gebhart/patrepeval huggingface dataset:
Effect of static magnetic fields on osteoblasts and fibroblasts in vitro (1993)

In vitro assays were made of the effect of a static magnetic field of a neodymium magnet on cellular behavior. The cell turnover rate was examined by the incorporation of radioactive thymidine, and anabolic processes were measured by the incorporation of radioactive proline. Cell cultures of fibroblast- and osteoblast-like cells of the neonatal rat calvarium were assayed to determine uptakes of radioactive thymidine and proline; these assays were performed in conjunction with examination of an explant of the rat calvarium. The cells were assayed after exposure to a field for 1-, 3-, 5-, 7-, and 10-day periods. Cells were exposed to north and south poles with a pole-face flux density of 0.61 T; control cultures were exposed to an unmagnetised piece of neodymium. After sham exposure or exposure to the magnetic field, 50 microCuries/ml of culture media of isotope were added to the culture medium. The cultures were returned to an incubator for 6 h. Then, following centrifugation, the supernatant was assayed for radioactivity in a scintillation counter after addition of 3 ml of scintillation fluid. A statistically significant magnetic stimulation of turnover rate and synthesis of fibroblasts was found, but stimulation of osteoblasts did not occur. Conversely, the explants, which represent the osteoblasts and fibroblasts in an organised system, showed a statistically significant inhibition in uptake of the radioactive label. The data indicate both variability and diversity of cellular behaviour, and they accentuate the need for caution in the interpretation of effects of static magnetic fields.
A Closer Look at Skip-gram Modelling (2006)

Data sparsity is a large problem in natural language processing that refers to the fact that language is a system of rare events, so varied and complex, that even using an extremely large corpus, we can never accurately model all possible strings of words. This paper examines the use of skip-grams (a technique where by n-grams are still stored to model language, but they allow for tokens to be skipped) to overcome the data sparsity problem. We analyze this by computing all possible skip-grams in a training corpus and measure how many adjacent (standard) n-grams these cover in test documents. We examine skip-gram modelling using one to four skips with various amount of training data and test against similar documents as well as documents generated from a machine translation system. In this paper we also determine the amount of extra training data required to achieve skip-gram coverage using standard adjacent tri-grams. 1.
Interleukin 2 augmentation of natural killer cell activity in homosexual men with acquired immune deficiency syndrome (1984)

Natural killer cell activity of peripheral blood mononuclear cells against K562 myeloid cells was studied in 8 normal heterosexual men, 5 healthy homosexual men, and 11 homosexual men with acquired immune deficiency syndrome. The overall natural killer cell activity was lower in healthy homosexual men and in homosexual men with acquired immune deficiency syndrome. Peripheral blood mononuclear cells from four normal heterosexual men were preincubated overnight in complete medium supplemented with various concentrations of lectin-free interleukin 2 lacking interferon. Cells from these cultures exhibited a dose-dependent augmentation of natural killer cell activity. Peripheral blood mononuclear cells obtained from 8 normal heterosexuals, 5 healthy homosexuals, and 11 homosexual men with acquired immune deficiency syndrome were preincubated overnight in complete medium supplemented with 20% interleukin 2. Natural killer cell activity cultured in 20% interleukin 2 increased to 78.4 +/- 8.4 (mean +/- standard deviation) from 30.8 +/- 11.0 in normal heterosexual men, to 68.3 +/- 17.6 from 16.8 +/- 13.6 in healthy homosexual men and to 49.3 +/- 15.3 from 11.6 +/- 6.1 in homosexual men with acquired immune deficiency syndrome at a 100:1 effector/target cell ratio. These results suggest that interleukin 2 is capable of directly stimulating natural cell-mediated cytotoxicity. Consideration of the use of interleukin 2 as a potential therapeutic agent to modify immune responses in disorders such as acquired immune deficiency syndrome appears warranted.
Cell Biology of Extracellular Matrix (1988)

At a recent meeting to discuss the domains of cell biology, I put forth a case for the extracellular matrix, even though my argument ran the risk of falling on deaf ears. After all, the matrix is EXTR
Role of Omi/HtrA2 in Apoptotic Cell Death After Myocardial Ischemia and Reperfusion (2004)

Taken together, these results demonstrate for the first time that ischemia/reperfusion results in Omi/HtrA2 translocation from the mitochondria to the cytosol, where it promotes cardiomyocyte apoptosis via a protease activity-dependent, caspase-mediated pathway.
Assessment of Tumor Necrosis Factor Alpha Blockade As an Intervention to Improve Tolerability of Dose-Intensive Chemotherapy in Cancer Patients (2006)

The addition of etanercept is safe and had no impact on docetaxel concentrations. The significant improvement in tolerability and the trend toward preservation of dose-intensity suggests further exploration of TNF blockade as an adjunct to cancer therapies.
Healing of Thermoplastic Polymers at an Interface under Nonisothermal Conditions (2002)

Fabrication of layered thermoplastic polymer products involves applying heat and pressure to contacting thermoplastic surfaces and consolidating the interface. Polymer healing, referring to the intermolecular diffusion across the interfaces of thermoplastic tape layers in intimate contact, is one of the important steps responsible for the development of interlaminar bond strength and is strongly influenced by the temperature history. While the theory for healing under isothermal conditions is well established in the literature, the available descriptions of healing under nonisothermal processing conditions lack a sound fundamental basis. In this paper, a model for the healing process under nonisothermal conditions is developed starting from a fundamental formulation of the reptation of polymer chains. Considering the temperature dependence of the welding time, the bond strength is described as a function of temperature history. It is shown that, under certain nonisothermal conditions, considerable errors could be introduced in the prediction of the healing development using the models in the literature.
Etk/Bmx, a tyrosine kinase with a pleckstrin-homology domain, is an effector of phosphatidylinositol 3′-kinase and is involved in interleukin 6-induced neuroendocrine differentiation of prostate cancer cells (1998)

Etk/Bmx is the newest member of Btk tyrosine kinase family that contains a pleckstrin homology domain, an src homology 3 domain, an src homology 2 domain, and a catalytic domain. Unlike other members of the Btk family kinases, which are mostly hemopoietic cell-specific, Etk/Bmx is preferentially expressed in epithelial and endothelial cells. We first identified this kinase in prostate cancer [Robinson, D., He, F., Pretlow, T. & Kung, H. J. (1996) Proc. Natl. Acad. Sci. USA 93, 5958-5962). Here we report that Etk is engaged in phosphatidylinositol 3-kinase (PI3-kinase) pathway and plays a pivotal role in interleukin 6 (IL-6) signaling in a prostate cancer cell line, LNCaP. Our evidence that PI3-kinase is involved in Etk activation includes: (i) Wortmannin, a specific inhibitor of PI3-kinase, abolished the activation of Etk by IL-6; (ii) a constitutively active p110 subunit of PI3-kinase was able to activate Etk in the absence of IL-6; and (iii) a dominant negative p85 subunit of PI3-kinase mutant blocked the activation of Etk by IL-6. Interestingly, IL-6 treatment of LNCaP induced a remarkable neuroendocrine-like differentiation phenotype, with neurite extension and enhanced expression of neuronal markers. This phenotype could be abrogated by the overexpression of a dominant-negative Etk, indicating Etk is required for this differentiation process.
Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers (2012)

In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity.
Percutaneous endovascular graft: experimental evaluation. (1987)

An arterial endovascular graft was constructed by wrapping a Dacron cylinder around the Gianturco expandable metallic stent. The device was passed through an 11-F Teflon catheter into the normal abdominal or thoracic aortas of nine dogs. At follow-up of 7-35 weeks, all but one graft remained patent. At necropsy, the grafts were almost completely covered by neo-intimal proliferation. Similar proliferation was observed between the graft and the wall of the vessel.
Incidence of Death and Acute Myocardial Infarction Associated With Stopping Clopidogrel After Acute Coronary Syndrome (2008)

We observed a clustering of adverse events in the initial 90 days after stopping clopidogrel among both medically treated and PCI-treated patients with ACS, supporting the possibility of a clopidogrel rebound effect. Additional studies are needed to confirm the clustering of events after stopping clopidogrel, including associations with cardiovascular mortality and reasons for stopping clopidogrel, as well as to determine the mechanism of this phenomenon, and to identify strategies to reduce early events after clopidogrel cessation.
Reactive Immunization (1995)

For almost 200 years inert antigens have been used for initiating the process of immunization. A procedure is now described in which the antigen used is so highly reactive that a chemical reaction occurs in the antibody combining site during immunization. An organophosphorus diester hapten was used to illustrate this concept coined "reactive immunization." The organophosphonate recruited chemical potential from the immune response that resembled the way these compounds recruit the catalytic power of the serine hydrolases. During this recruitment, a large proportion of the isolated antibodies catalyzed the formation and cleavage of phosphonylated intermediates and subsequent ester hydrolysis. Reactive immunization can augment traditional immunization and enhance the scope of catalytic antibody chemistry. Among the compounds anticipated to be effective are those that contain appropriate reactive functionalities or those that are latently reactive, as in the mechanism-based inhibitors of enzymes.
Potentiation of Catechin Gallate-Mediated Sensitization of Staphylococcus aureus to Oxacillin by Nongalloylated Catechins (2006)

(-)-Epicatechin gallate (ECg) and (-)-epigallocatechin gallate (EGCg) reduce oxacillin resistance in mecA-containing strains of Staphylococcus aureus. Their binding to staphylococcal cells is enhanced by the nongalloyl analogues (-)-epicatechin (EC) and (-)-epigallocatechin (EGC). EC and EGC significantly increased the capacity of ECg and EGCg to reduce levels of staphylococcal oxacillin resistance.
Advances in biotechnological production of butyric acid (2000)

The review is focused on several aspects of butyric acid production: butyric acid-producing bacterial strains, the characteristics of the genus Clostridium (the bacterium most used for butyrate production), and alternative methods of obtaining butyric acid by alcohol biotransformation. Further, the main metabolic pathways of butyrate production, and possibilities for their control are outlined. Batch, fed-batch or continuous fermentation combined with cell recycle or immobilization are applicable for anaerobic fermentations using Clostridium as the production strain. The best process comprises a combination of high cell concentration and slowly growing biomass, in addition to high production selectivity and low inhibitory effects of the end-product. Inhibitory effects may be avoided by on-line removal of the end-product. Extraction alone or extraction combined with simultaneous stripping of the organic phase (liquid membrane) into the second aqueous phase (pertraction) seem to be the most suitable methods for on-line butyrate removal. The biocompatibility and the distribution coefficient of the organic phase under fermentation conditions should be considered before designing a fermentation apparatus. Journal of Industrial Microbiology & Biotechnology (2000) 24, 153–160.
All ErbB Receptors Other Than the Epidermal Growth Factor Receptor Are Endocytosis Impaired (1996)

Four transmembrane tyrosine kinases constitute the ErbB receptor family: the epidermal growth factor (EGF) receptor, ErbB-2, ErbB-3, and ErbB-4. We have measured the endocytic capacities of all four members of the EGF receptor family, including ErbB-3 and ErbB-4, which have not been described previously. EGF-responsive chimeric receptors containing the EGF receptor extracellular domain and different ErbB cytoplasmic domains (EGFR/ErbB) have been employed. The capacity of these growth factor-receptor complexes to mediate 125I-EGF internalization, receptor down-regulation, receptor degradation, and receptor co-immunoprecipitation with AP-2 was assayed. In contrast to the EGF receptor, all EGFR/ErbB receptors show impaired ligand-induced rapid internalization, down-regulation, degradation, and AP-2 association. Also, we have analyzed the heregulin-responsive wild-type ErbB-4 receptor, which does not mediate the rapid internalization of 125I-heregulin, demonstrates no heregulin-regulated receptor degradation, and fails to form association complexes with AP-2. Despite the substantial differences in ligand-induced receptor trafficking between the EGF and ErbB-4 receptors, EGF and heregulin have equivalent capacities to stimulate DNA synthesis in quiescent cells. These results show that the ligand-dependent down-regulation mechanism of the EGF receptor, surprisingly, is not a property of any other known ErbB receptor family member. Since endocytosis is thought to be an attenuation mechanism for growth factor-receptor complexes, these data imply that substantial differences in attenuation mechanisms exist within one family of structurally related receptors.
Pre-eclampsia-associated alterations in Wharton's jelly proteoglycans. (2005)

Proteoglycans of Wharton's jelly contain mainly chondroitin/dermatan sulphate chains. The predominant proteoglycan is decorin (core proteins of 45 and 47 kDa), although the core proteins of biglycan (45 kDa), versican (260 kDa) and of other proteoglycans (90, 110, 220 kDa) were also detected (Gogiel et al., 2003). The aim of the present study was to compare the proteoglycan composition of Wharton's jelly of newborns delivered by healthy mothers and those with pre-eclampsia. Proteoglycans from pre-eclamptic Wharton's jelly had a higher sulphated glycosaminoglycan/protein ratio than those of normal tissue. Pre-eclampsia is associated with a lower level of all proteoglycan core proteins, especially those of higher molecular mass (such as versican), although the same set of core proteins were found in normal and pre-eclamptic Wharton's jelly. The alterations in the proteoglycan composition of Wharton's jelly may affect the mechanical properties of the umbilical cord and, in the case of pre-eclampsia, disturb foetal blood circulation.
Separation of “Light Fluorous” Reagents and Catalysts by Fluorous Solid-Phase Extraction:  Synthesis and Study of a Family of Triarylphosphines Bearing Linear and Branched Fluorous Tags (2000)

Practical syntheses of new triarylphosphines bearing both linear and branched fluorous tags (Rf) are reported. The phosphines have one, two, or all three aryl rings bearing fluorous tags: (Ph)(3)(-)(n)()P(C(6)H(4)(CH(2))(m)()Rf)(n)(). Fluorous-organic partition coefficients have been measured and the retention properties of both the phosphines and the derived phosphine oxides on fluorous reverse phase silica have been studied. While applications relying on liquid-liquid extractive separations of these phosphines may be limited to those bearing three fluorous chains, the technique of solid phase extraction should be broadly applicable to phosphines, phosphine oxides, and derived metal complexes. A parallel platinum-catalyzed allylation of aldehydes with fluorous allyl stannanes illustrates the usefulness of the new fluorous ligands in small-scale synthesis.
IMPORTANT COMPONENTS OF THE UW SOLUTION (1990)

The UW solution for preservation of the liver, kidney, and pancreas contains a number of components, and the importance of each of these has not been fully resolved. In the studies reported here the importance of glutathione and adenosine is demonstrated in isolated cell models (rabbit renal tubules and rat liver hepatocytes) of hypothermic preservation and reperfusion and in dog renal transplantation. Glutathione in the UW solution is necessary for the preservation of the capability of the cell to regenerate ATP and maintain membrane integrity. Adenosine in the UW solution provides the preserved cell with substrates for the regeneration of ATP during the reperfusion period following cold storage. The omission of GHS from the UW solution results in poorer renal function in the 48 hr dog kidney preservation-transplant model. The role of other components of the UW solution is discussed including lactobionic acid; other impermeants; and the colloid, hydroxyethyl starch. It is concluded that the development of improved preservation solutions will require a more detailed understanding of the mechanism of injury due to cold storage and, once obtained, solutions more complex than the UW solution may be required for improved long-term storage of organs.
Heat of Dissolution Measurements for CO2 in Mixed Alkanolamine Solvents (2007)

The main objective of this research was to measure heat of dissolution of CO{sub 2} in carefully mixed alkanolamine solvent systems, and provide such directly measured data that might be used for efficient design of CO{sub 2} capture process, and for better understanding of the thermodynamics of CO{sub 2}-Alkanolamine systems. An experimental set-up has been designed using the Isothermal Micro Calorimeter for measuring the solubilities and enthalpies of CO{sub 2} in mixed solvents made of MEA, MDEA, PZ, KF and water. All the measurements were done at temperatures 15, 40, and 75 C by maintaining a constant pressure of 100 psig. A detailed study has been done on the variation of solubilities and enthalpies over a wide range of temperatures, pressures and concentrations, by extracting the information from the literature.
Long-term Weight Control Study VI (1992)

We analyzed the individual response patterns of all 121 participants who entered the study. Fifty-one participants completed up to week 190. In 26 completers, the response pattern consisted of an initial beneficial effect (greater than or equal to 6 months of weight loss greater than or equal to 10% from baseline) and later success (weight loss of greater than or equal to 10% from baseline at week 160). These successful participants had lost 14.1 +/- 1.0 kg (mean +/- SEM); 15.9% +/- 0.9% of initial weight) at week 160 and 8.1 +/- 1.2 kg (9.1% +/- 1.3% of initial weight) at week 190. A second pattern observed in 16 completers consisted of initial benefit and later partial success (loss of 0.1% to 9.9% at week 160). Other response patterns observed in completers included showing initial benefit only (n = 3) and no success (n = 6). Seventy of the 121 participants left the study before week 190. There were 22 "dropout successes" who had consistent weight loss for 1 year or more and were greater than or equal to 10% below their initial weights at time of dropout. Fifteen "dropouts with initial benefit" stayed in the study for greater than or equal to 1 year with initial benefit (weight loss greater than or equal to 10% from baseline maintained for greater than or equal to 6 months). Medication-related reasons accounted for only 10 of the 37 dropouts in the group with initial or later benefit. Minimal benefit was seen in 17 dropouts. Another 16 were in the study less than 1 year. Analysis of individual participant responses made some other generalizations possible. Participants receiving continuous medication lost more weight and had fewer adverse effects than those receiving targeted intermittent medication. Upward dose adjustment appeared to help 24 participants achieve the criteria for late or partial success. Analyses of individual participant responses can suggest ways to optimize anorectic medication use for individual patients.
Autonomic Nervous System Activity Before and During Episodes of Myocardial Ischemia in Patients with Stable Coronary Artery Disease During Daily Life (2000)

Spectral analysis of heart rate variability (HRV) was used to assess changes in the autonomic nervous system (ANS) 10 minutes before, during, and 10 minutes after 110 ischemic episodes (IEs) in 38 patients (25 men, age 61 +/- 10 years) with stable coronary artery disease. In 26 of 77 diurnal IEs (07:00-22:59) there were no changes in the spectral indexes (LF and HF) during the study period. In the remainder there was an increase in the LF:HF ratio due to HF withdrawal that started before the onset of the IE. All 33 nocturnal episodes also showed an increase in the LF:HF ratio, which was due not only to HF withdrawal, but also to a simultaneous increase in LF. Although it is not the only cause, the ANS plays a significant role in triggering IEs during daily life in patients with stable coronary artery disease. The common factor in all such episodes is a gradual withdrawal of parasympathetic tone.
Sparse solutions to linear inverse problems with multiple measurement vectors (2005)

We address the problem of finding sparse solutions to an underdetermined system of equations when there are multiple measurement vectors having the same, but unknown, sparsity structure. The single measurement sparse solution problem has been extensively studied in the past. Although known to be NP-hard, many single-measurement suboptimal algorithms have been formulated that have found utility in many different applications. Here, we consider in depth the extension of two classes of algorithms-Matching Pursuit (MP) and FOCal Underdetermined System Solver (FOCUSS)-to the multiple measurement case so that they may be used in applications such as neuromagnetic imaging, where multiple measurement vectors are available, and solutions with a common sparsity structure must be computed. Cost functions appropriate to the multiple measurement problem are developed, and algorithms are derived based on their minimization. A simulation study is conducted on a test-case dictionary to show how the utilization of more than one measurement vector improves the performance of the MP and FOCUSS classes of algorithm, and their performances are compared.