gebhart/patrepeval huggingface dataset:
A Method To Detect Low Levels of Enteric Viruses in Contaminated Oysters (1999)

Direct isolation and identification of pathogenic viruses from oysters implicated in gastroenteritis outbreaks are hampered by inefficient methods for recovering viruses, naturally occurring PCR inhibitors, and low levels of virus contamination. In this study we focused on developing rapid and efficient oyster-processing procedures that can be used for sensitive PCR detection of viruses in raw oysters. Poliovirus type 3 (PV3) Sabin strain was used to evaluate the efficacy of virus recovery and the removal of PCR inhibitors during oyster-processing procedures. These procedures included elution, polyethylene glycol precipitation, solvent extraction, and RNA extraction. Acid adsorption-elution in which glycine buffer (pH 7.5) was used was found to retain fewer inhibitors than direct elution in which glycine buffer (pH 9.5) was used. RNA extraction in which a silica gel membrane was used was more effective than single-step RNA precipitation for removing additional nonspecific PCR inhibitors. The final 10-microl volume of RNA concentrates obtained from 2 g of oyster tissue (concentration factor, 200-fold) was satisfactory for efficient reverse transcription-PCR detection of virus. The overall detection sensitivity of our method was 1 PFU/g of oyster tissue initially seeded with PV3. The method was utilized to investigate a 1998 gastroenteritis outbreak in California in which contaminated oysters were the suspected disease transmission vehicle. A genogroup II Norwalk-like virus was found in two of three recalled oyster samples linked by tags to the harvest dates and areas associated with the majority of cases. The method described here improves the response to outbreaks and can be used for rapid and sensitive detection of viral agents in outbreak-implicated oysters.
Cooperative cognitive electronic warfare UAV game modeling for frequency hopping radar (2018)

In modern warfare concepts, the use of wireless communications and network-centric topologies with unmanned aerial vehicles (UAVs) creates an opportunity to combine the familiar concepts of wireless beamforming in opportunistic random arrays and swarm UAVs. Similar in concept to the collaborative beamforming used in ground-based randomly distributed array systems, our novel approach improves wireless beamforming performance by leveraging cooperative location and function knowledge. This enables the capabilities of individual UAVs to be enhanced, using swarming and cooperative beamforming techniques, for more-effective support of complex radar jamming and deception missions. In addition, a dedicated System Oversight function can be used to optimize the number of beamforming UAVs required to jam a given target and manage deception assets.
Inhibiting glutamine uptake represents an attractive new strategy for treating acute myeloid leukemia (2013)

Cancer cells require nutrients and energy to adapt to increased biosynthetic activity, and protein synthesis inhibition downstream of mammalian target of rapamycin complex 1 (mTORC1) has shown promise as a possible therapy for acute myeloid leukemia (AML). Glutamine contributes to leucine import into cells, which controls the amino acid/Rag/mTORC1 signaling pathway. We show in our current study that glutamine removal inhibits mTORC1 and induces apoptosis in AML cells. The knockdown of the SLC1A5 high-affinity transporter for glutamine induces apoptosis and inhibits tumor formation in a mouse AML xenotransplantation model. l-asparaginase (l-ase) is an anticancer agent also harboring glutaminase activity. We show that l-ases from both Escherichia coli and Erwinia chrysanthemi profoundly inhibit mTORC1 and protein synthesis and that this inhibition correlates with their glutaminase activity levels and produces a strong apoptotic response in primary AML cells. We further show that l-ases upregulate glutamine synthase (GS) expression in leukemic cells and that a GS knockdown enhances l-ase-induced apoptosis in some AML cells. Finally, we observe a strong autophagic process upon l-ase treatment. These results suggest that l-ase anticancer activity and glutamine uptake inhibition are promising new therapeutic strategies for AML.
A comparison of estimated proportional hazards models and regression trees (1989)

We present examples of the usage of regression trees for censored response via two real world datasets, one a rheumatoid arthritis survival study and the other a hip replacement study, and draw comparisons with the results of Cox proportional hazards modelling. The two methods pursue different goals. Motivation of the tree techniques is the desire to extract meaningful prognostic groups while the proportional hazards model enables assessment of the impact of risk factors. The methods are thus complementary. For the arthritis study the two techniques corroborate one another, although the flavour of the conclusions derived differ. For the hip replacement study, however, the regression tree approach reveals structure that would not emerge from a routine proportional hazards analysis. We also discuss the treatment of data analytic issues such as the handling of missing values and influence in the presence of non-uniform censoring.
Involvement of lipoproteins, free radicals, and calcium in cardiovascular disease processes. (1995)

Low density lipoproteins have the capacity to alter cell calcium concentrations of a wide variety of cell types. The precise mechanism of physical interaction of the LDL or its products with the cell is not defined yet. There is more agreement about the calcium transport pathway affected. Most studies show an ability of LDL to alter transsarcolemmal calcium flux, probably through the slow calcium channel. However, internal stores of calcium like the sarcoplasmic reticulum also appear to be altered. These effects of LDL on cellular calcium homeostasis have potential importance in both physiological and disease settings. Oxidised LDL has even more potential significance than the native LDL in disease conditions. Free radical mediated oxidation of LDL during atherosclerotic and ischaemic conditions creates a molecule with even greater potency for altering cell calcium and ultimately cell function and viability. The interaction of this trio of compounds--LDL, free radicals, and cellular calcium--may be critical for the mechanism of pathogenesis in specific cardiovascular diseases. It will be important in the future to identify new therapeutic strategies to prevent their interaction.
Vilsmeier formylation of tert-anilines: dibenzo[b,f  ][1,5]diazocines and quinazolinium salts via the ‘t-amino effect’1 (1998)

The attempted Vilsmeier ortho-formylation of p-substituted N,N-dimethylanilines 1 with N-formyl-N-alkylarylamides 2 unexpectedly gives dibenzo[b,f][1,5]diazocines 5 in 26–74% yield. This reaction proceeds by Vilsmeier formylation ortho to the dimethylamino group of 1 followed by hydride migration from the N-methyl group to the newly formed iminium CH group, followed by intramolecular cyclisation, a new example of the ‘t-amino effect’. Similar formylation of cyclic tert-anilines such as 4-tolyl-pyrrolidines 6a,e,g, -piperidines 6b,f,h, -perhydroazepines 6c,i and -morpholine 6d, however, shows a different chemistry giving diformylated enamines 7 as the major products (12–60%). A small amount of diazocines 8 (1–13%) with a substituted benzyl at the nitrogen and N-formylated diazocines 9 are also isolated in some cases. When N-formyl-1,2,3,4-tetrahydroquinoline is used as the Vilsmeier reagent, normal formylation is observed, while use of aliphatic Vilsmeier reagents such as DMF and N-formylmorpholine give quinazolinium salts 16 and 17, also by way of the ‘t-amino effect’. The key feature in these formylations is the hydride transfer from the α-position of a tertiary amine to an unsaturated ortho-substituent CHNR2+, the ‘t-amino effect’.
Comparison Of Discrete Cosine Transform And Vector Quantization Of Medical Imagery (1986)

This paper addresses the problem of data compression of medical imagery such as X-rays, Computer Tomography, Magnetic Resonance, Nuclear Medicine and Ultrasound. The Discrete Cosine Transform (DCT) has been extensively studied for image data compression, and good compression has been obtained without unduly sacrificing image quality. Vector Quantization has only recently been applied to image data compression, but shows promise of outperforming more traditional transform coding methods, especially at high compression. Vector Quantization is quite well suited for those applications where the images to be processed are very much alike, or can be grouped into a small number of classifications. These and similar studies continue to suffer from the lack of a uniformly agreed upon measure of image quality. This is also exacerbated by the large variety of electronic displays and viewing conditions.
pH-Dependent Processes in Protein (1985)

Recent improvements in the understanding of electrostatic interactions in proteins serve as a focus for the general topic of pH-dependent processes in proteins. The general importance of pH-dependent processes is first set out in terms of hydrogen ion equilibria, stability, ligand interactions, assembly, dynamics, and events in related molecular systems. The development of various theoretical treatments includes various formalisms in addition to the solvent interface model developed by Shire et al. as an extension of the Tanford-Kirkwood treatment. A number of detailed applications of the model are presented and future potentialities are sketched.
Hyperosmotic stimuli inhibit VCAM-1 expression in cultured endothelial cells via effects on interferon regulatory factor-1 expression and activity (2002)

Transcriptional up-regulation of the VCAM-1 gene, induced by proinflammatory cytokines such as IL-1beta and TNF-alpha, requires activation of not only NF-kappaB, but also involves interferon regulatory factor (IRF)-1. During a study of gene induction by mechanical stimuli in cultured human endothelial cells, we noted that medium hyperosmolarity appeared to influence cytokine-induced expression of VCAM-1. Indeed, addition of hyperosmotic, pathophysiologically relevant concentrations of NaCl effectively inhibited IL-1beta or TNF-alpha induction of VCAM-1, but not E-selectin, at the level of mRNA and cell surface protein. Because induction of both VCAM-1 and E-selectin by these cytokines is NF-kappaB dependent, we investigated whether the inhibitory effect of hyperosmotic medium might involve IRF-1. Electrophoretic mobility shift assays of the VCAM-1 promoter demonstrated that hyperosmotic medium suppressed IL-1beta- or TNF-alpha-activated binding activities of IRF-1, but not NF-kappaB, to their respective sites. Hyperosmotic medium also inhibited the expression of IRF-1 induced by TNF-alpha or IFN-gamma. Furthermore, hyperosmotic medium inhibited TNF-alpha or IFN-gamma induction of guanylate binding protein-1, another IRF-1-dependent gene. Taken together, hyperosmolarity selectively inhibits cytokine-induced VCAM-1 in endothelial cells, via an IRF-1-dependent mechanism. Thus, pathophysiological fluctuations in plasma osmolarity may influence certain endothelial-dependent components of the inflammatory response and host defense mechanisms.
The role of printing parameters and scaffold biopolymer properties in the efficacy of a new hybrid nano-bioprinting system (2009)

We created a hybrid nano-bioprinting system, which combines the initial patterning capabilities of direct cell writing with the active patterning capabilities of superparamagnetic nanoparticles. Biofabrication conditions, including printing parameters and scaffold biopolymer properties, may affect cell viability, nanoparticle manipulation and patterning capabilities. Nanoparticles were printed under varied conditions either in the biopolymer or loaded inside cells. Cell viability, alginate viscosity, nanoparticle movement and printing resolution were measured. We now show that while nanoparticles decreased cell viability, nozzle size had no significant effect. High printing pressure decreased cell viability, but viability loss was not accentuated by nanoparticles. High nanoparticle concentrations increased alginate viscosity at higher alginate concentrations. Nanoparticle velocity in response to a magnetic field was a function of nanoparticle diameter and scaffold viscosity, which agreed with a mathematical model of nanoparticle movement. Finally, the nano-bioprinting system resolution and patterning precision were not affected by nanoparticles in the prepolymer solution. These data suggest that nanoparticle incorporation in solid freeform fabrication does not change biofabrication parameters unless high nanoparticle concentrations are used. Future work includes developing vascularized tissue engineering constructs using the nano-bioprinting system.
MET and KRAS Gene Amplification Mediates Acquired Resistance to MET Tyrosine Kinase Inhibitors (2010)

The establishment of the role of MET in human cancer has led to the development of small-molecule inhibitors, many of which are currently in clinical trials. Thus far, nothing is known about their therapeutic efficacy and the possible emergence of resistance to treatment, a problem that has been often observed with other receptor tyrosine kinase (RTK) inhibitors. To predict mechanisms of acquired resistance, we generated resistant cells by treating MET-addicted cells with increasing concentrations of the MET small-molecule inhibitors PHA-665752 or JNJ38877605. Resistant cells displayed MET gene amplification, leading to increased expression and constitutive phosphorylation of MET, followed by subsequent amplification and overexpression of wild-type (wt) KRAS. Cells harboring KRAS amplification progressively lost their MET dependence and acquired KRAS dependence. Our results suggest that MET and KRAS amplification is a general mechanism of resistance to specific MET inhibitors given that similar results were observed with two small inhibitors and in different cell lines of different histotypes. To our knowledge, this is the first report showing that overexpression of wt KRAS can overcome the inhibitory effect of a RTK inhibitor. In view of the fact that cellular models of resistance to inhibitors targeting other tyrosine kinases have predicted and corroborated clinical findings, our results provide insights into strategies for preventing and/or overcoming drug resistance.
Samarium (III) iodide promoted preparation of α,α′-bis (substituted benzylidene)cyclohexanones from benzaldehydes and cyclohexanone (2000)

Promoted by SmI 3 , cyclohexanone condenses with benzaldehydes in the presence of catalytic amount of SiMe 3 Cl (TMSCl) to give 2,6-bis(substituted benzylidene)cyclohexanones under mild conditions in good yields.
Oestrogen receptors – an overview (1999)

The oestrogen receptor (ER) is a ligand-activated transcription factor that mediates the effects of the steroid hormone 17beta-oestradiol in both males and females. Since the isolation and cloning of ER, the prevailing opinion has been that only one such receptor exists. The finding of a second subtype of ER (ERbeta) has caused considerable excitement and has forced endocrinologists to re-evaluate many aspects of the actions of oestrogens. In this article, we will try to summarize the current knowledge about the two oestrogen receptor subtypes, with the emphasis on oestrogen receptor beta (ERbeta), and to comment on the observations in mice lacking either receptor or the hormone itself.
Cell-Penetrating Peptides: Mechanisms and Applications (2005)

A major obstacle in the development of new therapeutic agents is the low bioavailability of hydrophilic substances. Drugs that bind to intracellular targets must penetrate the lipid bilayer surrounding the cell in order to exert their effect. A relatively new research area that addresses this problem by introducing novel transport peptides that facilitate the cellular penetration of potential drugs has emerged. These peptides predominantly have a positive net charge and/or an amphipathic nature, but can otherwise have very different characteristics. This group of peptides, although sometimes called protein transduction domains (PTDs), is here referred to as cell-penetrating peptides (CPPs). For many years it was believed that these peptides were internalized into cells via a non-endocytotic, receptor-independent pathway. However, recent publications have suggested that an endocytotic pathway cannot be ruled out, and that earlier results might be based on artifacts associated with fixation of cells and membrane association of peptides. Although the mechanism of cellular uptake remains unclear, there is an increasing amount of reports on biological effects of CPPs and their cargos. Thus, CPPs are an attractive pharmaceutical and biochemical tool that needs more attention. This review will discuss some recent results in this research field with focus on the cell-penetrating peptide transportan.
RAP: Internet Route Access Protocol (1993)

This memo defines an Experimental Protocol for the Internet community. It does not specify an Internet standard. Discussion and suggestions for improvement are requested. Please refer
Accumulation of 2',5'-oligoadenylates in encephalomyocarditis virus-infected mice (1987)

Levels of 2',5'-oligoadenylates (2-5A) in various tissues of murine encephalomyocarditis virus (EMCV)-infected mice were determined and compared with those found in pathogen-free mice and in mice treated with the interferon inducer poly(I).poly(C). In control, pathogen-free mice, liver, spleen, brain, and kidney tissues possessed levels of 2-5A below 1 pmol/g of tissue, demonstrating that 2-5A was not a major component of uninfected mouse tissue. All control tissues had low basal levels (0.3 to 2.0 pmol/h per g) of 2-5A synthetase, the enzyme responsible for 2-5A production. After mice were injected intravenously with the interferon inducer poly(I).poly(C), circulating interferon, 2-5A synthetase, and 2-5A were elevated with increasing doses of double-stranded RNA. The greatest response to poly(I).poly(C) occurred in the kidney, in which enzyme levels increased 5-fold and 2-5A levels increased 24-fold to 15 pmol/g. Mice that were infected with EMCV also possessed elevated levels of 2-5A and 2-5A synthetase in the four tissues examined, although the relative distribution differed from that observed with poly(I).poly(C), indicating that the interferon inducer affects the concentration and location of intracellular 2-5A. Brain, spleen, and kidney tissues from EMCV-infected mice contained seven- to eightfold more 2-5A than control tissues did. The nanomolar levels of 2-5A in the tissues of EMCV-infected mice provide evidence that 2-5A may play a role in the antiviral response in an intact animal. In both poly(I).poly(C)- and EMCV-treated mice, the levels of 2-5A recovered from the tissues were not directly proportional to the amount of 2-5A synthetase present. These results indicate that factors other than the level of 2-5A synthetase controlled the accumulation of 2-5A in tissues.
Apoptosis-Associated Speck-like Protein Containing a CARD Forms Specks but Does Not Activate Caspase-1 in the Absence of NLRP3 during Macrophage Swelling (2015)

Apoptosis-associated speck-like protein containing a C-terminal caspase recruitment domain (ASC) is a key adaptor molecule required for the inflammatory processes. ASC acts by bridging NLRP proteins, such as NLRP3, with procaspase-1 within the inflammasome complex, which subsequently results in the activation of caspase-1 and the secretion of IL-1β and IL-18. In response to bacterial infection, ASC also forms specks by self-oligomerization to activate caspase-1 and induce pyroptosis. Hitherto, the role of these specks in NLRP3 inflammasome activation in response to danger signals, such as a hypotonic environment, largely has been unexplored. In this article, we report that, under hypotonic conditions and independently of NLRP3, ASC was able to form specks that did not activate caspase-1. These specks were not associated with pyroptosis and were controlled by transient receptor potential vanilloid 2 channel-mediated signaling. However, interaction with NLRP3 enhanced ASC speck formation, leading to fully functional inflammasomes and caspase-1 activation. This study reveals that the ASC speck can present different oligomerization assemblies and represents an essential step in the activation of functional NLRP3 inflammasomes.
Energy Harvesting From Human and Machine Motion for Wireless Electronic Devices (2008)

Energy harvesting generators are attractive as inexhaustible replacements for batteries in low-power wireless electronic devices and have received increasing research interest in recent years. Ambient motion is one of the main sources of energy for harvesting, and a wide range of motion-powered energy harvesters have been proposed or demonstrated, particularly at the microscale. This paper reviews the principles and state-of-art in motion-driven miniature energy harvesters and discusses trends, suitable applications, and possible future developments.
Determination of the primary structure of cholera toxin B subunit. (1977)

The primary structure of cholera toxin B subunit, responsible for the binding of the toxin to cell surface ganglioside Gm1, has been determined as: Thr-Pro-Gln-Asn-Ile-Thr-Asp-Leu-Cys-Ala-Glu-Tyr-His-Asn-Thr-Gln-Ile-His-Thr-Leu-Asn-Asn-Lys-Ile-Phe-Ser-Tyr-Thr-Glu-Ser-Leu-Ala-Gly-Lys-Arg-Glu-Met-Ala-Ile-Ile-Thr-Phe-Lys-Asn-Gly-Ala-Thr-Phe-Glu-Val-Glu-Val-Pro-Gly-Ser-Gln-His-Ile-Asp-Ser-Gln-Lys-Lys-Ala-Ile-Glu-Arg-Met-Lys-Asn-Thr-Leu-Arg-Ile-Ala-Tyr-Leu-Thr-Glu-Ala-Lys-Val-Glu-Lys-Leu-Cys-Val-Trp-Asn-Asn-Lys-Thr-Pro-His-Ala-Ile-Ala-Ala-Ile-Ser-Met-Ala-Asn The number and the sequence of amino acid residues has been established by separation and analyses of the peptides obtained through enzymatic and chemical cleavage of the B subunit. The chymotryptic peptides from the citraconylated B subunit proved to be useful in the alignment of the tryptic peptide.
Psoriasis (2005)

Research to define the pathogenesis of psoriasis, a common inflammatory skin disorder, has considerably increased the general understanding of T-cell–mediated autoimmune disorders. Psoriasis is increasingly a prime target for new pathogenesis-oriented biologic therapies. The authors of this article review genetic, clinical, and pathogenic aspects of psoriasis and discuss their implications for new therapies.
Langerhans' cells, veiled cells, and interdigitating cells in the mouse recognized by a monoclonal antibody. (1986)

An mAb, NLDC-145, is described that specifically reacts with a group of nonlymphoid dendritic cells including Langerhans cells (LC), veiled cells (VC), and interdigitating cells (IDC). The antibody does not react with precursor cells in bone marrow and blood. Macrophages are not stained by the antibody, but a subpopulation of Ia+ peritoneal exudate cells is recognized. Possible relationships of the various nonlymphoid dendritic cell (NLDC) types are discussed.
Development of the Logical Observation Identifier Names and Codes (LOINC) Vocabulary (1998)

The LOINC (Logical Observation Identifier Names and Codes) vocabulary is a set of more than 10,000 names and codes developed for use as observation identifiers in standardized messages exchanged between clinical computer systems. The goal of the study was to create universal names and codes for clinical observations that could be used by all clinical information systems. The LOINC names are structured to facilitate rapid matching, either automated or manual, between local vocabularies and the universal LOINC codes. If LOINC codes are used in clinical messages, each system participating in data exchange needs to match its local vocabulary to the standard vocabulary only once. This will reduce both the time and cost of implementing standardized interfaces. The history of the development of the LOINC vocabulary and the methodology used in its creation are described.