gebhart/patrepeval huggingface dataset:
Simple and complex models for studying muscle function in walking (2003)

While simple models can be helpful in identifying basic features of muscle function, more complex models are needed to discern the functional roles of specific muscles in movement. In this paper, two very different models of walking, one simple and one complex, are used to study how muscle forces, gravitational forces and centrifugal forces (i.e. forces arising from motion of the joints) combine to produce the pattern of force exerted on the ground. Both the simple model and the complex one predict that muscles contribute significantly to the ground force pattern generated in walking; indeed, both models show that muscle action is responsible for the appearance of the two peaks in the vertical force. The simple model, an inverted double pendulum, suggests further that the first and second peaks are due to net extensor muscle moments exerted about the knee and ankle, respectively. Analyses based on a much more complex, muscle-actuated simulation of walking are in general agreement with these results; however, the more detailed model also reveals that both the hip extensor and hip abductor muscles contribute significantly to vertical motion of the centre of mass, and therefore to the appearance of the first peak in the vertical ground force, in early single-leg stance. This discrepancy in the model predictions is most probably explained by the difference in model complexity. First, movements of the upper body in the sagittal plane are not represented properly in the double-pendulum model, which may explain the anomalous result obtained for the contribution of a hip-extensor torque to the vertical ground force. Second, the double-pendulum model incorporates only three of the six major elements of walking, whereas the complex model is fully 3D and incorporates all six gait determinants. In particular, pelvic list occurs primarily in the frontal plane, so there is the potential for this mechanism to contribute significantly to the vertical ground force, especially during early single-leg stance when the hip abductors are activated with considerable force.
Intranasal immunization with C5a peptidase prevents nasopharyngeal colonization of mice by the group A Streptococcus (1997)

Early inflammatory events are initiated by phased production of C5a and interleukin-8 in tissue. Most serotypes of group A streptococci express a surface-bound peptidase (SCPA) which specifically cleaves mouse and human C5a chemotaxins. This study investigates the impact of SCPA on colonization of the nasopharyngeal mucosa of mice and evaluates its potential to induce protective immunity. Two strains, serotypes M6 and M49, which contain insertion and deletion mutations in the SCPA gene (scpA) and represent the two major subdivisions of group A streptococci, were characterized and compared in a mouse intranasal infection model. In this model, SCPA mutants were more rapidly cleared from the nasopharynges of inoculated mice compared with wild-type strains. A 2,908-bp fragment of scpA49 gene, obtained by PCR, was ligated to the expression vector pGEX-4T-1 and expressed in Escherichia coli. The affinity-purified deltaSCPA49 protein proved to be highly immunogenic in mice and rabbits. Although the purified deltaSCPA49 immunogen lacked enzymatic activity, it induced high titers of rabbit antibodies which were able to neutralize peptidase activity associated with M1, M6, M12, and M49 streptococci in vitro. This result confirmed that antipeptidase antibodies lack serotype specificity. Intranasal immunization of mice with the deleted form of the SCPA49 protein stimulated significant levels of specific salivary secretory immunoglobulin A (IgA) and serum IgG antibodies and reduced the potential of wild-type M1, M2, M6, M11, and M49 streptococci to colonize. These experiments suggest a new approach to vaccine development for prevention of streptococcal pharyngitis.
Elevated Levels of Plasmin-α2 Antiplasmin Complexes in Unstable Angina (1999)

The evidence of elevated levels of several biochemical markers of prothrombotic state in patients with unstable angina suggests that thrombus formation and lysis play a pivotal role in acute coronary syndromes. The clinical syndrome of unstable angina encompasses a variety of clinical presentations of transient episodes of myocardial ischemia. This study was designed to assess plasmin generation in different settings of unstable angina. Evidence of plasmin generation in patients with unstable angina was measured by circulating plasmin-alpha2 antiplasmin complexes (PAP). A second objective was to identify whether PAP levels had a prognostic value to predict outcome. Eighty-five patients admitted to the coronary care unit for unstable angina were classified into three groups. Group A included 26 patients with postinfarction angina; group B comprised 26 patients with new onset angina; and group C included 33 patients with crescendo angina. Mean PAP levels were higher in the three groups compared to healthy controls. A significant correlation was found between levels of PAP and D-dimer, particularly in postinfarction angina (r = 0.6; p <0.0005). This trial adds new insights into the pathophysiology of unstable angina. It demonstrates that plasmin is generated in the different settings of unstable angina but particularly in postinfarction angina patients where a fibrin-rich thrombus is responsible of the symptoms. However, in this series PAP levels do not predict an uneventful outcome neither in the acute phase nor at long term (6 months).
Cardiac natriuretic peptides: new laboratory parameters in heart failure patients. (2001)

Natriuretic peptides, atrial natriuretic peptide and brain natriuretic peptide, are key regulators in the homeostasis of salt and water excretion and in the maintenance of blood pressure. During heart failure, these peptides are highly activated because of volume overload and increased myocardial wall tension. Among all natriuretic peptides and neurohormones, brain natriuretic peptide and its N-terminal prohormone fragment have been shown to be the best markers to identify patients with heart failure. They are useful prognostic markers as well. The stability of brain natriuretic peptides and N-terminal prohormones in ethylene-diamine-tetraacetic-acid whole blood is sufficient for routine use. Sensitive and specific assays without the need for plasma extraction are commercially available. The available data indicate that natriuretic peptides are powerful diagnostic and prognostic markers in heart failure patients. First data on treatment guidance are promising.
Does preventive vaccination with engineered tumor cells work in cancer-prone transgenic mice? (1998)

The use of genetically modified tumor cells as vaccines has been successful in numerous animal models of grafted syngenic tumors and has provided the groundwork for many clinical trials of gene therapy in cancer patients. To investigate the real efficacy of ex vivo gene therapy-based vaccines, we used transgenic mice that express the SV40 large T and small t antigens under the control of hepatic antithrombin III (ASV-B)-regulatory sequences. These mice systematically develop hepatocarcinoma. Hepatoma cells, derived from ASV-B transgenic mice, were gene-transduced to express either interleukin-2, interleukin-4, the granulocyte-macrophage colony-stimulating factor, or the T-cell costimulatory molecule B7.1. First, we demonstrated the vaccine potential of engineered hepatoma cells by immunizing nontransgenic mice with these cells, which prevented the growth of subsequent grafted nontransduced hepatoma cells. However, vaccination of pretumoral transgenic animals with various combinations of engineered hepatoma cells failed to inhibit hepatoma onset and progression. Rather, tumor development in ASV-B mice appears to be dependent on the immune system, since neonatal induction of immunotolerance to tumor in ASV-B mice cells was associated with a moderate, but significant, acceleration of tumor development. These results seriously call into question the efficacy of this strategy of active vaccinotherapy against natural tumors.
Replacement of the Saccharomyces cerevisiae acetyl-CoA synthetases by alternative pathways for cytosolic acetyl-CoA synthesis (2013)

Cytosolic acetyl-coenzyme A is a precursor for many biotechnologically relevant compounds produced by Saccharomyces cerevisiae. In this yeast, cytosolic acetyl-CoA synthesis and growth strictly depend on expression of either the Acs1 or Acs2 isoenzyme of acetyl-CoA synthetase (ACS). Since hydrolysis of ATP to AMP and pyrophosphate in the ACS reaction constrains maximum yields of acetyl-CoA-derived products, this study explores replacement of ACS by two ATP-independent pathways for acetyl-CoA synthesis. After evaluating expression of different bacterial genes encoding acetylating acetaldehyde dehydrogenase (A-ALD) and pyruvate-formate lyase (PFL), acs1Δ acs2Δ S. cerevisiae strains were constructed in which A-ALD or PFL successfully replaced ACS. In A-ALD-dependent strains, aerobic growth rates of up to 0.27 h(-1) were observed, while anaerobic growth rates of PFL-dependent S. cerevisiae (0.20 h(-1)) were stoichiometrically coupled to formate production. In glucose-limited chemostat cultures, intracellular metabolite analysis did not reveal major differences between A-ALD-dependent and reference strains. However, biomass yields on glucose of A-ALD- and PFL-dependent strains were lower than those of the reference strain. Transcriptome analysis suggested that reduced biomass yields were caused by acetaldehyde and formate in A-ALD- and PFL-dependent strains, respectively. Transcript profiles also indicated that a previously proposed role of Acs2 in histone acetylation is probably linked to cytosolic acetyl-CoA levels rather than to direct involvement of Acs2 in histone acetylation. While demonstrating that yeast ACS can be fully replaced, this study demonstrates that further modifications are needed to achieve optimal in vivo performance of the alternative reactions for supply of cytosolic acetyl-CoA as a product precursor.
YKL-40 in giant cells and macrophages from patients with giant cell arteritis (1999)

YKL-40 is found in CD68+ giant cells and mononuclear cells in the media of arteritic vessels of patients with GCA, and the concentration of serum YKL-40 may reflect the local activity of these cells in the inflamed artery.
A Rapid and Accurate Closed-Tube Immunoassay for Platelets on an Automated Hematology Analyzer (2000)

Accurate and precise platelet counts are important for patients with severe thrombocytopenia or who are receiving chemotherapy. We developed a novel flow cytometric analysis of platelets that may be particularly valuable for assessing the necessity for platelet transfusions. This ImmunoPlt (CD61) assay is based in part on CD61 monoclonal antibody labeling and has been automated and implemented on the CELL-DYN 4000 hematology analyzer. It is well suited for thrombocytopenic specimens, since it reduces interference by nonplatelet particles. It takes less than 5 minutes from closed-tube aspiration to report. Data for more than 350 thrombocytopenic specimens demonstrate that the ImmunoPlt (CD61) assay is more accurate than the optical scatter or the impedance count for specimens with platelet counts between 1 and 60 x 10(3)/microL (1 and 60 x 10(9)/L). The ImmunoPlt (CD61) assay is more precise than the optical scatter or the impedance count for specimens with platelet counts between 1 and 50 x 10(3)/microL (1 and 50 x 10(9)/L).
Survival advantage with decitabine versus intensive chemotherapy in patients with higher risk myelodysplastic syndrome (2007)

In this analysis, decitabine was associated with a survival advantage compared with intensive chemotherapy in patients with higher risk MDS. Future studies should evaluate prospectively the results of decitabine versus intensive chemotherapy in this setting.
Independent regulation of adipose tissue-specificity and obesity response of the adipsin promoter in transgenic mice. (1994)

Transcription of the adipocyte-specific adipsin gene is dramatically reduced in the adipose tissue of a number of genetically and chemically-induced obese rodents. To map the region of the adipsin gene that confers this response to obesity, transgenic mice were made containing -114, -250, -400, -700, and -938 base pairs (bp) to +35 bp of the promoter linked to the bacterial chloramphenicol acetyltransferase gene. Transgenic mice containing as few as 114 bp of the adipsin promoter had high levels of chloramphenicol acetyltransferase activity in adipose tissue. However, only those mice with 938 bp of the adipsin upstream regulatory region showed suppression of expression in adipose tissue in mice that were induced to become obese with monosodium glutamate. Using gel retardation assays, we showed that a 56-bp fragment of DNA mapping between -687 and -743 bp upstream from the start of adipsin expression was bound by protein factors in nuclear extracts prepared from adipose tissue. There was much greater retardation of this fragment with nuclear extracts prepared from adipose tissue of lean versus obese mice. These results indicate that a tissue-specific transcription factor(s) that regulates adipsin expression is less active in the adipose tissue of obese animals.
Correlation of Optic Nerve Sheath Diameter with Direct Measurement of Intracranial Pressure (2008)

Using an ROC curve the authors systematically confirmed the commonly used threshold of ONSD > 5 mm to detect ICP > 20 cm H2O. This study directly correlates ventriculostomy measurements of ICP with US ONSD measurements and provides further support for the use of ONSD measurements as a noninvasive test for elevated ICP.
Temporary ex vivo inhibition of the expression of the human oncogene HER2 (NEU) by a triple helix-forming oligonucleotide. (1996)

A 28-base phosphodiester triple helix-forming oligonucleotide, mostly G and A containing, targeted to a polypurine tract interrupted by a purine-pyrimidine inversion, situated upstream from the TATA box of the promoter of the human HER2 gene, was conceived by computer modeling. The "energetically best choice" was oligo 28(C), which formed the triple helix in vitro, as proved by gel retardation and Fourier transform infrared spectroscopy. When administered as a complex with lipofectin, fluorescence confocal microscopy and electrophoresis confirmed the delivery and persistence of this unprotected oligonucleotide inside MCF7 (breast cancer) cells. At a concentration of 2 microM, the oligonucleotide reduced within 6 h the HER2 mRNA level to 42% (Northern blot) but did not interfere with the transcription of a housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase. During the first day of administration at 0.22 microM, it lowered to 59% the HER2 protein in treated, as compared to nontreated, cells (ELISA). The effect was sequence specific when compared to that of five different negative controls, and it was target selective when compared to the expression of a related, nontargeted protein, the epidermal growth factor receptor. By day 2, the inhibitory effect was overcome by replenishment reactions.
The Activation-resistant Conformation of Recombinant Human Plasminogen Is Stabilized by Basic Residues in the Amino-terminal Hinge Region (1995)

Fully activable recombinant human plasminogen (rPlg) was expressed in mammalian cells employing either recombinant vaccinia virus or stable lines coexpressing alpha 2-plasmin inhibitor. A panel of eight variants of rPlg was constructed, in which progressively up to 6 basic amino acid residues in the hinge region of rPlg between the NH2-terminal acidic domain ("proactivation peptide") and kringle 1 were substituted by neutral residues. Analysis of the cleavage rates of these variants by plasmin revealed that the peptide bond at Arg68 is most susceptible, followed by Lys62 and Lys77. A variant with all 6 basic residues substituted was cleaved at Lys20. Three of these variants, PlgB (R68A, R70A), PlgF (R68A, R70A, K77H, K78H), and PlgG (R61A, K62A, R68A, R70A, K77H, K78H), as well as rPlg, were analyzed in more detail. The conformation of these plasminogens was analyzed by monitoring the change in intrinsic fluorescence upon binding of lysine analogs. This revealed that rPlg exhibits the native tight Glu1-plasminogen conformation, whereas PlgB, PlgF, and Plg G display an open conformation similar to Lys78-plasminogen, leading to an increased affinity for lysine analogs. This allowed a direct study of the impact of the activation-resistant conformation on the properties of Glu1-plasminogen. The open conformation of rPlg variants leads to an increased rate of activation by urokinase-type plasminogen activator and streptokinase and increased binding to a fibrin clot. Fibrin clot lysis mediated by tissue-type plasminogen activator was accelerated for the variants as a result of a lower Km for tissue-type plasminogen activator-mediated plasminogen activation, resulting from the increased affinity of rPlg (variants) for intact fibrin. We conclude that the basic residues in the extremely plasmin susceptible hinge region of plasminogen are directly involved in maintaining the activation resistant Glu1-plasminogen conformation.
Detailed glycan analysis of serum glycoproteins of patients with congenital disorders of glycosylation indicates the specific defective glycan processing step and provides an insight into pathogenesis (2003)

The fundamental importance of correct protein glycosylation is abundantly clear in a group of diseases known as congenital disorders of glycosylation (CDGs). In these diseases, many biological functions are compromised, giving rise to a wide range of severe clinical conditions. By performing detailed analyses of the total serum glycoproteins as well as isolated transferrin and IgG, we have directly correlated aberrant glycosylation with a faulty glycosylation processing step. In one patient the complete absence of complex type sugars was consistent with ablation of GlcNAcTase II activity. In another CDG type II patient, the identification of specific hybrid sugars suggested that the defective processing step was cell type-specific and involved the mannosidase III pathway. In each case, complementary serum proteome analyses revealed significant changes in some 31 glycoproteins, including components of the complement system. This biochemical approach to charting diseases that involve alterations in glycan processing provides a rapid indicator of the nature, severity, and cell type specificity of the suboptimal glycan processing steps; allows links to genetic mutations; indicates the expression levels of proteins; and gives insight into the pathways affected in the disease process.
The Parietal Cell as a Therapeutic Target (1986)

Inhibition of acid secretion or an improvement in mucosal resistance is central to treatment of upper gastrointestinal tract ulcers. Initiation of secretion is largely brought about by activation of the H2-histamine receptor, though other receptors are also involved to a lesser extent. Activation of the parietal cell by histamine is dependent on adenylate cyclase, and is a result of direct stimulation of the enzyme by histamine, Cyclic AMP can mimic the effect of H2-receptor activation. Mechanisms of cholinergic and gastrinergic stimulation involve different receptors and second messengers. These three systems can be used to construct a model of the parietal cell and its activation. On activation, changes in metabolism, structure and H+ pump function occur in the parietal cell, and these suggest the possibility of several sites of action for the phosphokinases activated by the second messengers cyclic AMP and Ca2+. Detailed studies have been carried out on the H+K+ATPase of hog gastric mucosa and a reaction sequence has been proposed, which can be correlated to the transport functions of the enzyme. The molecular weight of the enzyme is 94,000 and a part of its amino acid sequence has been determined. As knowledge about the enzyme becomes more precise, it should be possible to design a specific inhibitor. Such a terminal step inhibitor should be able to completely inhibit acid secretion in therapeutic doses.
Fuzzy Model Identification Based on Cluster Estimation (1994)

We present an efficient method for estimating cluster centers of numerical data. This method can be used to determine the number of clusters and their initial values for initializing iterative optimization-based clustering algorithms such as fuzzy C-means. Here we use the cluster estimation method as the basis of a fast and robust algorithm for identifying fuzzy models. A benchmark problem involving the prediction of a chaotic time series shows this model identification method compares favorably with other, more computationally intensive methods. We also illustrate an application of this method in modeling the relationship between automobile trips and demographic factors.
The Relative Importance of First- and Second-Phase Insulin Secretion in Countering the Action of Glucagon on Glucose Turnover in the Conscious Dog (1982)

While it is known that glucagon induces a biphasic release of insulin when infused into a normal animal, it is not known whether the resultant pattern of insulin secretion has important metabolic consequences. To ascertain whether such is the case, glucagon was elevated fourfold in the presence of first-, second-, or combined first- and second-phase insulin release to determine ability of the latter hormone to antagonize the effect of glucagon on glucose turnover in the conscious dog. To separate the effects of the different phases of insulin release the “pancreatic clamp” technique, in which somatostatin is given to inhibit the endocrine pancreas and replacement amounts of insulin and glucagon are given intraportally, was used. In this way, a rise in glucagon (∼220 pg/ml) was brought about in the presence of simulated first-phase (peak IRI 25 μU/ml at 5 min; basal by 30 min), secondphase (peak IRI 19 μU/ml at 30 min and sustained elevation thereafter), or first- plus second-phase (peak IRI 33 μU/ml at 5 min; 17 μU/ml at 30 min and sustained elevation thereafter) insulin release. Optimal glycemic control required both first- and second-phase insulin release. A selective deficiency of first-phase release resulted in a transient (2 h) worsening of the glucagon-induced hyperglycemia (twofold the normal increment). This defect was attributable to a larger initial rise in glucose production (3.6 ± 0.6 mg/kg · min) than that observed when both phases of insulin release were present (0.9 ± 0.4 mg/kg · min). First-phase insulin release had no significant effect on glucose clearance. A selective deficiency of second-phase release resulted in marked (sixfold) and prolonged worsening of the glucagon-induced hyperglycemia. In this case, however, the hyperglycemia was primarily the result of a defect in glucose clearance. Glucose clearance fell by 29 ± 7% instead of rising by 30 ± 4% as it did when both firstand second-phase release were present. Glucose production was mildly elevated between 15 and 75 min when second-phase insulin release was deficient relative to that apparent when both the first- and secondphases of release were present; this also contributed to the abnormal hyperglycemia. We conclude that both phases of insulin release are vital to full counterregulation of the action of glucagon on glucose metabolism. First-phase insulin release is important to counter the quick effect of glucagon on glucose production, while second-phase insulin release is important to sustain that inhibition and to augment glucose utilization. Absence of first-phase release results in a transient (2 h) and moderate (20–30 mg/dl) glycemic defect while an absence of second-phase release results in a prolonged and dramatic (70–100 mg/dl) defect.