gebhart/patrepeval huggingface dataset:
Folate and antifolate pharmacology. (1997)

Folic acid is a water-soluble vitamin associated with the other B vitamins. In its fully reduced form (tetrahydrofolate), folate serves as a 1-carbon donor for synthesis of purines and thymidine as well as in the remethylation cycle of homocysteine to methionine. Folate is essential for normal cell growth and replication. It therefore is not surprising that folate analogues have served and continue to serve well as antibiotics and cytotoxic drugs in the treatment of cancer, autoimmune diseases, psoriasis, and bacterial and protozoal infections. During the past 50 years, many of the enzymes requiring folate as a co-factor (ie, thymidylate synthase), and molecules critical in folate homeostasis (ie, the reduced folate carrier, folylpolyglutamate synthase), have been purified and even crystallized. The genes have been cloned, sequenced, and mapped, providing detailed knowledge of their regulation and three-dimensional structure. This has, in part, led to the rational synthesis of a large number of folate analogues that differ from methotrexate, the "classical antifolate," in transport, metabolism, and intracellular targets. Currently, several new folate analogues with unique biochemical properties and clinical applications are being tested. The goals of this brief review are to review folate homeostasis, to highlight the similarities and differences between natural folate and antifolates with respect to biochemistry and metabolism, and to present the pharmacology of methotrexate and several next-generation folate analogues, such as trimetrexate and raltritrexed, with an emphasis on mechanisms of drug resistance.
Effect of salinity on growth, cell size and silicification of an euryhaline freshwater diatom: Cyclotella meneghiniana Kütz (2013)

1 - The rivers transport plankton seawards which finally enters estuaries and often experiences lethal osmotic stress along an increasing salinity gradient. The tolerance of river phytoplankton to salinity increase can modify the nutrient cycles in estuaries. In this experimental study based on two culture experiments, the effect of salinity on growth, cell size and silicification of the euryhaline freshwater diatom Cyclotella meneghiniana was studied. 2 - Diatoms were first grown in batch cultures at 8 different salinities ranging from 0 to 33. The maximal growth rate (0.92 d-1 ±0.04) occured at salinity 18 and decreased continuously from this optimum toward higher or lower salinities reaching 0.44 (±0.06) and 0.64 d-1 (±0.13) at salinities 0 and 33 respectively. 3 - In a second experiment two continuous cultures of the diatom were studied at salinities of 1 and 30. At equilibrium, the difference in the amount of Si per cell between the two cultures was due to a decreased cell height at salinity 30 and did not reflect any change in cell silicification on a surface basis. 4 - This work reveals the importance of accounting for the effect of salinity on freshwater euryhaline diatoms in the study of the Si cycle in the river-sea transition zone.
New common nomenclature for glycoprotein genes of varicella-zoster virus and their glycosylated products (1986)

The accumulation of recent data concerning the reactivity of monoclonal antibodies with particular varicella-zoster virus (VZV) glycoproteins and the mapping of several of their respective genes on the VZV genome has led to a unified nomenclature for the glycoprotein genes of VZV and their mature glycosylated products. Homologs to herpes simplex virus glycoprotein genes are noted.
Detection of nucleophosmin gene mutations in plasma from patients with acute myeloid leukemia: Clinical significance and implications (2009)

Roughly one-third of acute myeloid leukemia (AML) patients exhibit mutations in the nucleophosmin (NPM1) gene, and multiple studies have linked these mutations with a more favorable clinical outcome. We developed an assay for the detection of NPM1 mutations in peripheral blood plasma, and compared the results with clinical outcomes from a single institution. Analyzing plasma from previously untreated AML patients revealed NPM1 insertion mutations in 24 of 98 (24%) patients, with greater sensitivity than existing peripheral blood cell-based tests which showed positivity in only 22 of the 24 patients. Plasma testing allowed the detection of a novel 4 bp deletion in NPM1 in one patient. Analysis of clinical data corroborated previous data linking NPM1 mutations with better clinical outcome. These data underline the significance of NPM1 in the biology and clinical behavior of AML, and demonstrate the reliability and efficacy of plasma-based testing for NPM1 mutations.
Classical IP and ARP over ATM (1994)

This memo defines an initial application of IP and ARP in an Asynchronous Transfer Mode (ATM) network environment configured as a Logical IP Subnetwork (LIS) as described in Section 3. This memo does not preclude the subsequent development of ATM technology into areas other than a LIS; specifically, as single ATM networks grow to replace many ethernet local LAN segments and as these networks become globally connected, the application of IP and ARP will be treated differently. This memo considers only the application of ATM as a direct replacement for the wires and local LAN segments connecting IP end-stations (members) and routers operating in the classical LAN-based paradigm. Issues raised by MAC level bridging and LAN emulation are beyond the scope of this paper.
Type III Secretion: a Virulence Factor Delivery System Essential for the Pathogenicity of Burkholderia mallei (2004)

By creating mutations in the Burkholderia mallei ATCC 23344 animal pathogen-like type III secretion system (TTSS), this study analyzes the correlation between type III secretion and the pathogenicity of ATCC 23344 in vivo. Mutagenesis demonstrated that a functional TTSS was required for the full pathogenicity of ATCC 23344 in the BALB/c mouse and Syrian hamster models of infection. However, vaccination with each mutant failed to elicit a protective immunity against challenge with wild-type ATCC 23344.
Mechanism of Persistent Ischemic Mitral Regurgitation After Annuloplasty (2005)

Although tethering of both leaflets is the major determinant of ischemic MR before surgical annuloplasty, both leaflets tethering but with predominant and augmented PML tethering is related to persistent ischemic MR after the annnuloplasty.
Recognizing exons in genomic sequence using GRAIL II. (1994)

We have described an improved neural network system for recognizing protein coding regions (exons) in human genomic DNA sequences. This coding region recognition system is part of a new version of GRAIL, GRAIL II, and represents a significant improvement over the coding recognition performance of the previous GRAIL system. GRAIL II divides the process of locating exons into four steps. It first generates an exon candidate pool consisting of all possible (translation start-donor), (acceptor-donor), and (acceptor-translation stop) pairs within all open reading frames of the test sequence. The vast majority of these exon candidates are eliminated from consideration by applying a set of heuristic rules. After reducing the size of the candidate pool, GRAIL II uses three trained neural networks to evaluate the coding potential and accuracy of the edges of starting exon, internal exon and terminal exon candidates. These networks output a set of overlapping candidates for each exon which differ by their scores and position of their edges. Multiple candidates for a given exon are grouped into a cluster based on their locations relative to candidates corresponding to other exons, and the highest scoring candidate for each cluster is used as the "best" prediction of the corresponding exon. Unlike the previous GRAIL version, GRAIL II uses variable-length windows to evaluate exon candidates and its performance is nearly independent of exon length. In addition to several strong indicators of coding potential, the system uses several other types of information including scores for splice junctions, GC composition, and the properties of the regions adjacent to an exon candidate, to aid in the discrimination process. On a large set of sequences from Genbank (3), GRAIL II located 93% of all exons regardless of size with a false positive rate of 12%. Among the true positives, 62% match the actual exons exactly (the exons edges are correct to the base), and 93% match at least one edge correctly. These statistics are further improved, especially the false positive rate and accuracy of the edges, through a process of gene model construction by the Gene Assembly Program (GAP III) (4) module of GRAIL II, which uses the scored exon candidates as input and constructs optimal gene models. The gene modeling system will be described elsewhere.
Friction compensation for a force-feedback telerobotic system (2006)

This paper presents a model-based approach to cancel friction in the joints of the manipulators of a force-feedback telerobotic system. Friction compensation can improve the transparency of telerobotic systems, where transparency is quantified in terms of a match between the impedance of the environment and the impedance transmitted to the user. We used Dahl friction models to compensate for physical friction in the device. Experiments performed on a telerobotic system demonstrated that teleoperation transparency is improved by using these models. Further, the stability of the teleoperation is analyzed using passivity theory, and it is shown that the master-slave system remains stable up to a certain level of friction compensation
Gd(DOTA): An alternative to Gd(DTPA) as a T1,2 relaxation agent for NMR imaging or spectroscopy (1986)

Methods have been devised for obtaining gadolinium(III) complexes of the ligands NOTA (1,4,7-triazacyclononane-N,N',N''-triacetic acid), DOTA (1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid), TETA (1,4,8,11-tetraazacyclotetradecane-N,N',N'',N'''-tetraacetic acid), and DTPA (diethylenetriaminepentaacetic acid) as solids for use as pharmaceuticals. Their effectiveness as in vitro and in vivo contrast agents for NMR imaging or T1,2 relaxation agents for spectroscopy has been investigated. The Gd(DOTA) complex was shown to be a more stable alternative to Gd(DTPA) by serum stability studies and measurement of stability constants. Images of tumors grown in athymic mice were obtained by NMR after injection of Gd(DOTA) and Gd(DTPA).
Reaction of acid gases with mixtures of amines (1985)

Detailed thermodynamic and kinetic models are presented in this paper which were developed for acid gas reactions with mixtures of amines. The models permit the extension of the nonequilibrium-stage approach in the simulation of gas treating plants using solvent blends. The prediction of these models indicate a potentially great improvement in sour gas treating processes. The mixing concept enables one to obtain the individual advantages of each amine for absorption as well as desorption without the disadvantages of either. In the absorber, the MEA in the blend at the top of the column serves to remove residual CO2 from the gas while throughout the rest of the column MDEA does a bulk removal job. The use of blended amines to treat natural, refinery and synthesis gases brings about a considerable improvement in absorption and a great savings in energy requirements.
Functional significance of the beta-subunit for heterodimeric P-type ATPases (1995)

We have reviewed the structural and functional role of the beta-subunit in a subfamily of the P-ATPases known as the alpha/beta-heterodimeric, cation-exchange ATPases. The subfamily consists of the various isoforms of Na+/K(+)-ATPase and H+/K(+)-ATPase, both of which pump a cation out of the cell (Na+ or H+, respectively) in recycle exchange for K+. Much of the earlier work has emphasized the functional activities of the alpha-subunit, which shares many characteristics with the broader P-ATPase family. It is now clear that the glycosylated beta-subunit is an essential component of the cation-exchange ATPase subfamily. All beta-subunit isoforms have three highly conserved disulfide bonds within the extracellular domain that serve to stabilize the alpha-subunit, alpha/beta interaction and functional activity of the holoenzyme. Evidence strongly suggests that the beta-subunit is involved in the K(+)-dependent reactions of the enzymes, such as the E1-E2 transition and K+ occlusion, and that the extracellular domain of the beta-subunit plays an important role in determining the kinetics of K+ interaction. In most vertebrate cells, the unassociated alpha-subunit is restricted to the endoplasmic reticulum (ER), and assembly of the alpha/beta complex occurs within the ER. Signals for exiting the ER and directing the correct intracellular trafficking are primarily determined by the beta-subunit; Na+/K(+)-ATPase typically terminates in the plasma membrane facing the basolateral membrane, whereas all isoforms of H+/K(+)-ATPase terminate in the apical membrane. The C-terminal extracellular domain of the beta-subunit is important for proper interaction with the alpha-subunit and for correct intracellular trafficking. Oligosaccharides on the beta-subunit are not essential for enzyme function, but do serve to enhance the efficiency of alpha/beta association by increasing the lifetime of the unassociated beta-subunit and the stability of the alpha/beta complex to tryptic attack. We propose that highly specialized glycosylation on the beta-subunit of the gastric H+/K(+)-ATPase may help to protect that enzyme from the harsh extracellular environment of the stomach.
Internet Message Format (2001)

This standard specifies a syntax for text messages that are sent between computer users, within the framework of "electronic mail" messages. This standard supersedes the one specified in Request For Comments (RFC) 822, "Standard for the Format of ARPA Internet Text Messages", updating it to reflect current practice and incorporating incremental changes that were specified in other RFCs.
Sequence‐selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli (1999)

The CspA family of Escherichia coli comprises nine homologous proteins, CspA to CspI. CspA, the major cold shock protein, binds RNA with low sequence specificity and low binding affinity. This is considered to be important for its proposed function as an RNA chaperone to prevent the formation of secondary structures in RNA molecules, thus facilitating translation at low temperature. The cellular functions of other Csp proteins are yet to be fully elucidated, and their sequence specific binding capabilities have not been identified. As a step towards identification of the target genes of Csp proteins, we investigated the RNA binding specificities of CspB, CspC and CspE by an in vitro selection approach (SELEX). In the present study, we show that these proteins are able to bind preferentially to specific RNA/single-stranded DNA sequences. The consensus sequences for CspB, CspC and CspE are U/T stretches, AGGGAGGGA and AU/AT-rich regions, especially AAAUUU, respectively. CspE and CspB have Kd values in the range 0.23-0.9 x 10(-6) M, while CspC has 10-fold lower binding affinity. Consistent with our recent findings of transcriptional regulation of cspA by CspE, we have identified a motif identical to the CspE consensus. This motif is the putative CspE-mediated transcription pause recognition site in a 5'-untranslated region of the cspA mRNA.
Workshop on the Essentiality of and Recommended Dietary Intakes for Omega-6 and Omega-3 Fatty Acids (1999)

The Workshop on the Essentiality of and Recommended Dietary Intakes (RDIs) for Omega-6 and Omega-3 Fatty Acids was held at The Cloisters, National Institutes of Health (NIH) in Bethesda, Maryland, ...
Intraocular photodisruption with picosecond and nanosecond laser pulses: tissue effects in cornea, lens, and retina. (1994)

The use of ps pulses improves the precision of intraocular Nd:YAG laser surgery and diminishes unwanted disruptive side effects, thereby widening the field of potential applications. Promising fields for further studies are intrastromal corneal refractive surgery, cataract fragmentation, membrane cutting, and vitreolysis close to the retina.
One-Pot Borylation/Amination Reactions:  Syntheses of Arylamine Boronate Esters from Halogenated Arenes (2006)

[reaction: see text] A one-pot protocol for converting 1,3- and 1,4-substituted aryl halides to arylamine boronate esters is described. This is achieved by sequential Ir-catalyzed aromatic borylation at the least hindered C-H bond of the aryl halide and subsequent Pd-catalyzed C-N coupling at the halide position of the crude arylboronic ester.
Electrical Properties of Atomic Layer Deposition HfO[sub 2] and HfO[sub x]N[sub y] on Si Substrates with Various Crystal Orientations (2008)

The use of high-k gate oxide on Si substrates with alternative orientations is expected to contribute for the fabrication of high mobility devices. In this paper, the interfacial and electrical properties of the plasma enhanced atomic layer deposition PE-ALD HfO 2 and HfO x N y gate oxides on Si substrates with three different crystal orientations, 001, 011, and 111, were comparatively studied. While PE-ALD HfO 2 films were prepared using oxygen plasma as a reactant, PE-ALD HfO x N y films were prepared by in situ nitridation using oxygen/nitrogen mixture plasma. For all crystal orientations, in situ nitridation using oxygen/nitrogen mixture plasma improved electrical properties producing lower leakage currents and smaller equivalent oxide thickness values. Both HfO 2 and HfO x N y films have shown the lowest leakage current and interface state density on Si001, whereas the poorest electrical properties were obtained on Si111. The results are discussed based on the experimental results obtained from various analytical techniques, including I-V, C-V, conductance methods, and X-ray photoelectron spectroscopy.
Cell-Penetrating Peptide TP10 Shows Broad-Spectrum Activity against both Plasmodium falciparum and Trypanosoma brucei brucei (2008)

Malaria and trypanosomiasis are diseases which afflict millions and for which novel therapies are urgently required. We have tested two well-characterized cell-penetrating peptides (CPPs) for antiparasitic activity. One CPP, designated TP10, has broad-spectrum antiparasitic activity against Plasmodium falciparum, both blood and mosquito stages, and against blood-stage Trypanosoma brucei brucei.
Causal Propagation of Constraints and the Canonical Form of General Relativity (1998)

Studies of new hyperbolic systems for the Einstein evolution equations show that the ``slicing density'' $\\alpha(t,x)$ can be freely specified while the lapse $N = \\alpha g^{1/2}$ cannot. Implementation of this small change in the Arnowitt-Deser-Misner action principle leads to canonical equations that agree with the Einstein equations whether or not the constraints are satisfied. The constraint functions, independently of their values, then propagate according to a first order symmetric hyperbolic system whose characteristic cone is the light cone. This result follows from the twice-contracted Bianchi identity and constitutes the central content of the constraint ``algebra'' in the canonical formalism.
Topology of SREBP Cleavage-activating Protein, a Polytopic Membrane Protein with a Sterol-sensing Domain (1998)

The NH2-terminal fragments of sterol regulatory element-binding proteins (SREBPs) are released from endoplasmic reticulum membranes by proteases whose activities depend upon SREBP cleavage-activating protein (SCAP), a polytopic endoplasmic reticulum membrane protein. The activity of SCAP is inhibited by sterols, which appear to interact with the polytopic membrane domain of SCAP. Here, we use protease protection and N-linked glycosylation site-mapping techniques to define the topology of the eight membrane-spanning domains of SCAP. The data indicate that the NH2 terminus and COOH terminus of SCAP face the cytosol. The long intralumenal loops after membrane-spanning segments 1 and 7 are glycosylated, confirming their lumenal location. The region comprising membrane-spanning segments 2-6 shows sequence resemblance to putative sterol-sensing domains in three other proteins: 3-hydroxy-3-methylglutaryl CoA reductase (HMG-CoA reductase), the Niemann-Pick C1 protein, and the morphogen receptor Patched. The orientation of the eight membrane-spanning segments in SCAP is consistent with the model proposed for HMG-CoA reductase (Olender, E. H., and Simoni, R. D. (1992) J. Biol. Chem. 267, 4223-4235). The membrane-spanning domains of SCAP and HMG-CoA reductase confer sterol sensitivity upon the functional activities of the two molecules. The common membrane topology of the two proteins is consistent with the notion that sterols regulate both proteins by a common mechanism.
Influence of complement depletion on sperm function in the female rabbit (1983)

Female rabbits were wholly depleted of complement by treatment with anti-complementary cobra venom factor (CVF) 36 h before mating. Complement depletion did not compromise occurrence of the acrosome reaction, as judged by sperm penetration of eggs collected 12-13 h post coitum. However, in CVF-treated females, significantly more spermatozoa had penetrated the egg vestments, more spermatozoa were present in flushings from the oviducts, and sometimes the uterus, than in control females mated to the same males. The results indicate that, although the acrosome reaction is unlikely to depend on complement activation, complement-dependent factors may exert a restrictive effect on spermatozoa after vaginal insemination of the normal female rabbit.
A multiple-capillary electrophoresis system for small-scale DNA sequencing and analysis (1999)

A five-capillary system has been developed for DNA sequencing and analysis. The post-column fluorescence detector is based on a sheath-flow cuvette. The instrument provides uniform and continuous illumination of the samples. The cuvette virtually eliminates cross-talk in the fluorescence signal between capillaries. Discrete single-photon counting avalanche photodiodes provide high efficiency light detection. The instrument has detection limits (3sigma) of 130 +/- 30 fluorescein molecules injected onto each capillary. Over 650 bases of sequence at 98.8% accuracy were generated in 100 min at 50 degrees C from M13mp18. Separation and detection of short tandem repeats proved efficient and accurate with the use of internal standards for direct comparison of migration times between capillaries.
Humoral, Mucosal, and Cellular Immune Response to Topical Immunization with a Subunit Respiratory Syncytial Virus Vaccine (1994)

The efficacy of topical immunization with the respiratory syncytial virus (RSV) fusion (F) protein was tested in mice using cholera toxin B chain (CTB) as an adjuvant. The dose of CTB required for the adjuvant effect (as measured by local and systemic antibody stimulation) and protection from viral challenge was > or = 5 micrograms. With this dose, mice immunized intranasally with CTB plus F protein were highly protected from viral replication in the upper and lower respiratory tract. This protection was associated with the induction of mucosal IgA and serum IgG and neutralizing antibody. Addition of parenteral immunization with F protein to the topical vaccination provided protection from viral challenge nearly equivalent to immunization with live RSV intranasally. Topical and parenteral immunization with F protein was not associated with induction of splenic cytotoxic T cells, in contrast to live virus given intranasally.