phase, selectively derivatizing the lysine side chain with 1-(p-isothiocyanatobenzyl)DTPA or DTPA dianhydride (CA-DTPA), deprotecting other functional groups, and finally derivatizing the peptide's N-terminus so it contained a maleimide group. Radioiodinations of the peptides followed by conjugations to disulfide-reduced mAbs, carried out as a one-vial procedure, resulted in 32-89% overall yields, at specific activities of 1.8-11. 1 mCi/mg, with less than 2% aggregation. Two internalizing mAbs, LL2 (anti-CD 22 B-cell lymphoma mAb) and RS7 (an anti-adenocarcinoma mAb which targets EGP-1 antigen), labeled with this procedure exhibited a 2-3-fold better cellular retention in Ramos and Calu-3 tumor cell lines, in vitro, respectively, compared to the same mAbs radioiodinated with the chloramine-T method. The rationale for the new approach, syntheses, radiochemistry and in vitro data are presented.
Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer (2012)

There is an immediate need for improved methods to systematically and precisely quantify large sets of peptides in complex biological samples. To date protein quantification in biological samples has been routinely performed on triple quadrupole instruments operated in selected reaction monitoring mode (SRM), and two major challenges remain. Firstly, the number of peptides to be included in one survey experiment needs to be increased to routinely reach several hundreds, and secondly, the degree of selectivity should be improved so as to reliably discriminate the targeted analytes from background interferences. High resolution and accurate mass (HR/AM) analysis on the recently developed Q-Exactive mass spectrometer can potentially address these issues. This instrument presents a unique configuration: it is constituted of an orbitrap mass analyzer equipped with a quadrupole mass filter as the front-end for precursor ion mass selection. This configuration enables new quantitative methods based on HR/AM measurements, including targeted analysis in MS mode (single ion monitoring) and in MS/MS mode (parallel reaction monitoring). The ability of the quadrupole to select a restricted m/z range allows one to overcome the dynamic range limitations associated with trapping devices, and the MS/MS mode provides an additional stage of selectivity. When applied to targeted protein quantification in urine samples and benchmarked with the reference SRM technique, the quadrupole-orbitrap instrument exhibits similar or better performance in terms of selectivity, dynamic range, and sensitivity. This high performance is further enhanced by leveraging the multiplexing capability of the instrument to design novel acquisition methods and apply them to large targeted proteomic studies for the first time, as demonstrated on 770 tryptic yeast peptides analyzed in one 60-min experiment. The increased quality of quadrupole-orbitrap data has the potential to improve existing protein quantification methods in complex samples and address the pressing demand of systems biology or biomarker evaluation studies.
Specific sequestering agents for the actinides. 3. Polycatecholate ligands derived from 2,3-dihydroxy-5-sulfobenzoyl conjugates of diaza- and tetraazaalkanes (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSpecific sequestering agents for the actinides. 3. Polycatecholate ligands derived from 2,3-dihydroxy-5-sulfobenzoyl conjugates of diaza- and tetraazaalkanesFrederick L. Weitl and Kenneth N. RaymondCite this: J. Am. Chem. Soc. 1980, 102, 7, 2289–2293Publication Date (Print):March 1, 1980Publication History Published online1 May 2002Published inissue 1 March 1980https://pubs.acs.org/doi/10.1021/ja00527a026https://doi.org/10.1021/ja00527a026research-articleACS PublicationsRequest reuse permissionsArticle Views457Altmetric-Citations44LEARN 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
Cholesterolemic Rabbit Lipoproteins: Serum Lipoproteins of the Cholesterolemic Rabbit (1955)

The chemical composition of the low density lipoproteins (S f 0 to 25. S f 15 to 100, and S f 20 to 400) has been investigated by isolating the molecules centrifugally and separating the various lipid constituents on silicic acid columns and analyzing the fractions so obtained by infrared spectrophotometry. Quantitative protein determinations were also made upon each group of lipoproteins. The molecules are shown to contain 40–60% cholesterol esters, 10–20% unesterified cholesterol, 10–20% phospholipid, and 3–30% protein, depending upon the sedimentation characteristics. The quantity of glyceride was usually less than 10% for all of the above mentioned groups of lipoproteins. The quantity of unesterified fatty acids was always less than 6%. Two of the four animals from which samples were withdrawn and analyzed had previously received daily heparin injections for a period of 10 weeks. The effects of heparin injections upon the ultracentrifugal patterns of a larger group of rabbits was also studied. No significant changes in the concentrations of the S f 5 to 15, S f 15 to 40, and S f 40 to 100 species of lipoproteins were found which could be attributed to the heparin injections. The major peak, usually to be found in the S f 5 to 15 region, did show a small but significant decrease in sedimentation coefficient in response to heparin injection. Serum from all of the animals receiving heparin did show a definite lipolytic activity in vitro.
Add-on Therapy of EPA Reduces Oxidative Stress and Inhibits the Progression of Aortic Stiffness in Patients with Coronary Artery Disease and Statin Therapy: A Randomized Controlled Study (2011)

EPA may reduce oxidative stress and inhibit the progression of arterial stiffness more efficiently than statin-only therapy in patients with dyslipidemia and CAD.
Lower extremity joint kinetics and lumbar curvature during squat and stoop lifting (2009)

In conclusion, the knee extension which is prominent kinematics during the squat lifting was produced by the contributions of the kinetic factors from the hip and ankle joints(extensor moment and power generation) and the lumbar extension which is prominent kinematics during the stoop lifting could be produced by the contributions of the knee joint kinetic factors(flexor moment, power absorption, bi-articular muscle function).
Kinetics of In-111-Platelets in the Baboon: I. Isolation and Labelling of a Viable and Representative Platelet Population (1985)

A fully representative and viable platelet population was isolated from the blood of 15 baboons by a multiwash procedure, and labelled with In-111-oxine. The recovery of the total platelet population in the circulation was 85% +/- 9. Mean platelet life span was 146 hr +/- 13. Correcting for plasma radioactivity (always less than 3.5%) did not significantly affect the estimate of platelet life span (145 hr +/- 16) or recovery (85% +/- 12). Platelet survival estimates, repeated at different times, were reproducible. In 5 baboons, platelets were also harvested by a single step differential centrifugation. The mean life span of a representative platelet population was significantly longer than that of platelets harvested by a single step. Recovery values of the representative and non-representative population were similar. We conclude that it may be important to harvest and label a fully representative platelet population for kinetic studies. The proposed method is simple and reproducible, and may be applied in studies in humans.
Use of adeno-associated virus as a mammalian DNA cloning vector: transduction of neomycin resistance into mammalian tissue culture cells. (1984)

Adeno-associated virus (AAV) is a human DNA virus that has a broad host range and can be grown both as an integrated provirus and as a lytic genome. These properties suggested that AAV may be useful as a mammalian transduction vector. To test this possibility, we have isolated a recombinant AAV viral stock in which the neomycin resistance gene was substituted for the AAV capsid genes. Using this recombinant stock, we have demonstrated that AAV can be used to transduce foreign DNA into human and murine tissue culture cells. In addition, we have demonstrated that, if the transductants are superinfected with a helper virus (adenovirus), the recombinant AAV genome is rescued from the proviral state and amplified to high copy number. These unique features of AAV vectors suggest that they may have a broad utility in the study of biological problems. Because AAV, itself, is nonpathogenic in both humans and animals, these vectors also may be useful for the purpose of gene therapy.
α-Helical Coiled-coil Oligomerization Domains Are Almost Ubiquitous in the Collagen Superfamily (2003)

Alpha-helical coiled-coils are widely occurring protein oligomerization motifs. Here we show that most members of the collagen superfamily contain short, repeating heptad sequences typical of coiled coils. Such sequences are found at the N-terminal ends of the C-propeptide domains in all fibrillar procollagens. When fused C-terminal to a reporter molecule containing a collagen-like sequence that does not spontaneously trimerize, the C-propeptide heptad repeats induced trimerization. C-terminal heptad repeats were also found in the oligomerization domains of the multiplexins (collagens XV and XVIII). N-terminal heptad repeats are known to drive trimerization in transmembrane collagens, whereas fibril-associated collagens with interrupted triple helices, as well as collagens VII, XIII, XXIII, and XXV, were found to contain heptad repeats between collagen domains. Finally, heptad repeats were found in the von Willebrand factor A domains known to be involved in trimerization of collagen VI, as well as in collagen VII. These observations suggest that coiled-coil oligomerization domains are widely used in the assembly of collagens and collagen-like proteins.
Realistic lower bounds for the factorization time of large numbers on a quantum computer (1996)

We investigate the time T a quantum computer requires to factorize a given number dependent on the number of bits L required to represent this number. We stress the fact that in most cases one has to take into account that the execution time of a single quantum gate is related to the decoherence time of the quantum bits (qubits) that are involved in the computation. Although exhibited here only for special systems, this interdependence of decoherence and computation time seems to be a restriction in many current models for quantum computers and leads to the result that the computation time T scales much stronger with L than previously expected. \textcopyright{} 1996 The American Physical Society.
Supramolecular Peptide Amphiphile Vesicles through Host–Guest Complexation (2012)

Tricky triggering: Supramolecular peptide amphiphiles were prepared by host–guest complexation of pyrene-labeled peptides and viologen lipid with cucurbit[8]uril. They self-assemble into vesicles, which are responsive to a variety of external triggers. Both “switching on” and “switching off” of fluoresence and cytotoxicity is demonstrated in vitro.