gebhart/patrepeval huggingface dataset:
Using 17 α-hydroxyprogesterone caproate to impact rates of recurrent preterm delivery in clinical practice (2010)

Objective. Evaluation of an outpatient 17 α-hydroxyprogesterone caproate (17P) administration programme.Methods. A retrospective analysis of data collected from patients with a history of preterm birth (PTB) and current singleton gestation enrolled between 16.0 and 20.9 weeks' gestational age (GA) for weekly outpatient 17P administration and nursing assessment between 7/2004 and 12/2007 was conducted (n = 3139).Results. The population was mostly white (50.3%), 18–35 years old (77.7%), and married (67.0%). Median GA at 17P initiation and stop was 17.4 (16.0, 20.9) weeks and 35.1 (18.6, 37.4) weeks. Mean injections per patient were 16.5 ± 4.9, at an interval of 7.2 days. Median GA at delivery was 37.3 (18.6, 44.0) weeks. Rate of recurrent spontaneous PTB was 29.8%, with 15.5% and 7.0% with PTB at <35 and <32 weeks.Conclusions. This represents the largest cohort reported to date of patients prescribed 17P therapy in clinical practice to prevent recurrent spontaneous PTB.
From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software (2012)

Scientists working with single-nucleotide variants (SNVs), inferred by next-generation sequencing software, often need further information regarding true variants, artifacts and sequence coverage gaps. In clinical diagnostics, e.g. SNVs must usually be validated by visual inspection or several independent SNV-callers. We here demonstrate that 0.5-60% of relevant SNVs might not be detected due to coverage gaps, or might be misidentified. Even low error rates can overwhelm the true biological signal, especially in clinical diagnostics, in research comparing healthy with affected cells, in archaeogenetic dating or in forensics. For these reasons, we have developed a package called pibase, which is applicable to diploid and haploid genome, exome or targeted enrichment data. pibase extracts details on nucleotides from alignment files at user-specified coordinates and identifies reproducible genotypes, if present. In test cases pibase identifies genotypes at 99.98% specificity, 10-fold better than other tools. pibase also provides pair-wise comparisons between healthy and affected cells using nucleotide signals (10-fold more accurately than a genotype-based approach, as we show in our case study of monozygotic twins). This comparison tool also solves the problem of detecting allelic imbalance within heterozygous SNVs in copy number variation loci, or in heterogeneous tumor sequences.
Structural study on the micelle formation of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) triblock copolymer in aqueous solution (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural study on the micelle formation of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) triblock copolymer in aqueous solutionKell Mortensen and Jan Skov PedersenCite this: Macromolecules 1993, 26, 4, 805–812Publication Date (Print):February 1, 1993Publication History Published online1 May 2002Published inissue 1 February 1993https://pubs.acs.org/doi/10.1021/ma00056a035https://doi.org/10.1021/ma00056a035research-articleACS PublicationsRequest reuse permissionsArticle Views3810Altmetric-Citations643LEARN 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
Transformation of Maize by Electroporation of Embryos (2003)

Plant cell walls present a barrier to DNA uptake not present in mammalian cells or plant protoplasts. Transformation methods that force DNA through this network of cellulose fibers include particle gun technology (ballistics; 1), imbibition of dried seeds (2), and use of silicon carbide “whiskers” (3). Each of these methods has associated limitations. Ballistics, the bombarding of cells or tissues with high-velocity, DNA-coated microprojectiles, has been used most widely and successfully with both cell cultures (4–6) and embryos serving as target tissues. Electroporation has several advantages over ballistics in that it does not require the expensive particle gun apparatus, associated consumable supplies, and licensing. We describe in this chapter an electroporation protocol that has been used successfully to introduce DNA into maize embryos and has resulted in the recovery of stably transformed, fertile, transgenic maize plants.
Establishment and characterization of conditions required for tumor colonization by intravenously delivered bacteria (2008)

Intravenously injected bacteria have the ability to enter and replicate within tumors in mice. Here, we further characterized this dynamic process by investigating the conditions required for tumor colonization by bacteria. We discovered that a broad range of bacteria, including both Gram-negative and Gram-positive strains, colonize a panel of syngeneic and xenogeneic tumors, as well as spontaneous tumors in mice. The colonization process is dependent on the stage of tumor development, but independent of tumor type. The entry and replication of bacteria in tumors was consistently achieved in nude mice when approximately 1 x 10(5) bacteria were injected. The majority of the bacteria were found in the central portion of the tumors, coinciding with the necrotic regions of sectioned tumors. We also found that, although cancer can be characterized as a chronic inflammation, inflammation alone, as seen in cutaneous wounds and in sites artificially induced by Sephadex, was not sufficient to sustain bacterial colonization. Furthermore, we found that "sensitizing" the tumors by oncolytic vaccinia virus colonization prior to bacterial delivery may help to enhance tumor colonization at least twofold by bacteria that were delivered subsequently. Taken together, the data from this and previous studies, lead us to propose the concept that blood-borne bacteria enter tumors to amplify in the central necrotic region; and that, due to impaired immunosurveillance in the tumors as known previously, the clearance of bacteria is inhibited. Bacterial colonization of tumors could be achieved without any specific gene modifications either in bacteria or in the host.
Glucosylation of Steviol and Steviol-Glucosides in Extracts from Stevia rebaudiana Bertoni (1991)

To evaluate and characterize stevioside biosynthetic pathway in Stevia rebaudiana Bertoni cv Houten, two enzyme fractions that catalyze glucosylation of steviol (ent-13-hydroxy kaur-16-en-19-oic acid) and steviol-glucosides (steviol-13-O-glucopyranoside, steviolbioside and stevioside), utilizing UDP-glucose as the glucose donor, were prepared from the soluble extracts of S. rebaudiana leaves. Enzyme fraction I, passed through DEAE-Toyopearl equilibrated with 50 millimolar K-phosphate pH 7.5, catalyzed the glucosylation to steviol and 19-O-methylsteviol, but not to iso-steviol and 13-O-methylsteviol, indicating that 13-hydroxyl group of the steviol skeleton is glucosylated first from UDP-glucose to produce steviol-13-O-glucopyranoside. Enzyme fraction II, eluted from the DEAE-Toyopearl column with 0.15 molar KCI, catalyzed the glucose transfer from UDP-glucose to steviol-13-O-glucopyranoside, steviolbioside and stevioside, but not to rubusoside (13, 19-di-O-glucopyranoside) and rebaudioside A. The reaction products glucosylated from steviol-13-O-glucopyranoside, steviolbioside and stevioside were identified to be steviolbioside, stevioside and rebaudioside A, respectively. These results indicate that in the steviol-glucoside biosynthetic pathway, steviol-13-O-glucopyranoside produced from the steviol glucosylation is successively glucosylated to steviolbioside, then to stevioside producing rebaudioside A.
Amelioration of Insulin Resistance in Streptozotocin Diabetic Mice by Transgenic Overexpression of GLUT4 Driven by an Adipose-Specific Promoter (1997)

In diabetic rodents and humans, glucose transporter 4 (GLUT4) expression is suppressed in adipocytes in association with insulin resistance. Transgenic mice overexpressing GLUT4 selectively in fat have enhanced glucose disposal in vivo and massively increased glucose transport in adipocytes. To determine whether overexpression can be maintained in diabetes and whether it can prevent insulin resistance, we rendered wild-type and transgenic mice diabetic with streptozotocin. After 12–14 days, blood glucose was more than 21.4 mm and plasma insulin was 1.06 ng/ml or less in both diabetic groups in the fed state. Body weight was reduced and gonadal fat pad weight and adipocyte size were 52–75% smaller in both nontransgenic and transgenic diabetic mice, compared with nondiabetic. Basal and maximally-stimulated rates of lipolysis were similar in adipocytes from nontransgenic and transgenic mice, but the ED50 for isoproterenol stimulation was 50% lower in transgenic mice. There was no difference in the sensitivity to insulin to inhibit lipolysis. In adipocytes of nontransgenic diabetic mice, GLUT4 protein was reduced 34%, with a 46% reduction in insulin stimulated glucose transport. In contrast, in adipocytes of transgenic diabetic mice, GLUT4 remained 21-fold overexpressed, resulting in 21-fold increased basal and 10-fold increased insulin stimulated glucose transport. Injection of insulin (0.7 mU/g BW) resulted in a 35% decrease in blood glucose in transgenic diabetic mice (P < 0.05), with no effect in nontransgenic diabetic mice. Thus, high-level overexpression of GLUT4 driven by a fat specific promoter can be maintained with insulinopenic diabetes, even when fat cell metabolism is markedly altered. Overexpression of GLUT4 in adipocytes prevents insulin resistant glucose transport at the cellular level and improves insulin action in vivo, even with overt diabetes.
Propagation of polarized light in birefringent turbid media: time-resolved simulations (2001)

A Monte Carlo model was used to analyze the propagation of polarized light in linearly birefringent turbid media, such as fibrous tissues. Linearly and circularly polarized light sources were used to demonstrate the change of polarizations in turbid media with different birefringent parameters. Videos of spatially distributed polarization states of light backscattered from or propagating in birefringent media are presented.
Effects of Hydrogen Plasma Treatments on the Atomic Layer Deposition of Copper (2008)

The effects of hydrogen plasma substrate pretreatments on the subsequent material and integration properties of a previously developed plasma-enhanced atomic layer deposition Cu process have been investigated. Plasma treatments were observed to improve Cu nucleation and enable lower Cu resistivity, which have important technological implications with respect to the use of copper in nanoelectronic interconnect structures. The observed results can be explained by the removal of substrate surface hydroxyl groups achieved by the hydrogen plasma pretreatments. The removal of hydroxyl groups and subsequent H-termination of the substrate is favorable for the initial Cu nucleation, which results in higher nucleation density, a smoother surface, and lower resistivity.
Age-Dependent Neuronal and Synaptic Degeneration in Mice Transgenic for the C Terminus of the Amyloid Precursor Protein (1996)

The molecular basis for the degeneration of neurons and the deposition of amyloid in plaques and in the cerebrovasculature in Alzheimer's disease (AD) is incompletely understood. We have proposed that one molecule common to these abnormal processes is a fragment of the Alzheimer amyloid precursor protein (APP) comprising the C-terminal 100 amino acids of this molecule (APP-C100). We tested this hypothesis by creating transgenic mice expressing APP-C100 in the brain. We report here that aging (18-28 month) APP-C100 transgenic mice exhibit profound degeneration of neurons and synapses in Ammon's horn and the dentate gyrus of the hippocampal formation. Of the 106 transgenic mice between 8 and 28 months of age that were examined, all of those older than 18 months displayed severe hippocampal degeneration. The numerous degenerating axonal profiles contained increased numbers of neurofilaments, whorls of membrane, and accumulations of debris resembling secondary lysosomes near the cell body. The dendrites of degenerating granule and pyramidal cells contained disorganized, wavy microtubules. Cerebral blood vessels had thickened refractile basal laminae, and microglia laden with debris lay adjacent to larger venous vessels. Mice transgenic for Flag-APP-C100 (in which the hydrophilic Flag tag was fused to the N terminus of APP-C100) showed a similar degree of neurodegeneration in the hippocampal formation as early as 12 months of age. The 45 control mice displayed only occasional necrotic cells and no extensive cell degeneration in the same brain regions. These findings show that APP-C100 is capable of causing some of the neuropathological features of AD.
Martensite start temperature as a weldability index (1996)

Traditionally, welding experts have used carbon equivalent type expressions, which include chemical composition and cooling rates, to determine the susceptibility of a steel and its weldment to hydrogen damage. Experimental diagrams that map cracking versus non-cracking behavior as a function of hydrogen and carbon equivalent have also been proposed for practical applications. More recently, however, there is a growing concern that the hydrogen distribution across the weldment is non-uniform. Depending on the hardenability of the heat affected zone (base metal) and the weld metal, the two regions may undergo austenite decomposition, more specifically, martensite transformation at different times. As a result of the earlier or later transformation of the weld metal (compared with the heat affected zone), hydrogen may accumulate in the weld metal or in the heat affected zone. Selective distribution of hydrogen will lead to decreased or increased hydrogen damage susceptibility of the welded joint. By investigating the martensite start temperature of the weld metal and of the base metal, together with the amount of hydrogen pickup, the hydrogen outgassing behavior and distribution across the weldment can be modeled.
Effect of Sequence on Peptide Geometry in 5-tert-Butylprolyl Type VI β-Turn Mimics (2002)

The influence of sequence on turn geometry was examined by incorporating (2S,5R)-5-tert-butylproline (5-(t)BuPro) into a series of dipeptides and tetrapeptides. (2S,5R)-5-tert-Butylproline and proline were respectively introduced at the C-terminal residue of N-acetyl dipeptide N'-methylamides 1 and 2. The conformational analysis of these analogues was performed using NMR and CD spectroscopy as well as X-ray diffraction to examine the factors that control the prolyl amide (in this text, the term "prolyl amide" refers to the tertiary amide composed of the pyrrolidine nitrogen of the prolyl residue and the carbonyl of the N-terminal residue) equilibrium and stabilize type VI beta-turn conformation. The high cis-isomer population with aromatic residues N-terminal to proline was shown to result from a stacking interaction between the partial positive charged prolyl amide nitrogen and the aromatic pi-system as seen in the crystal structure of 1c. The effect of sequence on the prolyl amide equilibrium of 5-(t)BuPro-tetrapeptides (Ac-Xaa-Yaa-5-(t)BuPro-Zaa-XMe, 13 and 14) was studied by varying the amino acids at the Xaa, Yaa, and Zaa positions. High (>80%) cis-isomer populations were obtained with alkyl groups at the Xaa position, an aromatic residue at the Yaa position, and either an alanine or a lysine residue at the Zaa position of the 5-(t)BuPro-tetrapeptide methyl esters in water. Tetrapeptides Ac-Ala-Phe-5-(t)BuPro-Zaa-OMe (Zaa = Ala, Lys), 14d and 14f, with high cis-isomer content adopted type VIa beta-turn conformations as shown by their NMR and CD spectra. Although a pattern of amide proton temperature coefficient values indicative of a hairpin geometry was observed in peptides 14d and 14f, the value magnitudes did not indicate strong hydrogen bonding in water.
New Tripeptide‐Based Macrocyclic Calpain Inhibitors Formed by N‐Alkylation of Histidine (2012)

Two new series of 15-membered macrocyclic peptidomimetics, in which the P1 and P3 residues of the peptide backbone are linked by a bridge containing a 1,4-disubstituted 1H-imidazole, are reported. The structure with an aldehyde at the C-terminus and the imidazole at P3, i.e., 4c, shows significant inhibitory activity against calpain 2, with an IC(50) value of 238 nM. The macrocyclic aldehyde with the imidazole at the alternative P1 position, i.e., 5c, is significantly less active. The relative activities are linked to the ability of the component macrocycles to mimic a β-strand geometry that is known to favor active-site binding. This ability is defined by conformational searches and docking studies with calpain.
The NMDA Receptor Hypofunction Model of Psychosis (2003)

Antagonists of the NMDA glutamate receptor, including phencyclidine (PCP), ketamine, and CGS-19755, produce cognitive and behavioral changes in humans. In rodents these agents produce a myriad of histopathological and neurochemical changes. Several lines of evidence suggest that a large number of these drug-induced effects are dose-dependent manifestations of the same general disinhibition process in which NMDA antagonists abolish GABAergic inhibition, resulting in the simultaneous excessive release of acetylcholine and glutamate. Progressive increases in the severity of NMDA receptor hypofunction (NRHypo) within the brain produce an increasing range of effects on brain function. Underexcitation of NMDA receptors, induced by even relatively low doses of NMDA antagonist drugs, can produce specific forms of memory dysfunction without clinically evident psychosis. More severe NRHypo can produce a clinical syndrome very similar to a psychotic schizophrenic exacerbation. Finally, sustained and severe NRHypo in the adult brain is associated with a form of neurotoxicity with well-characterized neuropathological features. In this paper several of these effects of NMDA antagonists and a likely mechanism responsible for producing them will be reviewed. In addition the possible role of NRHypo in the pathophysiology of idiopathic psychotic disorders will be considered.
One‐Pot Synthesis of Biomimetic Shell Cross‐Linked Micelles and Nanocages by ATRP in Alcohol/Water Mixtures (2010)

Shell shock: The one-pot synthesis of shell cross-linked (SCL) micelles was achieved using an ABC triblock copolymer in a 9:1 alcohol/water mixture. These SCL micelles were dialyzed against water, leading to solvation of the core-forming PMPC chains. If the cross-linking is not too high, these chains migrate through the inner shell to join the coronal PEO chains, hence forming nanocages. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The Mpl-ligand or thrombopoietin or megakaryocyte growth and differentiative factor has both direct proliferative and differentiative activities on human megakaryocyte progenitors (1995)

Previously, it was believed that megakaryocytopoiesis was regulated by two types of humoral factors: megakaryocyte colony-stimulating factor (MK-CSF), which acts on progenitors inducing their proliferation, and thrombopoietin (TPO), a megakaryocyte(s) (MK) maturational factor that induces platelet formation. The recently cloned Mpl-ligand (Mpl-L) seems to have both properties in vivo and in vitro and has also been called TPO. However, it cannot be excluded that a part of these activities is due to a synergistic effect with growth factors present in the serum or synthesized by accessory cells. To delineate the precise TPO (Mpl-L) biologic activities, we performed serum-free cultures at limiting cell dilution. Target cells were adult human marrow CD34+CD41+ cells, which represent a highly selected population of late MK progenitor or transitional cells. Cells were purified using a flow cytometer equipped with an automatic cloning design unit. We determined that the recombinant molecule had a biologic activity that reached a plateau at 10 ng/mL. At this concentration, a linear relationship between the average MK number per well and the number of cells seeded (between 1 to 50 cells per well) was observed. At one cell per well, 60% of the wells contained a single MK at day 5 of culture. Half of these wells contained only one large MK, whereas the other half contained several MK (up to 25), demonstrating that TPO has direct proliferative biologic activity. In contrast, at limiting dilution, none of the other cytokines tested (stem cell factor [SCF], interleukin- 6 [IL-6], and erythropoietin [Epo]) were effective, whereas IL-3 showed a mild effect. However, a combination of SCF plus IL-6 plus IL-3 produced similar results as TPO alone. Addition of the other cytokines to TPO did not enhance the cloning efficiency of the CD34+CD41+ cells but increased twofold the average number of MKs per clone. MKs reached a ploidy of 32N and 64N in the presence of TPO. The mean ploidy value was approximately 6 and was not modified by addition of the other cytokines. At the ultrastructural level, a majority of the MKs showed maturational defects related to an imbalance between the synthesis of alpha-granules and demarcation membranes. However, a fraction (about 30%) had a cytoplasmic maturation that exactly mimicked that of marrow MKs. In addition, proplatelet-shedding MKs were observed in the cultures, even at limiting dilution. Such a result was not observed with any other individual cytokines, including the combination of three cytokines.(ABSTRACT TRUNCATED AT 400 WORDS)
There are no bad anticancer agents, only bad clinical trial designs--twenty-first Richard and Hinda Rosenthal Foundation Award Lecture. (1998)

Unfortunately, the vast majority (90%) of new anticancer agents designed in the laboratory never make it into routine clinical use. The hypothesis of this lecture is that many new agents fail in the clinic because the appropriate clinical trial(s) that could exploit the attributes of the new agent are not performed. An appreciation that both bench and clinical investigations are difficult endeavors should aid in improving clinical trial designs and give the best chance for new agents to be added to our therapeutic armamentarium.
Latin Vocabulary Acquisition: An Experiment Using Information-Processing Techniques of Chunking and Imagery (2001)

The purpose of the study was to determine the effect on student performance and attitude toward high school Latin by Latin I students when provided with vocabulary instruction through chunking and imagery.