gebhart/patrepeval huggingface dataset:
Structural organization of the genes for murine and human leukemia inhibitory factor. Evolutionary conservation of coding and non-coding regions. (1990)

Leukemia inhibitory factor, LIF, is a glycoprotein with multiple activities in both the adult and the embryo. LIF appears to be encoded by a unique gene in both mouse and man, although the 3'-untranslated region of the mouse LIF gene gives a complex hybridization pattern on Southern blots. The complete nucleotide sequences of both the murine and human LIF genes and their flanking regions (8.7 and 7.6 kilobase pairs, respectively) were determined and compared. Both genes comprise three exons, two introns and an unusually long 3'-untranslated region (3.2 kilobase pairs), specificying a mRNA of approximately 4.1 kilobases. Two start sites of LIF-transcription were determined, by S1-nuclease protection and by a novel approach involving the polymerase chain reaction. S1-nuclease protection revealed a start site 60-64 base pairs upstream of the translational start codon and immediately downstream of a TATA box (TATATAAAT). The PCR approach identified a second transcriptional start site 160 base pairs 5' of the start codon and adjacent to a "TATA-like" element (CATAATTT). A comparison of the murine and human LIF gene sequences revealed a high degree of conservation in the coding regions and in segments of the untranslated and flanking regions. Seven segments displaying greater than 75% homology were identified, with the 5' and 3' ends of the transcription unit revealing the highest degree of homology. These conserved regions represents potential cis-acting control elements.
Soluble intercellular adhesion molecule-1, E-selectin, vascular cell adhesion molecule-1 and von Willebrand factor in stroke (1999)

We investigated the role of endothelial cell and leukocyte adhesion in the pathophysiology of acute stroke. The immunocytochemical expression of adhesion molecules in brain tissue from six patients who died following acute ischaemic stroke showed weak endothelial expression of intercellular adhesion molecule-1 (ICAM-1), but intense expression of vascular cell adhesion molecule-1 (VCAM-1) by astrocytes and endothelial cells from the infarcted, but not the non-infarcted areas. We also measured soluble adhesion molecules E-selectin, ICAM-1, VCAM-1 and von Willebrand factor (all by enzyme-linked immunosorbent assay) in 21 patients after an acute ischaemic stroke (ictus < 12 h), and again 3 months later. Blood levels in the stroke patients were compared with 82 healthy controls and 22 subjects with carotid atherosclerosis. Compared with healthy controls, both patient groups had raised levels of von Willebrand factor (P < 0.02) but the level of soluble VCAM-1 was raised only in patients with acute stroke (P < 0.02). Levels of von Willebrand factor and soluble VCAM-1 in the stroke patients were still high at 3 months follow-up. We suggest that there might be changes in adhesion molecule expression and release in the acute and chronic stages of ischaemic stroke, where blood levels are related to immunocytochemical findings on infarcted brain. These changes may perhaps be part of the complex pathophysiological responses to infarction and repair of brain tissue following stroke.
Effective generation of transgenic pigs and mice by linker based sperm-mediated gene transfer. (2002)

Our data suggests that LB-SMGT could be used to generate transgenic animals efficiently in many different species.
Plasma Soluble (Pro)Renin Receptor Is Independent of Plasma Renin, Prorenin, and Aldosterone Concentrations But Is Affected by Ethnicity (2013)

A soluble (pro)renin receptor (sPRR) circulates in plasma and is able to bind renin and prorenin. It is not known whether plasma sPRR concentrations vary with the activity of the renin-angiotensin system. We measured plasma sPRR, renin, prorenin, and aldosterone concentrations in 121 white and 9 black healthy subjects, 40 patients with diabetes mellitus, 41 hypertensive patients with or without renin-angiotensin system blockers, 9 patients with primary aldosteronism, and 10 patients with Gitelman syndrome. Median physiological plasma sPRR concentration was 23.5 ng/mL (interquartile range, 20.9-26.5) under usual uncontrolled sodium diet. sPRR concentration in healthy subjects, unlike renin and prorenin, did not display circadian variation or dependence on age, sex, posture, or hormonal status. sPRR concentrations were ≈25% lower in black than in white subjects, whereas renin concentrations were ≈40% lower. Patients with diabetes mellitus (average renin-high prorenin levels) and with hypertension only (average renin-average prorenin levels) had sPRR concentrations similar to healthy subjects. Renin-angiotensin system blockade was associated with increase of sPRR concentration by ≈12%. sPRR in patients with primary aldosteronism (low renin-low prorenin) and Gitelman syndrome (high renin-high prorenin) were similar and ≈10% higher than in healthy subjects. There was no correlation between sPRR and renin or prorenin. In conclusion, our results show that plasma sPRR concentrations are dependent on ethnicity and independent of renin, prorenin, and aldosterone concentrations in healthy subjects and in patients with contrasted degrees of renin-angiotensin system activity.
Thin observation module by bound optics (TOMBO): concept and experimental verification (2001)

A compact image-capturing system called TOMBO (an acronym for thin observation module by bound optics) is presented in which the compound-eye imaging system is utilized to achieve a thin optical configuration. The captured multiple images are processed to retrieve the image of the target object. For image retrieval, two kinds of processing method are considered: image sampling and backprojection. Computer simulations and preliminary experiments were executed on an evaluation system to verify the principles of the system and to clarify the issues related to its implementation.
Graph-based approach for interference free integration of pervasive applications (2012)

Smart-space modeling is a fundamental requirement towards the achievement of safe integration of pervasive systems and devices. Traditional behavior models lack explicit representation of rich semantic for ubicomp systems. We propose a graph-based model supporting ubicomp's computational, physical, user and temporal contextual information. The model is part of a solution to tackle the interference problem, which results from unexpected interactions involving users and entertainment, communication, and health-related devices. This is a major concern when, for instance, daily routines are affected by different types of applications. The proposed graph-based interference detection is integrated in the Safe Home Care reflective platform, and allows reifying system's state and simulating home care scenarios. A set of home care scenarios are used to assess the applicability and correctness of our approach.
Kinetic and Mechanistic Analysis of Nonenzymatic, Template-Directed Oligoribonucleotide Ligation (1996)

The role of divalent cations in the mechanism of pyrophosphate-activated, template-directed oligoribonucleotide ligation has been investigated. The dependence of the reaction rate on Mg2+ concentration suggests a kinetic scheme in which a Mg2+ ion must bind before ligation can proceed. Mn2+, Ca2+, Sr2+, and Ba2+ can also catalyze the reaction. Although Pb2+ and Zn2+ do not catalyze the reaction in the absence of other divalent ions, they significantly modulate the reaction rate when added in the presence of Mg2+, with Pb2+ stimulating the reaction (up to 65-fold) and Zn2+ inhibiting the reaction. The logarithm of the ligation rate increases linearly, with slope of 0.95, as a function of pH, indicating that the reaction involves a single critical deprotonation step. The ligation rates observed with the different divalent metal ion catalysts (Mn2+ > Mg2+ > Ca2+ > Sr2+ = Ba2+) vary inversely with the pKa values of their bound water molecules. The pH profile and these relative ligation rates suggest a mechanism in which a metal-bound hydroxide ion located near the ligation junction promotes catalysis, most likely by deprotonation of the hydroxl nucleophile. The effects of changing either the leaving group or the attacking hydroxyl, together with the large delta S(++) value for oligonucleotide ligation (about -20 eu), are consistent with an associative transition state.
Partial characterization of a bovine group A rotavirus with a short genome electropherotype (1988)

A group A rotavirus (ID isolate) recovered from a diarrheic beef calf possessed a short genome electropherotype. This short genome electropherotype was a stable characteristic of the ID isolate as it remained unchanged through 3 passages in gnotobiotic calves or through 19 passages in MA104 cell cultures. Subgroup analysis with monoclonal antibodies in an enzyme-linked immunosorbent assay established that the isolate was a subgroup 1 rotavirus. Neutralization tests demonstrated that this isolate was a distinct serotype from the human group A rotavirus S2 isolate (short genome electropherotype) and the turkey group A rotavirus 174 isolate (semi-short genome electropherotype). The ID isolate was pathogenic for 5- to 21-day-old gnotobiotic calves, inducing diarrhea within 48 h postinoculation.
Prolonged Disease-Free Survival in Hodgkin's Disease with MOPP Reinduction After First Relapse (1979)

Thirty-two patients with Hodgkin's disease who relapsed after a first complete remission induced by nitrogen mustard, vincristine, procarbazine, and prednisone (MOPP) were retreated with MOPP chemotherapy. Nineteen patients achieved a second complete remission. Median duration of the second complete remission was 21 months. The likelihood of achieving a second complete response could be predicted by the duration of the first response. Fourteen of 15 patients whose first complete remission was longer than 12 months achieved a second complete response in contrast to five of 17 patients whose initial complete remission lasted less than 12 months (P less than 0.001). Median survival of all patients in this study who were re-treated with MOPP was longer than 4 years after their first relapse. We conclude that patients with Hodgkin's disease who relapse after a first complete remission induced by MOPP are not necessarily resistant to further MOPP therapy and can achieve long-term survival with MOPP reinduction.
Protein Engineering:  Design of Single-Residue-Anchored Metal-Uptake Systems (1999)

From the vantage of inorganic chemistry, the inability of any of the coded amino acid side chains to carry metal ions should appear as a grave omission in the genetic code, particularly since, metalloenzymes play a pivotal role in diverse facets of life processes. The ready transformation of the coded amino acid tyrosine to metal-uptake systems in a peptide environment forms the core of the present work, thus enabling a minimalistic design of metalloproteins, where the peptide segment that generally constitutes the metal-binding region in copper electron-transfer proteins can be replaced by a single amino acid.
Array-driven ultrasonic microactuators (2002)

The authors present the design of an array-driven ultrasonic microactuator. Unlike a conventional ultrasonic motor, the array-driven ultrasonic microactuator consists of many distributed modules, using a concept similar to that of the distributed microactuator array. With a conventional ultrasonic motor, it is difficult to control an object locally and to obtain sufficient resolution of the rotor position and orientation without closed-loop control, since the motion of the rotor is produced by traveling waves on the whole diaphragm. However, an array-driven ultrasonic microactuator can control the motion with high accuracy even in open-loop control, because it can control the motion of each distributed module. It uses perpendicular motion, which is suitable for an electrostatic-force-type actuator. Perpendicular motions produced by two transducers in each module are mechanically transformed into circular motion, and a set of circular motions of the micromodules induces motion in the object.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The R‐type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F‐type is related to lambda phage (2000)

Pseudomonas aeruginosa produces three types of bacteriocins: R-, F- and S-type pyocins. The S-type pyocin is a colicin-like protein, whereas the R-type pyocin resembles a contractile but non-flexible tail structure of bacteriophage, and the F-type a flexible but non-contractile one. As genetically related phages exist for each type, these pyocins have been thought to be variations of defective phage. In the present study, the nucleotide sequence of R2 pyocin genes, along with those for F2 pyocin, which are located downstream of the R2 gene cluster on the chromosome of P. aeruginosa PAO1, was analysed in order to elucidate the relationship between the pyocins and bacteriophages. The results clearly demonstrated that the R-type pyocin is derived from a common ancestral origin with P2 phage and the F-type from lambda phage. This notion was supported by identification of a lysis gene cassette similar to those for bacteriophages. The gene organization of the R2 and F2 pyocin gene cluster, however, suggested that both pyocins are not simple defective phages, but are phage tails that have been evolutionarily specialized as bacteriocins. A systematic polymerase chain reaction (PCR) analysis of P. aeruginosa strains that produce various subtypes of R and F pyocins revealed that the genes for every subtype are located between trpE and trpG in the same or very similar gene organization as for R2 and F2 pyocins, but with alterations in genes that determine the receptor specificity.
Anticancer agents. IV. Antitumor activity of some 1,4- and 1,5-(bisthiosemicarbazones) and of related heterocycles (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnticancer agents. IV. Antitumor activity of some 1,4- and 1,5-(bisthiosemicarbazones) and of related heterocyclesVincent C. Barry, Michael L. Conalty, Joan E. McCormick, Robert S. McElhinney, Mary R. McInerney, and John F. O'SullivanCite this: J. Med. Chem. 1970, 13, 3, 421–427Publication Date (Print):May 1, 1970Publication History Published online1 May 2002Published inissue 1 May 1970https://pubs.acs.org/doi/10.1021/jm00297a021https://doi.org/10.1021/jm00297a021research-articleACS PublicationsRequest reuse permissionsArticle Views268Altmetric-Citations8LEARN 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
Teratogenicity induced by targeting a placental immunoglobulin transporter (2002)

Approximately 3% of children in developed countries are born with nongenetic birth defects. However, the nature and mechanisms of teratogenesis are poorly understood. We investigated mechanisms of teratogen-mediated blockade of maternofetal transport by screening a combinatorial library for peptides that bind nonendothelial placental vasculature in pregnant mice. Here, we identified a peptide motif, TPKTSVT, that homes to the yolk sac, induces placental necrosis, and disrupts embryo development. We show that TPKTSVT promotes transcytosis of phage into the embryo and blocks the transplacental transport of immunoglobulins. Based on these data, we propose a model in which TPKTSVT targets a placental Fc receptor. Absence of TPKTSVT placental homing in mice lacking beta(2)-microglobulin (beta(2)m) suggests FcRn/beta(2)m as a target for the TPKTSVT, which is unexpected, given the normal development of FcRn/beta(2)m-deficient progeny. High-throughput screening for embryotoxins that target placental receptors could be developed to systematically identify and avoid exposure to teratogenic drugs.
Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents (2014)

Limited chemical diversity of nucleic acid libraries has long been suspected to be a major constraining factor in the overall success of SELEX (Systematic Evolution of Ligands by EXponential enrichment). Despite this constraint, SELEX has enjoyed considerable success over the past quarter of a century as a result of the enormous size of starting libraries and conformational richness of nucleic acids. With judicious introduction of functional groups absent in natural nucleic acids, the "diversity gap" between nucleic acid-based ligands and protein-based ligands can be substantially bridged, to generate a new class of ligands that represent the best of both worlds. We have explored the effect of various functional groups at the 5-position of uracil and found that hydrophobic aromatic side chains have the most profound influence on the success rate of SELEX and allow the identification of ligands with very low dissociation rate constants (named Slow Off-rate Modified Aptamers or SOMAmers). Such modified nucleotides create unique intramolecular motifs and make direct contacts with proteins. Importantly, SOMAmers engage their protein targets with surfaces that have significantly more hydrophobic character compared with conventional aptamers, thereby increasing the range of epitopes that are available for binding. These improvements have enabled us to build a collection of SOMAmers to over 3,000 human proteins encompassing major families such as growth factors, cytokines, enzymes, hormones, and receptors, with additional SOMAmers aimed at pathogen and rodent proteins. Such a large and growing collection of exquisite affinity reagents expands the scope of possible applications in diagnostics and therapeutics.
Epitope determines efficacy of therapeutic anti-Tau antibodies in a functional assay with human Alzheimer Tau (2018)

In Alzheimer’s disease (AD) and other tauopathies, the cytosolic protein Tau misfolds and forms intracellular aggregates which accumulate within the brain leading to neurodegeneration. Clinical progression is tightly linked to the progressive spread of Tau pathology throughout the brain, and several lines of evidence suggest that Tau aggregates or “seeds” may propagate pathology by spreading from cell to cell in a “prion like” manner. Accordingly, blocking the spread of extracellular seeds with an antibody could be a viable therapeutic approach. However, as the structure of Tau seeds is unknown, it is only possible to rationally design therapeutic Tau antibodies by making a priori assumptions. To avoid this, we developed a robust and quantitative cell based assay and employed an unbiased screening approach to identify the antibody with the highest activity against human Tau seeds. The selected antibody (D), directed to the mid-region of Tau (amino acids 235–250), potently blocked the seeding of human AD Tau and was also fully efficacious against seeds from progressive supranuclear palsy. When we compared this antibody with previously described reference antibodies, we were surprised to find that none of these antibodies showed comparable efficacy against human pathological seeds. Our data highlight the difficulty of predicting antibody accessible epitopes on pathological Tau seeds and question the potential efficacy of some of the Tau antibodies that are currently in clinical development.
Catalytic Properties of Botulinum Neurotoxin Subtypes A3 and A4 (2009)

Botulinum toxins (BoNT) are zinc proteases (serotypes A-G) which cause flaccid paralysis through the cleavage of SNARE proteins within motor neurons. BoNT/A was originally organized into two subtypes, BoNT/A1 and BoNT/A2, which are approximately 95% homologous and possess similar catalytic activities. Subsequently, two additional subtypes were identified, BoNT/A3 (Loch Maree) and BoNT/A4 (657Ba), which are 81 and 88% homologous with BoNT/A1, respectively. Alignment studies predicted that BoNT/A3 and BoNT/A4 were sufficiently different from BoNT/A1 to affect SNAP25 binding and cleavage. Recombinant light chain (LC) of BoNT/A3 (LC/A3) and BoNT/A4 (LC/A4) were subjected to biochemical analysis. LC/A3 cleaved SNAP25 at 50% of the rate of LC/A1 but cleaved SNAPtide at a faster rate than LC/A1, while LC/A4 cleaved SNAP25 and SNAPtide at slower rates than LC/A1. LC/A3 and LC/A4 had similar K(m) values for SNAP25 relative to LC/A1, while the k(cat) for LC/A4 was 10-fold slower than that for LC/A1, suggesting a defect in substrate cleavage. Neither LC/A3 nor LC/A4 possessed autocatalytic activity, a property of LC/A1 and LC/A2. Thus, the four subtypes of BoNT/A bind SNAP25 with similar affinity but have different catalytic capacities for SNAP25 cleavage, SNAPtide cleavage, and autocatalysis. The catalytic properties identified among the subtypes of LC/A may influence strategies for the development of small molecule or peptide inhibitors as therapies against botulism.
A molecular trigger of lipid binding-induced opening of a helix bundle exchangeable apolipoprotein (1999)

Apolipophorin III (apoLp-III) from the sphinx moth, Manduca sexta, is a helix bundle protein that interacts reversibly with lipoproteins. Its five elongated amphipathic alpha-helices are organized in an antiparallel fashion, with helices 3 and 4 connected by a short 6-residue (PDVEKE) linker helix, termed helix 3'. Upon interaction with lipoproteins, apoLp-III opens to expose a continuous hydrophobic interior. It was postulated that helix bundle opening is preceded by an initiation step wherein helix 3' serves to recognize available lipoprotein surface binding sites. To test this hypothesis, helix 3' was replaced by residues that have a propensity to form a type I beta-turn, NPNG. This mutant apoLp-III was defective in lipoprotein binding assays. To define a more precise mode of interaction, the relevance of the presence of the hydrophobic Val-97 flanked by Asp-96 and Glu-98 was investigated by site-directed mutagenesis. V97N and D96N/V97N/E98Q apoLp-III were unable to compete with wild-type apoLp-III to initiate an interaction with lipoproteins, whereas D96N/E98Q apoLp-III was as competent as wild-type apoLp-III. The results suggest that Val-97 is critical, whereas Asp-96 and Glu-98 are irrelevant for initiating binding to lipoproteins. A model of binding is presented wherein apoLp-III is oriented with the helix 3' end of the molecule juxtaposed to the lipoprotein surface. Recognition of lipoprotein surface hydrophobic defects by Val-97 triggers opening of the helix bundle and facilitates formation of a stable binding interaction.
The IC50: an exactly defined measure of antibiotic sensitivity (1992)

The concentration of gentamicin that inhibits the growth of half of an inoculum of Pseudomonas aeruginosa (IC50) was estimated by doing viable bacterial counts with varying concentrations of gentamicin and fitting a probit inhibition curve to the results. This is a more precisely defined measure than the MIC and its standard error is readily calculable.