gebhart/patrepeval huggingface dataset:
Establishment of long-term monocyte suspension cultures from normal human peripheral blood. (1982)

The long-term suspension growth of normal, immature myeloid cells from fresh human cord blood was recently reported and required cells separated on supplemented discontinuous Percoll gradients, growth in media containing hydrocortisone and vitamins D3, and gentle, continuous agitation (13). When normal adult bone marrow (six donors) or blood from Epstein-Barr virus (EBV)-seropositive donors (nine donors) was used as a source of fresh human leukocytes, only short-term proliferation of myeloid cells was achieved with the same techniques. However, when leukocytes prepared from EBV seronegative normal adult peripheral blood were used, pure populations of monocytes and macrophages that replicate slowly in liquid suspension culture for greater than 5 mo were repeatedly obtained from three independent donors. These cultures consists of several morphologically distinguishable monocytic cell types, including an approximately 20% adherent macrophage population. The monocytic nature of these cultures was confirmed by cytochemical, immunological, and functional criteria. These monocytes retain a normal chromosome pattern and can be induced to differentiate to phagocytic cells by treatment with tetradecanylphorbal acetate. Eventually, the cultures terminate as nonreplicating mature macrophages. These liquid suspension cultures should be a valuable resource for morphological, biochemical, and functional studies of developing monocyte-macrophages and their interaction with other cell types in normal and various pathological situations.
TGF‐β Latency: Biological Significance and Mechanisms of Activation (1997)

Transforming growth factor (TGF-) beta is secreted as a latent complex in which the mature growth factor remains associated with its propeptide. In order to elicit a biological response, the cytokine must be released from the latent complex, a process termed latent TGF-beta activation or TGF-beta formation. Although latent TGF-beta activation is a critical step in the regulation of its activity, little is known about the molecular mechanisms that lead to the production of active TGF-beta. In this article, we present an overview of the data available on this topic, and we propose a tentative model for the mechanism of TGF-beta formation based upon the observations with different cell systems and on recent findings on the structure of the latent TGF-beta complex.
A one way public key cryptosystem for the linkage of nominal files in epidemiological studies. (1995)

An encryption method is proposed for nominal files to allow their linkage while respecting confidentiality rules. In contrast to most encryption algorithms, this encryption method must be non-reversible. The method is based on congruence, like the SAN MARCO algorithm, and satisfies the two following conditions. 1) Non-reversible enciphering, which implies the possibility of collisions. 2) The collision rate must be minimized, to allow file linkage. The security of this method is, in addition, guaranteed by a key, which is destroyed after enciphering and is not given to the recipient of the coded file.
Ciprofloxacin-tinidazole combination, fluconazole- azithromicin-secnidazole-kit and doxycycline- metronidazole combination therapy in syndromic management of pelvic inflammatory disease: a prospective randomized controlled trial. (2003)

All the three treatment combinations were found to be equally effective in the syndromic management of pelvic inflammatory disease.
Direct plasmadynamic conversion of plasma thermal power to electricity (2002)

The generation of electrical energy using direct plasmadynamic conversion (PDC) is studied experimentally for small-scale, chemically-assisted plasmas (CA-plasma) for the first time. Glow discharge and microwave-generated plasma sources are operated at power levels on the order of a few to 50 W in the discharge case and up to 12.83 W/cm/sup 3/ in the microwave case. Extracted power approaching 1/4 W has been achieved as a demonstration. It is envisioned that such a system may be readily scaled to a few hundred Watts to several tens of kilowatts output power for microdistributed commercial applications (e.g., household, automotive, light industry, and space based power). Three-quarter inch long by 0.040-in diameter cylindrical PDC electrodes have been tested in a 10-50 W direct current, glow discharge plasma device with He or Ar as the working gas at 0.3-3.0 torr. The PDC anode was magnetized in the range of 0-700 G with a 1.5-in water cooled Helmholtz electromagnet. Open circuit voltages up to 6.5 V were obtained across the PDC electrodes at 1 torr He and 350-G field. The collector voltage was shown to be a function of applied magnetic field strength B and peaking at about 300 G. A variety of resistive loads were connected across the PDC electrodes, extracting continuous electrical power up to 0.44 mW. The power/load curve peaks at 0.44 mW for a 20 k/spl Omega/ load indicating the impedance matching condition with the plasma source. The most severe limitation to collector output performance is shown to be plasma conductivity. Collector power drops sharply with increasing neutral gas fill pressure in the glow discharge chamber at constant discharge current indicating that electron collisions with neutral gas atoms are responsible for the reduction in conductivity. Scale-up to higher power has been achieved with the use of a microwave plasma generator. A 0.75-in long by 0.094-in diameter PDC anode was magnetized to /spl sim/140 G resulting in open circuit PDC voltages in excess of 11.5 V for He plasmas at /spl sim/0.75-1 torr and 50 sccm flow. Due to higher conductivity, load matching was now obtained at /spl sim/600 /spl Omega/. Langmuir probe results indicate good agreement between the conductivity change and the electron to neutral density ratio scale-up. For this source and electrode configuration, PDC power as high as /spl sim/200 mW was demonstrated in He at 0.75 torr for a microwave input power density of /spl sim/8.55 W/cm/sup 3/. Considering an electron mean-free path as the scale for collector probe influence in the plasma, the peak extracted power density is /spl sim/1.61 W/cm/sup 3/, corresponding to a volumetric conversion efficiency of /spl sim/18.8%.
Localization of an alpha 1,2 galactosyltransferase activity to the Golgi apparatus of Schizosaccharomyces pombe. (1994)

We have cloned a gene encoding an alpha 1,2 galactosyltransferase activity from Schizosaccharomyces pombe. The open reading frame of the gene (gma12 for galactomannan, alpha 1,2), combined with the previous protein purification (Chappell and Warren, 1989), predicts an O-linked glycoprotein with type II transmembrane topology. By homologous gene disruption, we have demonstrated that the gma12 gene product (gma12p) is nonessential. The deletion strain (gma12-D10::ura4) has a significantly reduced level of galactosyltransferase activity relative to the parental strain, but both in situ lectin binding and in vitro biochemical assays demonstrate the presence of further galactosyltransferase activity in addition to gma12p. Although gma12p is not the only galactosyltransferase in S. pombe, it produces a unique carbohydrate structure on the surface of the yeast cells. We have generated a polyclonal antiserum against this carbohydrate epitope and shown that gma12p is capable of synthesizing the epitope both in vitro and in vivo. Electron microscopic localization of the gma12+ specific epitope in gma12+ cells revealed that gma12p synthesizes the carbohydrate structure in the Golgi apparatus, and subsequent intracellular transport distributes the epitope to later stages of the secretory pathway. The immunolocalization studies confirm the presence of one or more galactosyltransferase activities in the Golgi apparatus in fission yeast.
AP1-Dependent Galectin-1 Expression Delineates Classical Hodgkin and Anaplastic Large Cell Lymphomas from Other Lymphoid Malignancies with Shared Molecular Features (2008)

These findings establish a functional AP1 signature that includes Gal1 expression in cHL and ALCL and suggests a common mechanism for tumor immunotolerance in these diseases. In addition, the combination of Gal1 and c-Jun serve as diagnostic biomarkers that delineate cHL and ALCL from other lymphomas with shared morphologic and/or molecular features.
Amperometric enzyme electrodes (1987)

Three different types of amperometric enzyme electrode are described. The first type uses a conducting organic-salt electrode to oxidize NADH. Results for sensors for ethanol and for bile acids are presented. In the second type of sensor, flavoenzymes are directly oxidized on the surface of the conducting organic-salt electrode. Results for five different enzymes are described. The mechanism of the enzyme oxidation is discussed and the reaction is shown to take place by heterogeneous redox catalysis and not by homogeneous mediation. The enzymes are strongly adsorbed on the electrode; microelectrodes for in vivo studies can be constructed without a membrane. Results for in vivo studies of changing glucose levels in the brain of a freely moving rat are presented. The third type of sensor is designed to measure low levels of toxic gases such as H2S and HCN. This is done by monitoring the inhibition by the toxic gas of the activity of the respiratory enzyme cytochrome oxidase.
Primary structure of Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase determined by mass spectrometry sequence analysis and molecular cloning. Evidence for a protein motif in the sialyltransferase gene family. (1992)

The Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase forms the NeuAc alpha 2,3Gal beta 1,3(4)GlcNAc sequences found in terminal carbohydrate groups of glycoproteins and glycolipids. High energy collision-induced dissociation analysis of tryptic peptides from only 300 pmol of the purified Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase provided 25% of the total amino acid sequence and led to the successful cloning of this enzyme. The peptide sequence information was used to design short degenerate primers for use in the polymerase chain reaction. A long specific cDNA fragment was amplified which was used to isolate a clone from a rat liver cDNA library. The cloned cDNA encodes a 374-amino acid protein containing an amino-terminal signal-anchor sequence characteristic of all cloned glycosyltransferases and produced sialyltransferase activity when transiently expressed in COS-1 cells. When compared with two other cloned sialyltransferases, the primary structure of Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase revealed a homologous region in all three enzymes consisting of a stretch of 55 amino acids located in their catalytic domains. This feature together with lack of homology in the remaining 85% of the sequence of the three sialyltransferases defines a pattern of sequence homology not found in cloned cDNAs of other glycosyltransferase families.
Security modeling and quantification of intrusion tolerant systems using attack-response graph (2004)

Increasing deployment of computer systems in critical applications has made study and quantifiable analysis of the security aspects of these systems an important issue. Security quantification analysis can either be done by logging large amounts of operational data and analyzing this data or by developing analytic models. First approach, though straight forward, is less desirable, since such an analysis is typically done in a post-facto manner, after the damage caused by a security breach has already occurred. The modeling approach, on the other hand, can be done in an a-priori manner and is also much less costly. Another aspect of designing secure systems that is gaining acceptance is that while preventing security attacks is an important goal. it is not always possible to be able to prevent all types of attacks, particularly since attackers are always creating newer attacks. Recent approaches to designing dependable systems suggest treating intrusion prevention as a first line of defence to be followed by building intrusion tolerence measures that do not entirely preclude the possibility of security intrusion from succeeding. Such systems take appropriate responsive measures to mitigate the adverse effects of security intrusions. In this paper, we utilize the attack and privilege graph models that have been successfully used to model the attack progression to incorporate the system's response to an attack and for verifying if the system is secure or not. The proposed model is referred to as the attack response graph. Security quantification uses a Markov chain model to compute mean time taken to reach security failed states. However, getting to the Markov chain directly is rather difficult. Instead, we first obtain the SPN from the ARG description. The reachability graph of this SPN gives the absorbing state Markov chain which in turn is used to quantify the security in terms of the mean-time-to-security-failure measure for an intrusion tolerant system. Finally, we utilize sensitivity analysis to evaluate the effects of inaccuracies in estimating the model parameters.
Zea systematics: ribosomal ITS evidence (1996)

Ribosomal internal transcribed spacer (ITS) sequences were used to evaluate the phylogenetics of Zea and Tripsacum. Maximum likelihood and polymorphism parsimony were used for phylogenetic reconstructions. Zea ITS nucleotide diversity was high compared to other plant species, but approximately equivalent to other maize loci. Coalescence of ITS alleles was rapid relative to other nuclear loci; however, there was still much diversity within populations. Zea and Tripsacum form a clade clearly differentiated from all other Poaceae. Four Zea ITS pseudogenes were identified by phylogenetic position and nucleotide composition. The phylogenetic position of Z. mays ssp. huehuetenangensis was clearly established as basal to the other Z. mays. The ITS phylogeny disfavored a Z. luxurians and Z. diploperennis clade, which conflicted with some previous studies. The introgression of Z. mays alleles into Z. perennis and Z. diploperennis was also established. The ITS data indicated a near contemporary divergence of domesticated maize and its two closest wild relatives.
Proteolysis of SNAP‐25 Isoforms by Botulinum Neurotoxin Types A, C, and E (1999)

Tetanus toxin and the seven serologically distinct botulinal neurotoxins (BoNT/A to BoNT/G) abrogate synaptic transmission at nerve endings through the action of their light chains (L chains), which proteolytically cleave VAMP (vesicle-associated membrane protein)/synaptobrevin, SNAP-25 (synaptosome-associated protein of 25 kDa), or syntaxin. BoNT/C was reported to proteolyze both syntaxin and SNAP-25. Here, we demonstrate that cleavage of SNAP-25 occurs between Arg198 and Ala199, depends on the presence of regions Asn93 to Glu145 and Ile156 to Met202, and requires about 1,000-fold higher L chain concentrations in comparison with BoNT/A and BoNT/E. Analyses of the BoNT/A and BoNT/E cleavage sites revealed that changes in the carboxyl-terminal residues, in contrast with changes in the amino-terminal residues, drastically impair proteolysis. A proteolytically inactive BoNT/A L chain mutant failed to bind to VAMP/synaptobrevin and syntaxin, but formed a stable complex (KD = 1.9 x 10(-7) M) with SNAP-25. The minimal essential domain of SNAP-25 required for cleavage by BoNT/A involves the segment Met146-Gln197, and binding was optimal only with full-length SNAP-25. Proteolysis by BoNT/E required the presence of the domain Ile156-Asp186. Murine SNAP-23 was cleaved by BoNT/E and, to a reduced extent, by BoNT/A, whereas human SNAP-23 was resistant to all clostridial L chains. Lys185Asp or Pro182Arg mutations of human SNAP-23 induced susceptibility toward BoNT/E or toward both BoNT/A and BoNT/E, respectively.
Quantitative cardiac 31P spectroscopy at 3 Tesla using adiabatic pulses (2009)

Cardiac phosphorus magnetic resonance spectroscopy (MRS) with surface coils promises better quantification at 3 Tesla (T) from improved signal-to-noise ratios and spectral resolution compared with 1.5 T. However, Bloch equation and field analyses at 3T show that for efficient quantitative MRS protocols using small-angle adiabatic (BIR4/BIRP) pulses the excitation-field is limited by radiofrequency (RF) power requirements and power deposition. When BIR4/BIRP pulse duration is increased to reduce power levels, T2-decay can introduce flip-angle dependent errors in the steady-state magnetization, causing errors in saturation corrections for metabolite quantification and in T1s measured by varying the flip-angle. A new dual-repetition-time (2TR) T1 method using frequency-sign-cycled adiabatic-half-passage pulses is introduced to alleviate power requirements, and avoid the problem related to T2 relaxation during the RF pulse. The 2TR method is validated against inversion-recovery in phantoms using a practical transmit/receive coil set designed for phosphorus MRS of the heart at depths of 9-10 cm with 4 kW of pulse power. The T1s of phosphocreatine (PCr) and adenosine triphosphate (gamma-ATP) in the calf-muscle (n=9) at 3 T are 6.8+/-0.3 s and 5.4+/-0.6 s, respectively. For heart (n=10) the values are 5.8+/-0.5 s (PCr) and 3.1+/-0.6 s (gamma-ATP). The 2TR protocol measurements agreed with those obtained by conventional methods to within 10%.
Experimental demonstration of guiding and confining light in nanometer-size low-refractive-index material (2004)

We experimentally demonstrate a novel silicon waveguide structure for guiding and confining light in nanometer-wide low-refractive-index material. The optical field in the low-index material is enhanced because of the discontinuity of the electric field at high-index-contrast interfaces. We measure a 30% reduction of the effective index of light propagating in the novel structure due to the presence of the nanometer-wide low-index region, evidencing the guiding and confinement of light in the low-index material. We fabricate ring resonators based on the structure and show that the structure can be implemented in highly integrated photonics.
Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes (2010)

Knowledge of elaborate structures of protein complexes is fundamental for understanding their functions and regulations. Although cross-linking coupled with mass spectrometry (MS) has been presented as a feasible strategy for structural elucidation of large multisubunit protein complexes, this method has proven challenging because of technical difficulties in unambiguous identification of cross-linked peptides and determination of cross-linked sites by MS analysis. In this work, we developed a novel cross-linking strategy using a newly designed MS-cleavable cross-linker, disuccinimidyl sulfoxide (DSSO). DSSO contains two symmetric collision-induced dissociation (CID)-cleavable sites that allow effective identification of DSSO-cross-linked peptides based on their distinct fragmentation patterns unique to cross-linking types (i.e. interlink, intralink, and dead end). The CID-induced separation of interlinked peptides in MS/MS permits MS(3) analysis of single peptide chain fragment ions with defined modifications (due to DSSO remnants) for easy interpretation and unambiguous identification using existing database searching tools. Integration of data analyses from three generated data sets (MS, MS/MS, and MS(3)) allows high confidence identification of DSSO cross-linked peptides. The efficacy of the newly developed DSSO-based cross-linking strategy was demonstrated using model peptides and proteins. In addition, this method was successfully used for structural characterization of the yeast 20 S proteasome complex. In total, 13 non-redundant interlinked peptides of the 20 S proteasome were identified, representing the first application of an MS-cleavable cross-linker for the characterization of a multisubunit protein complex. Given its effectiveness and simplicity, this cross-linking strategy can find a broad range of applications in elucidating the structural topology of proteins and protein complexes.
Energy deficit in Huntington disease: why it matters (2011)

Huntington disease (HD) is an autosomal dominant neurodegenerative disease with complete penetrance. Although the understanding of the cellular mechanisms that drive neurodegeneration in HD and account for the characteristic pattern of neuronal vulnerability is incomplete, defects in energy metabolism, particularly mitochondrial function, represent a common thread in studies of HD pathogenesis in humans and animal models. Here we review the clinical, biochemical, and molecular evidence of an energy deficit in HD and discuss the mechanisms underlying mitochondrial and related alterations.
A unique deoxyguanosine triphosphatase is responsible for the optA1 phenotype of Escherichia coli. (1988)

Escherichia coli optA1, a mutant unable to support the growth of T7 phage containing mutations in gene 1.2, contains reduced amounts of dGTP. Extracts of E. coli optA1 catalyze the hydrolysis of dGTP at a rate 50-fold greater than do extracts of E. coli optA+. The dGTPase responsible for the increased hydrolysis has been purified to apparent homogeneity. Purification of the protein is facilitated by its high affinity for single-stranded DNA. By using this purification scheme an identical dGTPase has been purified from E. coli optA+. The purified proteins catalyze the hydrolysis of dGTP to yield deoxyguanosine and tripolyphosphate. The products of hydrolysis, chromatographic properties, denatured molecular mass of 56 kDa, N-terminal amino acid sequence, substrate specificity, and heat inactivation indicate that the proteins purified from optA1 and from optA+ cells are identical and identify the enzyme as the deoxyguanosine 5'-triphosphate triphosphohydrolase purified to homogeneity from wild-type E. coli [Seto, D., Bhatnagar, S. K. & Bessman, M. J. (1988) J. Biol. Chem. 263, 1494-1499]. OptA1 cells contain approximately equal to 50-fold more active molecules of the 56-kDa dGTPase than do E. coli optA+ cells.
Eliminating cache conflict misses through XOR-based placement functions (1997)

functions for cache memories. It shows that these XOR-mapping<br/>schemes can eliminate many conflict misses for direct-mapped and<br/>victim caches and practically all of them for (pseudo) two-way<br/>associative organizations. The paper evaluates the performance of<br/>XOR-mapping schemes for a number of different cache<br/>organizations: direct-mapped, set-associative, victim, hash-rehash,<br/>column-associative and skewed-associative. It also proposes novel<br/>replacement policies for some of these cache organizations. In<br/>particular, it presents a low-cost implementation of a pure LRU<br/>replacement policy which demonstrates a significant improvement<br/>over the pseudo-LRU replacement previously proposed. The paper<br/>shows that for a 8 Kbyte data cache, XOR-mapping schemes<br/>approximately halve the miss ratio for two-way associative and<br/>column-associative organizations. Skewed-associative caches,<br/>which already make use of XOR-mapping functions, can benefit<br/>from the LRU replacement and also from the use of more<br/>sophisticated mapping functions. For two-way associative, columnassociative<br/>and two-way skewed-associative organizations, XORmapping<br/>schemes achieve a miss ratio that is not higher than 1.10<br/>times that of a fully-associative cache. XOR mapping schemes also<br/>provide a very significant reduction in the miss ratio for the other<br/>cache organizations, including the direct-mapped cache.<br/>Ultimately, the conclusion of this study is that XOR-based<br/>placement functions unequivocally provide highly significant<br/>performance benefits to most cache organizations.