gebhart/patrepeval huggingface dataset:
Lanthanides in magnetic resonance imaging (2006)

Magnetic Resonance Imaging is perhaps the most important and prominent technique in diagnostic clinical medicine and biomedical research. Its success and development as an imaging technique has been aided by the characteristics of contrast agents that enhance signal intensities and improve specificity. Gadolinium(iii) remains the dominant starting material for contrast agent design but other lanthanide ions (and other oxidation states i.e. +2) are also being increasingly investigated as alternatives to gadolinium(III) within laboratory conditions. This critical review provides a concise summary of the MRI-active gadolinium(III) complexes to date--their pros and cons, an outline of contrast agents based on other lanthanide ions (e.g. europium, dysprosium), and directs the reader to newer, more speculative areas of lanthanide-containing contrast agent design.
Two-step model of stop codon recognition by eukaryotic release factor eRF1 (2013)

Release factor eRF1 plays a key role in the termination of protein synthesis in eukaryotes. The eRF1 consists of three domains (N, M and C) that perform unique roles in termination. Previous studies of eRF1 point mutants and standard/variant code eRF1 chimeras unequivocally demonstrated a direct involvement of the highly conserved N-domain motifs (NIKS, YxCxxxF and GTx) in stop codon recognition. In the current study, we extend this work by investigating the role of the 41 invariant and conserved N-domain residues in stop codon decoding by human eRF1. Using a combination of the conservative and non-conservative amino acid substitutions, we measured the functional activity of >80 mutant eRF1s in an in vitro reconstituted eukaryotic translation system and selected 15 amino acid residues essential for recognition of different stop codon nucleotides. Furthermore, toe-print analyses provide evidence of a conformational rearrangement of ribosomal complexes that occurs during binding of eRF1 to messenger RNA and reflects stop codon decoding activity of eRF1. Based on our experimental data and molecular modelling of the N-domain at the ribosomal A site, we propose a two-step model of stop codon decoding in the eukaryotic ribosome.
Bovine pneumonic pasteurellosis: Model for Pasteurella haemolytica- and Pasteurella multocida-induced pneumonia in cattle (1984)

Pneumonic lesions in calves were induced with Pasteurella haemolytica or P multocida. The inoculum, consisting of a suspension of either organism, was administered by transthoracic intrapulmonic injection to 23 calves. Three died of septicemia; the 20 remaining, killed 96 hours after inoculation, had an expanding unifocal pneumonia qualitatively comparable with that of acute pneumonic pasteurellosis (shipping fever). The concentration of bacteria that consistently produced a lesion was a 5-ml volume containing 10(9) colony-forming units of bacteria; a concentration of 10(6) colony-forming units inconsistently produced lesions. Bacteria, except in calves that developed septicemia and died, remained localized at the injection site. The inflammatory process spread within the lungs, not only through airways, but through the interlobular and interalveolar septa as well.
Multicellular Tumor Spheroids as a Model for Assessing Delivery of Oligonucleotides in Three Dimensions (2014)

Oligonucleotides have shown promise in selectively manipulating gene expression in vitro, but that success has not translated to the clinic for cancer therapy. A potential reason for this is that cells behave differently in monolayer than in the three-dimensional tumor, resulting in limited penetration and distribution of oligonucleotides in the tumor. This may be especially true when oligonucleotides are associated with nanocarriers such as lipoplexes and polyplexes, commonly used delivery vehicles for oligonucleotides. The multicellular tumor spheroid (MCTS), a three-dimensional model that closely resembles small avascular tumors and micrometastases, has been utilized as an intermediate between monolayer culture and in vivo studies for the screening of small-molecule drugs. However, spheroids have been little used for the study of various oligonucleotide delivery formulations. Here, we have evaluated the uptake and efficacy of splice-switching antisense oligonucleotides using various delivery modalities in two- and three-dimensional culture models. We find that the size of the delivery agent dramatically influences penetration into the spheroid and thus the biological effect of the oligonucleotides. We hypothesize that the MCTS model will prove to be a useful tool in the future development of oligonucleotide delivery formulations.Molecular Therapy-Nucleic Acids (2014) 3, e153; doi:10.1038/mtna.2014.5; published online 11 March 2014.
Soluble Silica with High Affinity for Aluminum under Physiological and Natural Conditions (1997)

Soluble silica reduces aluminum availability and ameliorates toxicity in several biological systems. It has therefore been suggested that these two species strongly interact in solution. However, there is only weak affinity between monomeric silicic acid and aluminum with reported log Keff of between 4 and 6 at pH 7.2. We now show the existence of a soluble low molecular weight form of silica that is nonmonomeric but has an affinity for aluminum at least 1 000 000 times greater than the monomeric form (log Keff = 11.70 ± 0.30 at pH 7.2). This was established by competition, for binding of aluminum, between different preparations of soluble silica and the powerful M3+ chelator, 1,2-dimethyl-3-hydroxy-4-pyridinone (DMHP). At pH 7.2, this nonmonomeric silica quantitatively displaced one equiv of DMHP for every 34.42 ± 0.77 equiv of total silica, suggesting that the soluble silica that so avidly binds aluminum is an oligomer containing fewer than 35 silicon atoms. The presence of oligomeric or monomeric silica in solution depends on how the solution is prepared. The oligomer is formed when alkali stock solutions of silica (42 mM in this work) are pH neutralized prior to dilution, to physiological and natural levels of soluble silica (<2.5 mM). The diluted oligomeric silica is at least transiently stable (<1 day or >17 days; absence or presence of aluminum) and would compete effectively with endogenous physiological chelators for aluminum, such as citrate (log Keff aluminum citrate = 7.15 at pH 7.2). Oligomeric silica is probably responsible for the many experimental observations on the amelioration of aluminum availability and toxicity, but whether this silica species occurs naturally in the environment or is formed in vivo, remains to be established.
Early intensive care unit intervention for trauma care: what alters the outcome? (2002)

This review focuses on early management of multiple trauma patients with traumatic brain injury. Early usage of multislice computed tomography can substantially shorten the time spent on diagnostic workup in the emergency room and, therefore, speeds the initiation of lifesaving interventions for the control of hemorrhage. The important role of hemostatic angiographic embolization and its timing, in addition to surgical control of bleeding in patients suffering from pelvic fracture or organ lesions, is emphasized. The ongoing controversy regarding the strategy of fluid resuscitation is discussed. The concept of permissive hypotension seems to be promising but is absolutely contraindicated in patients with traumatic brain injury. Coagulation management should be guided by coagulation monitoring, including thromboelastography. A novel approach to reduce major bleeding is the application of recombinant factor VIIa. Strong effort should be directed toward the management of traumatic brain injury and the maintenance of cerebral perfusion pressure. The optimization of treatment of patients with multiple trauma, including brain injury, is a multidisciplinary task.
Effect of Sb doping on the thermoelectric properties of Ti-based half-Heusler compounds, TiNiSn1−xSbx (2000)

Half-Heusler alloys (MgAgAs type) with the general formula MNiSn where M is a group IV transition metal (Hf, Zr, or Ti) are currently under investigation for potential thermoelectric materials. These materials exhibit a high negative thermopower (−40 to −250 μV/K) and low electrical resistivity values (0.1–8 mΩ cm) both of which are necessary for a potential thermoelectric material. Results are presented in this letter regarding the effect of Sb doping on the Sn site (TiNiSn1−xSbx). The Sb doping leads to a relatively large power factor of (0.2–1.0) W/m K at room temperature for small concentrations of Sb. These values are comparable to that of Bi2Te3 alloys, which are the current state-of-the-art thermoelectric materials. The power factor is much larger at T≈650 K where it is over 4 W/m K making these materials very attractive for potential power generation considerations.
Inhibition of restriction endonuclease Nel I cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis (1986)

M13 RF IV DNA where phosphorothioate groups are incorporated at restriction endonuclease Nci I recognition sites in the (-)strand is efficiently nicked by the action of this enzyme. Incubation of such nicked DNA with exonuclease III produces gapped DNA. The gap can be filled by reaction with deoxynucleoside triphosphates and DNA polymerase I. When this sequence of reactions is performed with DNA containing a mismatch oligonucleotide primer in the (-)-strand mutational frequencies of 70-90% can be obtained upon transformation. The general nature of this methodology has been further shown to be applicable to other restriction enzymes such as Hind II, Pst I and Fsp I. The mutational frequency obtained using these enzymes is between 40-80% mainly because of less efficient nicking and gapping. Studies on inhibition of Nci I cleavage show that in addition to a phosphorothioate group at the position of cleavage an additional group in the 5'-neighbouring position is necessary for complete inhibition.
The Liaison of Sweet and Savory (2005)

The sense of taste provides humans with necessary information about the composition and quality of food. For humans, five basic tastes are readily distinguishable and include sweet, bitter, salty, sour, and savory (or umami). Although each of these qualities has individualized transduction pathways, sweet and umami tastes are believed to share a common receptor element, the T1R3 receptor subunit. The two G-protein-coupled heteromer receptors that comprise an umami stimulus receptor (T1R1-T1R3) and a sweetener receptor (T1R2-T1R3) constitute a potential link between these two qualities of perception. While the role of the individual monomers in each human heteromer has been examined in vitro, very little is known of the implication of this research for human perception, or specifically, how sweet and savory taste perceptions may be connected. Using a psychophysical approach, we demonstrate that lactisole, a potent sweetness inhibitor that binds in vitro to hT1R3, also inhibits a significant portion of the perception of umami taste from monosodium glutamate. Following the molecular logic put forward by Xu et al. (2004, Proc. Natl Acad. Sci. USA, 101, 14258-14263), our psychophysical data support the in vitro hypothesis that the shared T1R3 monomer moderates the activation of both T1R2 and T1R1 in humans and impairs suprathreshold perception, respectively, of sweetness and, to a lesser degree, umaminess in the presence of lactisole.
Molecular Species of Choline and Ethanolamine Phospholipids in Rat Cerebellum During Development (1990)

The molecular species composition of rat cerebellar phospholipid subclasses has been studied by HPLC after phospholipase C treatment and dinitrophenyl derivatization. During rat cerebellum development (3-90 days postpartum), cholinephosphoglycerides and ethanolamine phosphoglycerides represented approximately 80% of all phospholipids, with their relative amount changing after 1 month. Among ethanolamine phosphoglycerides, the molar ratio of diacylglycerophosphoethanolamine (diacylGPE) to alkenylacylGPE decreased from approximately 1.4 at 3 days to approximately 0.5 after 10 days. The phospholipids investigated contained up to 12 different molecular species. The rate of accumulation of the various molecular species of diacylglycerophosphocholine (diacylGPC), diacylGPE, and alkenylacylGPE during cerebellar development allowed a classification into three main groups. The overall increase of the molecular species of the first group (6-diacylGPC, 5-diacylGPE, and 4-alkenylacylGPE) was approximately 18-fold between 3 and 90 days, with a faster rate of accumulation between 3 and 30 days. Those of the second group (3-diacylGPC, 5-diacylGPE, and 5-akenylacylGPE) increased by approximately 45-fold during the same developmental period, at a slow rate before day 15 and a faster one thereafter. The molecular species of the third group (3-alkenylacylGPE) increased by greater than 250-fold between 3 and 90 days, at a very slow rate before day 21 and more quickly thereafter. The different rates of accumulation of the components of the three groups during cerebellar development suggest a preferential location of the first group in membranes of neuronal perikaryons, glial cells, and synaptosomal structures. Those of the second group appear to be located in both synaptosomal membranes and myelin sheets, and those of the third group can be considered as myelin markers.
Energy Metabolic Phenotype of the Cardiomyocyte During Development, Differentiation, and Postnatal Maturation (2010)

Dramatic maturational changes occur in cardiac energy metabolism during cardiac development, differentiation, and postnatal growth. These changes in energy metabolism have important impacts on the ability of the cardiomyocyte to proliferate during early cardiac development, as well as when cardiomyocytes terminally differentiate during later development. During early cardiac development, glycolysis is a major source of energy for proliferating cardiomyocytes. As cardiomyocytes mature and become terminally differentiated, mitochondrial oxidative capacity increases, with fatty acid beta-oxidation becoming a major source of energy for the heart. The increase in mitochondrial oxidative capacity seems to coincide with a decrease in the proliferative ability of the cardiomyocyte. The switch from glycolysis to mitochondrial oxidative metabolism during cardiac development includes both alterations in the transcriptional control and acute alterations in the control of each pathway. Interestingly, if a hypertrophic stress is placed on the adult heart, cardiac energy metabolism switches to a more fetal phenotype, which includes an increase in glycolysis and decrease in mitochondrial fatty acid beta-oxidation. In this article, we review the impact of alterations in energy substrate metabolism on cardiomyocyte proliferation, differentiation, and postnatal maturation.
Analytical ultracentrifugation as a contemporary biomolecular research tool. (1999)

Analytical ultracentrifugation has again become a widely used biomolecular research technique for determining sample purity, characterizing assembly and disassembly mechanisms of biomolecular complexes, determining subunit stoichiometries, detecting and characterizing macromolecular conformational changes, and measuring equilibrium constants and thermodynamic parameters for self- and hetero-associating systems. Concomitant with the availability of modern instrumentation is a strong need for biomedical scientists to become acquainted with the fundamental principles of analytical ultracentrifugation and the new data analysis methodologies that have greatly transformed this technique as it exists today.
Highly Coordinated Gene Regulation in Mouse Skeletal Muscle Regeneration (2003)

Mammalian skeletal muscles are capable of regeneration after injury. Quiescent satellite cells are activated to reenter the cell cycle and to differentiate for repair, recapitulating features of myogenesis during embryonic development. To understand better the molecular mechanism involved in this process in vivo, we employed high density cDNA microarrays for gene expression profiling in mouse tibialis anterior muscles after a cardiotoxin injection. Among 16,267 gene elements surveyed, 3,532 elements showed at least a 2.5-fold change at one or more time points during a 14-day time course. Hierarchical cluster analysis and semiquantitative reverse transcription-PCR showed induction of genes important for cell cycle control and DNA replication during the early phase of muscle regeneration. Subsequently, genes for myogenic regulatory factors, a group of imprinted genes and genes with functions to inhibit cell cycle progression and promote myogenic differentiation, were induced when myogenic stem cells started to differentiate. Induction of a majority of these genes, including E2f1 and E2f2, was abolished in muscles lacking satellite cell activity after gamma radiation. Regeneration was severely compromised in E2f1 null mice but not affected in E2f2 null mice. This study identifies novel genes potentially important for muscle regeneration and reveals highly coordinated myogenic cell proliferation and differentiation programs in adult skeletal muscle regeneration in vivo.
Allergic contact dermatitis to cyanamide (carbodiimide) (1981)

Occupational allergic dermatitis to cyanamide is described in a psychiatric ward assistant who handled several anti‐alcoholic products, one of which contained 6% cyanamide.
Primary Human Ovarian Epithelial Cancer Cells Broadly Express HER2 at Immunologically-Detectable Levels (2012)

The breadth of HER2 expression by primary human ovarian cancers remains controversial, which questions its suitability as a universal antigen in this malignancy. To address these issues, we performed extensive HER2 expression analysis on a wide panel of primary tumors as well as established and short-term human ovarian cancer cell lines. Conventional immunohistochemical (IHC) analysis of multiple tumor sites in 50 cases of high-grade ovarian serous carcinomas revealed HER2 overexpression in 29% of evaluated sites. However, more sensitive detection methods including flow cytometry, western blot analysis and q-PCR revealed HER2 expression in all fresh tumor cells derived from primary ascites or solid tumors as well as all established and short-term cultured cancer cell lines. Cancer cells generally expressed HER2 at higher levels than that found in normal ovarian surface epithelial (OSE) cells. Accordingly, genetically-engineered human T cells expressing an HER2-specific chimeric antigen receptor (CAR) recognized and reacted against all established or primary ovarian cancer cells tested with minimal or no reactivity against normal OSE cells. In conclusion, all human ovarian cancers express immunologically-detectable levels of HER2, indicating that IHC measurement underestimates the true frequency of HER2-expressing ovarian cancers and may limit patient access to otherwise clinically meaningful HER2-targeted therapies.
Hemostasis in Spontaneous Subarachnoid Hemorrhage (1995)

To comprehensively examine changes in the hemostatic systems early after spontaneous subarachnoid hemorrhage (SAH) and to assess the relationships between those changes and neurological findings, computed tomographic findings, and clinical outcomes, we reviewed 167 patients who were admitted within 24 hours of the onset of SAH. Blood was taken from all of the patients at admission for detailed examinations of the hemostatic systems. The following results were obtained: 1) the levels of the thrombin-antithrombin complex (elevation indicating the activation fo the blood coagulation system), plasmin-antiplasmin complex, and D-dimer (elevation indicating the activation of the fibrinolytic system) significantly increased with the neurological severity, amount of subarachnoid clot, and severity of clinical outcome; 2) the levels of the thrombin-antithrombin complexes and plasmin-antiplasmin complexes were significantly higher in patients with intracerebral or intraventricular hematomas than in patients without those hematomas; 3) in each of almost all the neurological and computed tomographic grades, the levels of the thrombin-antithrombin complexes were significantly higher in the patients with poor outcomes than in those with good outcomes; 4) the poor outcome rate significantly increased with neurological severity and the amount of subarachnoid clot. These data suggest that the activation of the blood coagulation system as well as of the fibrinolytic system occurred early in the course of SAH and that these systems were activated to a greater extent with the severity of neurological grades, computed tomographic findings, and clinical outcome.(ABSTRACT TRUNCATED AT 250 WORDS)
Microporous materials with negative Poisson's ratios. I. Microstructure and mechanical properties (1989)

A microporous, anisotropic form of expanded polytetrafluoroethylene has been found to have a large negative major Poisson's ratio. The value of Poisson's ratio varies with tensile strain and can attain values as large as -12. The microporous structure of the material is described and the mechanisms that lead to this large negative Poisson's ratio are identified. Micro-rotational degrees of freedom are observed, suggesting that a micropolar elasticity theory may be required to describe the mechanical properties.
Achieving Stable, Reverse Water‐in‐Fluorocarbon Emulsions (1996)

Dispersing water in a fluorocarbon seems against nature , since two more antipathetic types of liquids, in terms of intermolecular interactions, just do not exist. Every single characteristic relevant to water‐in‐fluorocarbon reverse emulsion stability (solubility and diffusivity parameters, interfacial tension and densities) is unfavorable. Yet stable emulsions of this type can be prepared with an appropriate fluorinated surfactant. Such reverse emulsions have potential as a new class of pulmonary drug‐delivery system.
A Severe Acute Respiratory Syndrome Coronavirus That Lacks the E Gene Is Attenuated In Vitro and In Vivo (2006)

A deletion mutant of severe acute respiratory syndrome coronavirus (SARS-CoV) has been engineered by deleting the structural E gene in an infectious cDNA clone that was constructed as a bacterial artificial chromosome (BAC). The recombinant virus lacking the E gene (rSARS-CoV-DeltaE) was rescued in Vero E6 cells. The recovered deletion mutant grew in Vero E6, Huh-7, and CaCo-2 cells to titers 20-, 200-, and 200-fold lower than the recombinant wild-type virus, respectively, indicating that although the E protein has an effect on growth, it is not essential for virus replication. No differences in virion stability under a wide range of pH and temperature were detected between the deletion mutant and recombinant wild-type viruses. Although both viruses showed the same morphology by electron microscopy, the process of morphogenesis seemed to be less efficient with the defective virus than with the recombinant wild-type one. The rSARS-CoV-DeltaE virus replicated to titers 100- to 1,000-fold lower than the recombinant wild-type virus in the upper and lower respiratory tract of hamsters, and the lower viral load was accompanied by less inflammation in the lungs of hamsters infected with rSARS-CoV-DeltaE virus than with the recombinant wild-type virus. Therefore, the SARS-CoV that lacks the E gene is attenuated in hamsters, might be a safer research tool, and may be a good candidate for the development of a live attenuated SARS-CoV vaccine.