gebhart/patrepeval huggingface dataset:
Tetranucleotide GGGA Motif in Primary RNA Transcripts (1998)

Selecting effective antisense target sites on a given mRNA molecule constitutes a major problem in antisense therapeutics. By trial-and-error, only 1 in 18 (6%) of antisense oligonucleotides designed to target the primary RNA transcript of tumor necrosis factor-alpha (TNF-alpha) strongly inhibited TNF-alpha synthesis. Subsequent studies showed that the area in RNA targeted by antisense oligonucleotides could be moved effectively 10-15 bases in either direction from the original area. We observed that only molecules that incorporated a tetranucleotide motif TCCC (complementary to GGGA on RNA) yielded potent antisense oligonucleotides against TNF-alpha. A comprehensive literature survey showed that this motif is unwittingly present in 48% of the most potent antisense oligonucleotides reported in the literature. This finding was prospectively used to predict the sequences of additional antisense oligonucleotides for the rat TNF-alpha primary RNA transcript. Over 50% of antisense constructs (13 of 22) containing the TCCC motif were found to effectively inhibit TNF-alpha synthesis. Marked reductions in mRNA were also observed. This motif was found to be most effective when targeting introns in the primary RNA transcript, suggesting a nuclear localization for the antisense action. Predicting target sites based on the presence of this motif in primary RNA transcripts should be of value in the development on new antisense pharmacotherapy.
Understanding pluripotency--how embryonic stem cells keep their options open (2008)

Embryonic stem (ES) cells have the capacity to proliferate indefinitely in culture while maintaining the ability to differentiate to form any of the cells of the body. This unique combination of functions suggests that these cells could provide a potentially unlimited source of differentiated cells for the treatment of disease and aging. Understanding the molecular processes that underpin these functions in ES cells will allow us to harness their potential and develop strategies that control their differentiation. Combination of controlled differentiation with ground-breaking technologies for the reversal of somatic cells to an ES cell-like state promise the generation of patient-derived pluripotent cell lines for the treatment of disease in the future.
Presentation of SIVgag to monkey T cells using dendritic cells transfected with a recombinant adenovirus (2000)

To pursue the capacity of monkey dendritic cells (DC) to be modified by adenoviral vectors and present the encoded antigens, we generated DC from blood monocytes and infected them with recombinant adenoviruses encoding GFP reporter and SIVgag or nef genes. Recombinant, E1- and E3-deleted, adenoviruses could transfect immature DC to >90% efficiency. When differentiated in the presence of a maturation stimulus, the infected cells were identical to control uninfected DC in surface markers and potent stimulatory activity for the mixed leukocyte reaction. Recombinant adeno-SIVgag was comparable to vaccinia-gag in stimulating IFN-gamma-secreting CD8(+) T cells from PBMC of macaques vaccinated with SIV(mac239) Deltanef and challenged with pathogenic SIV or chimeric SIV/HIV. Small numbers of adeno-SIVgag-infected DC were sufficient to trigger specific ELISPOT responses by CD8(+) T cells from these animals. Some CD4(+) IFN-gamma-secreting cells were also found in the three of eight vaccinated animals with the highest CD8(+) responses. T cells from control animals did not respond to DC transfected with adeno-gag. Therefore recombinant adenoviruses efficiently transfect monkey DC in a nonperturbing fashion, and these DC efficiently present antigens to SIVgag immune CD8(+) T cells. These findings will allow autologous DC, expressing SIV genes with high efficiency, to be tested in vivo to achieve strong specific T cell immunity.
Immunity to falciparum and vivax malaria induced by irradiated sporozoites: a review of the University of Maryland studies, 1971-75. (1990)

The immunogenicity in adult male volunteers of sporozoites of Plasmodium falciparum and P. vivax was evaluated at the University of Maryland from 1971 to 1975. Inoculation of large numbers of sporozoites by mosquitos that had been X-irradiated proved safe and well tolerated, and the sporozoites were rendered noninfective. Three volunteers were protectively immunized by this method, one against P. falciparum, one against P. vivax, and one against both species. Protection was species- and stage-specific, but effective against all strains tested within a species, and was reflected by a rise in titre of antibody to the circumsporozoite protein.
Effects of Creatine on Synthesis and Release of γ‐[3H]Aminobutyric Acid (1990)

Creatine has been used previously to alter the energy balance of neurons in brain slices. In the present experiments, it was found to reduce the accumulation of gamma-[3H]aminobutyric acid ([3H]GABA) as synthesized from [3H]glutamine or [3H]glutamic acid in slices of rat neostriatum. The lowest effective concentration was 5 mM. Creatine (25 mM) was also effective when the degrading enzyme of GABA, i.e., GABA-alpha-oxoglutarate transaminase, was blocked by gabaculine. Creatine (25 mM) did not inhibit the uptake and subsequent accumulation of [3H]GABA. Thus, indirect evidence was obtained that creatine decreased the activity of the synthesizing enzyme of GABA, i.e., glutamate decarboxylase. When the direct effect of creatine (25 mM) on glutamate decarboxylase was studied in vitro, the agent indeed decreased the activity of the enzyme. Creatine (25 mM) also diminished the release of [3H]GABA (expressed as dpm/mg wet weight) from rat neostriatal slices, probably by reducing its synthesis and thus its readily releasable pool. These data are of importance for studies with creatine in complex neuronal systems, because they show that the agent changes not only neuronal energy balance, but also synthesis and release of the ubiquitous transmitter GABA.
Single-Cell Sequencing Tackles Basic and Biomedical Questions (2012)

At the meeting, four groups described new insights derived from sequencing DNA from individual human cells.
NEW TYPE OF PREFABRICATED FULLY PROTECTED RIBONUCLEOTIDE MONOMER UNITS AS USEFUL SYNTHETIC INTERMEDIATES IN RAPID OLIGORIBONUCLEOTIDE SYNTHESIS (1982)

Abstract Oligoribonucleotide synthesis has been done by employing newly constructed fully protected ribonucleotide units, S,S-diphenyl 5′-O-dimethoxytrityl-2′-O-tetrahydropyranyl-N-monomethoxytritylnucleoside 3′-phosphorodithioates 7. The units were found to be useful synthetic intermediates for rapid oligoribonucleotide synthesis.
Human immunodeficiency virus type 1 Vif does not influence expression or virion incorporation of gag-, pol-, and env-encoded proteins (1996)

The Vif protein of human immunodeficiency virus type 1 is required for productive replication in peripheral blood lymphocytes and a limited number of immortalized T-lymphoid lines (nonpermissive cells). In contrast, Vif is fully dispensable for virus replication in other T-cell lines (permissive cells). Because the infection phenotype of released virions is determined by producer cells and by the presence of Vif in those cells, we have analyzed the protein contents of purified viral particles in an attempt to define compositional differences that could explain the infection phenotype. Surprisingly, we were unable to discern any Vif- or cell-type-dependent quantitative or qualitative difference in the Gag, Pol, and Env proteins of virions or virus-producing cells that correlates with virus infectivity. We were, however, able to demonstrate that Vif itself is present in virions and, using semiquantitative Western blotting (immunoblotting), that there is an average of 30 to 80 molecules of Vif incorporated into each virion. Importantly, parallel analyses of total lysates of the producer cells revealed that the cell-associated expression levels of Vif are close to those of the Gag proteins. Given the dramatically higher abundance of Vif in cells than in virions, we speculate that Vif exerts its principal activity during the processes of virus assembly and budding and that this function could be of a structural-conformational nature.
Regulation of las and rhl quorum sensing in Pseudomonas aeruginosa (1997)

The production of several virulence factors by Pseudomonas aeruginosa is controlled according to cell density through two quorum-sensing systems, las and rhl. The las system is comprised of the transcriptional activator protein LasR and of LasI, which directs the synthesis of the autoinducer PAI-1. Similarly, the rhl system consists of the transcriptional activator protein RhlR and of RhlI, which directs synthesis of the autoinducer PAI-2 (formerly referred to as factor 2). To study the interrelation between the two P. aeruginosa quorum-sensing systems, we fused a lacZ reporter gene to lasR, rhlR, and rhlA and monitored expression of these three genes under various conditions. Our data indicate that lasR and rhlR are expressed in a growth-dependent manner, with activation of each gene occurring during the last half of log-phase growth. We also show that the las quorum-sensing system controls the rhl quorum-sensing system in two ways. First, we found that LasR and PAI-1 activated rhlR transcription. Second, we showed that PAI-1 blocked PAI-2 from binding to RhlR, thereby inhibiting the expression of rhlA. Our data thus indicate that the las system exerts two levels of control on RhlR, transcriptional and posttranslational.
Properties of cyclodextrins: Part IX Specific inclusion compound formation of cyclodextrin derivatives with hexane and 2,3‐dimethylbutane in aqueous solution (1972)

Abstract On the basis of thermodynamic data concerning inclusion compounds of α and β‐cyclodextrin derivatives with hexane (hex) and 2,3‐dimethylbutane (DMB) in aqueous solution, as reported in earlier publications in this series, a model of the inclusion complex is suggested. This model comprises: A real inclusion compound (“fit in”) is formed in solution. Almost all derivatives form inclusion compounds with hex and DMB in which the mole ratio is 1:1 (conclusion of Part VIII of this series). α‐Cyclodextrin derivatives include in the voids hex molecules in their stretched form, whereas DMB molecules do not fit entirely into the voids. In both cases this causes a considerable disturbance in the water structure around the cyclodextrin molecules. β‐Cyclodextrin derivatives include hex molecules in their coiled form and DMB molecules fit entirely into the voids. The water structure is hardly affected. This model appears to be in agreement with considerations of space filling of the guest molecules in the cyclodextrin voids. Furthermore, in comparing the inclusion process with the dissolution of apolar compounds in different solvents, the model is confirmed. Also, comparison of the interaction among the different cyclodextrin derivatives is in agreement with the model.
Electrochemical Designing of Au/Pt Core Shell Nanoparticles as Nanostructured Catalyst with Tunable Activity for Oxygen Reduction (2007)

Abstract Au/Pt core shell nanoparticles (NPs) have been prepared via a layer‐by‐layer growth of Pt layers on Au NPs using underpotential deposition (UPD) redox replacement technique. A single UPD Cu monolayer replacement with Pt(II) yielded a uniform Pt film on Au NPs, and the shell thickness can be tuned by controlling the number of UPD redox replacement cycles. Oxygen reduction reaction (ORR) in air‐saturated 0.1 M H 2 SO 4 was used to investigate the electrocatalytic behavior of the as‐prepared core shell NPs. Cyclic voltammograms of ORR show that the peak potentials shift positively from 0.32 V to 0.48 V with the number of Pt layers increasing from one to five, suggesting the electrocatalytic activity increases with increasing the thickness of Pt shell. The increase in electrocatalytic activity may originate mostly from the large decrease of electronic influence of Au cores on surface Pt atoms. Rotating ring‐disk electrode voltammetry and rotating disk electrode voltammetry demonstrate that ORR is mainly a four‐electron reduction on the as‐prepared modified electrode with 5 Pt layers and first charge transfer is the rate‐determining step.
Anaerobic biodegradation of gasoline oxygenates in soils (1994)

ABSTRACT: This study evaluated the biodegradation of methyl tertiary butyl ether (MTBE), ethyl tertiary butyl ether (ETBE), and tertiary butyl alcohol (TBA)—three chemicals used as gasoline additives. The biodegradation under sulfate reducing, methanogenic and denitrifying conditions was measured in static soil and water microcosms using soils of different origin and varying characteristics. The results indicate that TBA was the easiest compound to biodegrade, whereas MTBE was the most recalcitrant. It is thought that cleavage of the ether bond in MTBE and ETBE is the first and rate‐limiting step in the degradation of these organics. TBA degradation was enhanced by nutrient addition in the nutrient poor soils but hindered by the presence of other easily‐degraded organic compounds. Degradation of MTBE and ETBE occurred only in the soil with the lowest organic matter content and with a pH around 5.5. No degradation of MTBE and ETBE was observed in the organic‐rich soils, and in the organically poor soil the addition of easily degradable organic compounds inhibited MTBE and ETBE degradation.
Organic electroluminescent device having a hole conductor as an emitting layer (1989)

We have succeeded in fabricating a novel thin-film electroluminescent device with a luminescent hole transport layer as an emitter. The cell structure is composed of an indium-tin-oxide substrate, a luminescent hole transport layer (emitter), an electron transport layer, and a MgAg electrode. The most essential feature of our device owes for adoption of an oxadiazole derivative as an electron transport layer. The emission intensity of 1000 cd/m2 was achieved at a current of 100 mA/cm2.
Eddy Current Effects on Rotor Position Estimation and Magnetic Pole Identification of PMSM at Zero and Low Speeds (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> High-frequency current responses of a permanent magnet synchronous machine (PMSM), with and without considering eddy current effects, are significantly different. This paper investigates the eddy current effects on rotor position estimation. A compensation method is developed to improve the high-frequency-injection-based rotor position estimation of a PMSM at zero and low speeds. The paper also contributes to an improved magnetic pole identification based on space vector pulse width modulation for an arbitrary initial rotor position. The estimation and sensorless control method of PMSM, considering eddy current effects, has been verified by experimental results. </para>
Spontaneous pancreatic islet amyloidosis in 40 baboons (2002)

Spontaneous amyloidosis occurs in many nonhuman primate species but remains difficult to diagnose and treat. Nonhuman primates continue to offer promise as animal models in which to study amyloidosis in humans. Amyloidosis was not diagnosed clinically but was found histologically in four male and 36 female baboons. The baboons averaged 18 years of age at death (range, 7-28 years). Clinical signs, if present, were hyperglycemia and cachexia. Blood glucose values were elevated in 12 of 30 baboons with available clinical pathology data. Four baboons had been clinically diagnosed as diabetic and three were treated with insulin. Amyloid was found in the islets of Langerhans of the pancreas in 40 baboons; 35 baboons had amyloid only in the islets of Langerhans. Amyloid was found in nonislet tissue of baboons as follows: five, nonislet pancreas; four, intestine and adrenal; three, kidney; two, prostate and spleen; and one each, lymph node, liver, gall bladder, stomach, tongue, urinary bladder, and salivary gland. Sections of paraffin-embedded tissues were evaluated for amyloid with hematoxylin and eosin (HE) and congo red (CR) staining, and using immunohistochemistry for human islet amyloid polypeptide (IAPP), calcitonin gene-related peptide (CGRP), glucagon, pancreatic polypeptide (PP), somatostatin (SS), and porcine insulin. Islet amyloid was positive with HE in 40 baboons, with CR in 39 baboons, and with IAPP and CGRP in 35 baboons. IAPP and CGRP only stained islet amyloid. PP, SS, glucagon, and porcine insulin did not stain amyloid. Islet amyloidosis in the baboon appears to be difficult to diagnose clinically, age-related, and similar to islet amyloidosis in other species. The baboon may be a good model for the study of islet amyloidosis in humans.
Ion Channels and Epilepsy (2005)

The role of voltage-gated and ligand-gated ion channels in epileptogenesis of both genetic and acquired epilepsies, and as targets in the development of new antiepileptic drugs (AEDs) is reviewed. Voltage-gated Na+ channels are essential for action potentials, and their mutations are the substrate for generalised epilepsy with febrile seizures plus and benign familial neonatal infantile seizures; Na+ channel inhibition is the primary mechanism of carbamazepine, phenytoin and lamotrigine, and is a probable mechanism for many other classic and novel AEDs. Voltage-gated K+ channels are essential in the repolarisation and hyperpolarisation that follows paroxysmal depolarisation shifts (PDSs), and their mutations are the substrate for the benign neonatal epilepsy and episodic ataxia type 1; they are new targets for AEDs such as retigabine. Voltage-gated Ca2+ channels are involved in neurotransmitter release, in the sustained depolarisation-phase of PDSs, and in the generation of absence seizures; their mutations are a substrate for juvenile myoclonic epilepsy and the absence-like pattern seen in some mice; the antiabsence effect of ethosuximide is due to the inhibition of thalamic T-type Ca2+ channels. Voltage-gated Cl- channels are implicated in GABA(A) transmission, and mutations in these channels have been described in some families with juvenile myoclonic epilepsies, epilepsy with grand mal seizures on awakening or juvenile absence epilepsy. Hyperpolarisation-activated cation channels have been implicated in spike-wave seizures and in hippocampal epileptiform discharges. The Cl- ionophore of the GABA(A) receptor is responsible for the rapid post-PDS hyperpolarisation, it has been involved in epileptogenesis both in animals and humans, and mutations in these receptors have been found in families with juvenile myoclonic epilepsy or generalised epilepsy with febrile seizures plus; enhancement of GABA(A) inhibitory transmission is the primary mechanism of benzodiazepines and phenobarbital and is a mechanistic approach to the development of novel AEDs such as tiagabine or vigabatrin. Altered GABA(B)-receptor function is implicated in spike-wave seizures. Ionotropic glutamate receptors are implicated in the sustained depolarisation phase of PDS and in epileptogenesis both in animals and humans; felbamate, phenobarbital and topiramate block these receptors, and attenuation of glutamatergic excitatory transmission is another new mechanistic approach. Mutations in the nicotinic acetylcholine receptor are the substrates for the nocturnal frontal lobe epilepsy. The knowledge of the role of the ion channels in the epilepsies is allowing the design of new and more specific therapeutic strategies.
NMR Solution Structure of Complement-like Repeat CR8 from the Low Density Lipoprotein Receptor-related Protein (1999)

The low density lipoprotein receptor-related protein is a member of the low density lipoprotein receptor family and contains clusters of cysteine-rich complement-like repeats of about 42 residues that are present in all members of this family of receptors. These clusters are thought to be the principal binding sites for protein ligands. We have expressed one complement-like repeat, CR8, from the cluster in lipoprotein receptor-related protein that binds certain proteinase inhibitor-proteinase complexes and used three-dimensional NMR on the 13C/15N-labeled protein to determine the structure in solution of the calcium-bound form. The structure is very similar in overall fold to repeat 5 from the low density lipoprotein receptor (LB5), with backbone root mean square deviation of 1.5 A. The calcium-binding site also appears to be homologous, with four carboxyl and two backbone carbonyl ligands. However, differences in primary structure are such that equivalent surfaces that might represent the binding interfaces are very different from one another, indicating that different domains will have very different ligand specificities.
A Risk-Based Framework for Assessing the Effectiveness of Stratospheric Aerosol Geoengineering (2014)

Geoengineering by stratospheric aerosol injection has been proposed as a policy response to warming from human emissions of greenhouse gases, but it may produce unequal regional impacts. We present a simple, intuitive risk-based framework for classifying these impacts according to whether geoengineering increases or decreases the risk of substantial climate change, with further classification by the level of existing risk from climate change from increasing carbon dioxide concentrations. This framework is applied to two climate model simulations of geoengineering counterbalancing the surface warming produced by a quadrupling of carbon dioxide concentrations, with one using a layer of sulphate aerosol in the lower stratosphere, and the other a reduction in total solar irradiance. The solar dimming model simulation shows less regional inequality of impacts compared with the aerosol geoengineering simulation. In the solar dimming simulation, 10% of the Earth's surface area, containing 10% of its population and 11% of its gross domestic product, experiences greater risk of substantial precipitation changes under geoengineering than under enhanced carbon dioxide concentrations. In the aerosol geoengineering simulation the increased risk of substantial precipitation change is experienced by 42% of Earth's surface area, containing 36% of its population and 60% of its gross domestic product.
Agonist-antagonist active knee prosthesis: a preliminary study in level-ground walking. (2009)

We present a powered knee prosthesis with two series-elastic actuators positioned in parallel in an agonist-antagonist arrangement. To motivate the knee's design, we developed a prosthetic knee model that comprises a variable damper and two series-elastic clutch units that span the knee joint. Using human gait data to constrain the model's joint to move biologically, we varied model parameters using an optimization scheme that minimized the sum over time of the squared difference between the model's joint torque and biological knee values. We then used these optimized values to specify the mechanical and control design of the prosthesis for level-ground walking. We hypothesized that a variable-impedance control design could produce humanlike knee mechanics during steady-state level-ground walking. As a preliminary evaluation of this hypothesis, we compared the prosthetic knee mechanics of an amputee walking at a self-selected gait speed with those of a weight- and height-matched nonamputee. We found qualitative agreement between prosthetic and human knee mechanics. Because the knee's motors never perform positive work on the knee joint throughout the level-ground gait cycle, the knee's electrical power requirement is modest in walking (8 W), decreasing the size of the onboard battery required to power the prosthesis.