gebhart/patrepeval huggingface dataset:
One-step assay for detecting influenza virus using dynamic light scattering and gold nanoparticles (2011)

Herein we detail the development of a simple, rapid, and sensitive method for quantitative detection of influenza A virus using dynamic light scattering (DLS) and gold nanoparticle (AuNP) labels. Influenza-specific antibodies are conjugated to AuNPs, and aggregation of the AuNP probes is induced upon addition of the target virus. DLS is used to measure the extent of aggregation and the mean hydrodynamic diameter is correlated to virus concentration. The effects of nanoparticle concentration and size on the analytical performance of the assay were systematically investigated. It was determined that decreasing the AuNP probe concentration improves the detection limit while the effect of changing the AuNP size is minimal. Optimization of the assay provided a detection limit of <100 TCID(50)/mL which is 1-2 orders of magnitude improved over commercial diagnostic kits without increasing the assay time or complexity. Additionally, this assay was demonstrated to perform equivalently for influenza virus prepared in different biological matrices.
Singlet–Singlet Exciton Annihilation in an Exciton-Coupled Squaraine-Squaraine Copolymer: A Model toward Hetero-J-Aggregates (2014)

Low-band-gap polymers with broad spectral absorption are highly sought after for application in organic photovoltaic cells and other optoelectronic devices. Thus, a conjugated copolymer based on two different indolenine squaraine dyes SQA and SQB was synthesized by Suzuki coupling, and its steady-state and time-resolved optical properties were investigated in detail. In CHCl3 the copolymer [SQA-SQB]n shows a strongly broadened and red-shifted absorption compared to that of its monomers, which was explained by exciton coupling of localized transition moments. The theoretical background of exciton coupling theory for copolymers was worked out in detail. In toluene, [SQA-SQB]n displays a spectral narrowing of the lowest excitation band which resembles the exchange narrowing effect found in cyanine J-aggregates. In this way [SQA-SQB]n behaves like a one-dimensional covalently bound hetero-J-aggregate. The photoinduced dynamics of the copolymer was investigated by transient absorption pump–probe spectroscopy with femtosecond resolution. Because of the unusually high exciton diffusion constant, singlet–singlet annihilation is the rate-limiting step for deactivation of the copolymer in solution at high laser fluencies. This is unlike the situation for many conjugated polymers in the solid state, where diffusion-limited annihilation is usually found. Thus, the [SQA-SQB]n copolymer is a unique model system which combines the excitonic features of J-aggregates with the chemical robustness of a polymer.
The Testicular Receptor for Follicle Stimulating Hormone: Structure and Functional Expression of Cloned cDNA (1990)

Cloned cDNA encoding the rat Sertoli cell receptor for FSH was isolated from a cognate library and functionally expressed in cultured mammalian cells. The FSH receptor (FSH-R), as predicted from the cDNA, is a single 75K polypeptide with a 348 residue extracellular domain which contains three N-linked glycosylation sites. This domain is connected to a structure containing seven putative transmembrane segments which displays sequence similarity to G protein-coupled receptors. Thus, the FSH-R is identical in its structural design to the LH/CG receptor (LH/CG-R). Furthermore, both receptors display 50% sequence similarity in their large extracellular domains and 80% identity across the seven transmembrane segments. Expression of the cloned cDNA in mammalian cells conferred FSH-dependent cAMP accumulation. The selectivity for FSH is attested by the fact that the related human glycoprotein hormones human CG and human TSH do not stimulate adenylyl cyclase in FSH-R expressing cells even when these hormones are present at high concentrations.
Time of Implantation of the Conceptus and Loss of Pregnancy (1999)

In most successful human pregnancies, the conceptus implants 8 to 10 days after ovulation. The risk of early pregnancy loss increases with later implantation.
Coil Design for Neuromuscular Magnetic Stimulation Based on a Detailed 3-D Thigh Model (2014)

Magnetic stimulation is gaining importance as an alternative to electrical stimulation in neurorehabilitation because it offers deep penetration and low pain. However, presently available equipment is not ideal for this purpose and sometimes even unsuitable. Furthermore, it is not known what physical conditions a coil has to provide for efficient stimulation. To solve these two problems, we set up a detailed 3-D computational model of the thigh to evaluate various coil designs with previously reported experimental performance. Comparison of the stimulation results with known experimental performance shows that a high absolute electric field seems to be sufficient for effective stimulation. Coil-generated field gradients, in contrast, do apparently not play a role. As a more appropriate metric, the electromagnetic coupling between different coil designs and the muscles of the thigh is found to be characteristic and explains the previously reported experimental performance differences. Furthermore, it is a good predictor for the achievable muscle torque (more than 99% correlation), whereas the gradient fails in this context. Accordingly, the model is able to test the performance of coils virtually and reveal both general relationships as well as design rules. In addition, the coupling factor formalism predicts a theoretical maximum level of the possible field induction and thus a guideline for potential improvements in the future.
The murI gene of Escherichia coli is an essential gene that encodes a glutamate racemase activity (1993)

The murI gene of Escherichia coli was recently identified on the basis of its ability to complement the only mutant requiring D-glutamic acid for growth that had been described to date: strain WM335 of E. coli B/r (P. Doublet, J. van Heijenoort, and D. Mengin-Lecreulx, J. Bacteriol. 174:5772-5779, 1992). We report experiments of insertional mutagenesis of the murI gene which demonstrate that this gene is essential for the biosynthesis of D-glutamic acid, one of the specific components of cell wall peptidoglycan. A special strategy was used for the construction of strains with a disrupted copy of murI, because of a limited capability of E. coli strains grown in rich medium to internalize D-glutamic acid. The murI gene product was overproduced and identified as a glutamate racemase activity. UDP-N-acetylmuramoyl-L-alanine (UDP-MurNAc-L-Ala), which is the nucleotide substrate of the D-glutamic-acid-adding enzyme (the murD gene product) catalyzing the subsequent step in the pathway for peptidoglycan synthesis, appears to be an effector of the racemase activity.
Activation of Group II Metabotropic Glutamate Receptors Attenuates Both Stress and Cue-Induced Ethanol-Seeking and Modulates c-fosExpression in the Hippocampus and Amygdala (2006)

Major precipitating factors for relapse to drug use are stress and exposure to drug-related environmental stimuli. Group II (mGlu(2/3)) metabotropic glutamate receptors (mGluRs) are densely expressed within circuitries mediating the motivating effects of stress and drug cues and, therefore, may participate in regulating drug-seeking linked to both of these risk factors. Thus, we tested the hypothesis that pharmacological activation of group II mGluRs modifies both stress- and cue-induced ethanol-seeking, using reinstatement models of relapse. In parallel, brain c-fos expression was examined to identify neural substrates for the behavioral effects of group II mGluR activation. The selective mGlu(2/3) agonist LY379268 (1R,4R,5S,6R-2-oxa-4-aminobicyclo[3.1.0]hexane-4,6-dicarboxylate) (0.3, 1.0, and 3.0 mg/kg, s.c.) dose dependently blocked the recovery of extinguished ethanol-seeking induced by either footshock stress or ethanol-associated discriminative stimuli. These effects were accompanied by modulation of c-fos expression in the hippocampus, central nucleus of the amygdala, bed nucleus of the stria terminalis, and medial parvocellular paraventricular nucleus of the hypothalamus. The results implicate group II mGluRs as a shared neuropharmacological substrate for ethanol-seeking elicited by both drug cues and stress and identify group II mGluRs as promising treatment targets for relapse prevention.
A Method for Particle Size Amplification by Water Condensation in a Laminar, Thermally Diffusive Flow (2005)

A new method is presented for the enlargement of particle size through condensation of water vapor in a laminar, thermally diffusive flow. The method involves the introduction of an air flow at temperature T i into a wet-walled tube at a temperature Tw > Ti . This approach yields higher supersaturation values than either mixing or cold-walled condensers when operating between the same temperature extremes. Model results for the saturation profiles within the condensing region show that the peak supersaturations are reached along the centerline of the flow, and that the activation efficiency curves are steeper for large temperature differences when the cutpoint diameter is smaller. Experiments conducted with three types of aerosol, oleic acid (a water-insoluble oil), a mixture of oxalic acid and sulfate, and with ambient laboratory aerosol confirmed that condensational growth is achieved with this approach, although experimental cutpoints are somewhat higher than predicted for wettable particles.
Heterostructure bipolar transistors and integrated circuits (1982)

Two new epitaxial technologies have emerged in recent years (molecular beam epitaxy (MBE) and metal-organic chemical vapor deposition (MOCVD)), which offer the promise of making highly advanced heterostructures routinely available. While many kinds of devices will benefit, the principal and first beneficiary will be bipolar transistors. The underlying central principle is the use of energy gap variations beside electric fields to control the forces acting on electrons and holes, separately and independently of each other. The resulting greater design freedom permits a re-optimization of doping levels and geometries, leading to higher speed devices. Microwave transistors with maximum oscillation frequencies above 100 GHz and digital switching transistors with switching times below 10 ps should become available. An inverted transistor strucure with a smaller collectors on top and a larger emitter on the bottom becomes possible, with speed advantages over the common "emitter-up" design. Double-heterostructure (DH) transistors with both wide-gap emitters and collectors offer additional advantages. They exhibit better performance under saturated operation. Their emitters and collectors may be interchanged by simply changing biasing conditions, greatly simplifying the architecture of bipolar IC's. Examples of heterostructure implementations of I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> L and ECL are discussed. The present overwhelming dominance of the compound semiconductor device field by FET's is likely to come to an end, with bipolar devices assuming an at least equal role, and very likely a leading one.
Wnt/FZD signaling and colorectal cancer morphogenesis (2006)

Malignant progression of colorectal carcinomas is characterized by an epithelial-mesenchymal transition (EMT)-like de-differentiation of the invading tumor cells. However a re-differentiation towards an epithelial phenotype, resembling a mesenchymal-epithelial transition (MET), is detectable in metastases. This indicates that malignant progression is based on dynamic processes, which can not be explained solely by irreversible genetic alterations, but must be additionally regulated by the tumor environment. The main oncoprotein in colorectal cancer is the Wnt-pathway effector beta-catenin, which in most cases is overexpressed due to mutations in the adenomatous polyposis coli (APC) tumor suppressor. EMT of tumor cells is associated with a nuclear accumulation of the transcriptional activator beta-catenin, which is reversed in metastases. Nuclear beta-catenin is involved in two fundamental processes in embryonic development: EMT and stem cell formation. Accumulating data demonstrate that aberrant nuclear expression of beta-catenin can also confer these two abilities to tumor cells, indicating the crucial role of aberrant Wnt-signaling for malignant tumor progression.
Surface of glassyGeS2: A model based on a first-principles approach (2014)

First-principles calculations within the framework of the density functional theory are used to construct realistic models for the surface of glassy $\mathrm{GeS}{}_{2}\phantom{\rule{0.3em}{0ex}}(g\text{\ensuremath{-}}\mathrm{GeS}{}_{2})$. Both calculations at $T=0$ K and at finite temperature ($T=300$ K) are considered. This allows for a comparison between the structural and electronic properties of surface and bulk $g\text{\ensuremath{-}}\mathrm{GeS}{}_{2}$. Although the $g\text{\ensuremath{-}}\mathrm{GeS}{}_{2}$ surface recovers the main tetrahedral structural motif of bulk $g\text{\ensuremath{-}}\mathrm{GeS}{}_{2}$, the number of fourfold coordinated Ge atoms and twofold coordinated S atoms is smaller than in the bulk. On the contrary, the surface system features a larger content of overcoordinated S atoms and threefold coordinated Ge atoms. This effect is more important for the $g\text{\ensuremath{-}}\mathrm{GeS}{}_{2}$ surface relaxed at 0 K. Maximally localized Wannier functions (WF) are used to inspect the nature of the chemical bonds of the structural units present at the $g\text{\ensuremath{-}}\mathrm{GeS}{}_{2}$ surface. We compare the ability of several charge derivation methods to capture the atomic charge variations induced by a coordination change. Our estimate for the charges allows exploiting the first-principles results as a data base to construct a reliable interatomic force field.
Expression of Fab fragment of catalytic antibody 6D9 in an Escherichia coli in vitro coupled transcription/translation system (2002)

The heavy chain (Hc) and light chain (Lc) genes of the Fab fragment of a catalytic antibody 6D9 were simultaneously expressed in an Escherichia coli in vitro transcription/translation system without a reducing agent. The intermolecular disulfide bond between the Hc and Lc was found formed, suggesting a correct formation of the Fab fragment in the in vitro system. In enzyme-linked immunosorbent assay, the Fab fragment synthesized in vitro exhibited an antigen-binding activity. Addition of reduced glutathione, oxidized glutathione, protein disulfide-isomerase and molecular chaperones, GroEL and GroES, increased the solubility and the antigen-binding activity of the Fab fragment greatly. The in vitro synthesized Fab was purified by means of a hexa-histidine tag attached to the C-terminus of the Hc. Catalytic assay of the purified Fab fragment showed that the His-tagged Fab fragment synthesized in vitro had a catalytic activity comparable to that produced in vivo.
Administration of angiotensin II and a bradykinin B2 receptor blocker in midpregnancy impairs gestational outcome in guinea pigs (2014)

The acute effects on fetal viability, and the persistently impaired renal/placental sufficiency and incomplete arterial remodeling implicate the RAS and KKS in the adaptations in pregnancy. The results partially confirm our hypothesis, as a preeclampsia-like syndrome was not induced. We demonstrate the feasibility of characterizing systemic and local modifications in pregnant guinea-pig, supporting its use to study normal placentation and related disorders.
Comparison of Novel Tacrine and 7-MEOTA Derivatives with Aromatic and Alicyclic Residues: Synthesis, Biological Evaluation and Docking Studies (2013)

Cholinesterase inhibitors play an essential role in the treatment of Alzheimer’s disease. Since their first introduction over a decade ago, they are an indispensable part of Alzheimer’s disease therapy and remain at the forefront of scientific interest worldwide. In this manuscript new analogs of THA and 7-MEOTA were designed, synthesized, and evaluated for their inhibitory activity against both acetylcholinesterase and butyrylcholinesterase. Cholinergic properties were investigated and quantified with respect to their side chain residues (aromatic or alicyclic). All synthesized compounds proved to have potent inhibitory activity at micromolar range. Moreover, compound 4 demonstrated promising efficacy and appears to be an ideal candidate for further testing. Keywords: 7-methoxytacrine, acetylcholinesterase, Alzheimer`s disease, butyrylcholinesterase, inhibition selectivity, molecular modelling.
A tripartite structure of the signals that determine protein insertion into the endoplasmic reticulum membrane. (1989)

Multilineage colony stimulating factor is a secretory protein with a cleavable signal sequence that is unusually long and hydrophobic. Using molecular cloning techniques we exchanged sequences NH2- or COOH-terminally flanking the hydrophobic signal sequence. Such modified fusion proteins still inserted into the membrane but their signal sequence was not cleaved. Instead the proteins were now anchored in the membrane by the formerly cleaved signal sequence (signal-anchor sequence). They exposed the NH2 terminus on the exoplasmic and the COOH terminus on the cytoplasmic side of the membrane. We conclude from our results that hydrophilic sequences flanking the hydrophobic core of a signal sequence can determine cleavage by signal peptidase and insertion into the membrane. It appears that negatively charged amino acid residues close to the NH2 terminal side of the hydrophobic segment are compatible with translocation of this segment across the membrane. A tripartite structure is proposed for signal-anchor sequences: a hydrophobic core region that mediates targeting to and insertion into the ER membrane and flanking hydrophilic segments that determine the orientation of the protein in the membrane.
Clopidogrel and Ticlopidine: P2Y12Adenosine Diphosphate-Receptor Antagonists for the Prevention of Atherothrombosis (2005)

Ticlopidine and clopidogrel belong to the same chemical family of thienopyridine adenosine diphosphate (ADP)-receptor antagonists. They have shown their efficacy as platelet antiaggregant and antithrombotic agents in many animal models, both ex vivo and in vivo. Although ticlopidine was discovered more than 30 years ago, it was only recently that the mechanism of action of ADP-receptor antagonists was characterized in detail. Ticlopidine and clopidogrel both behave in vivo as specific antagonists of P2Y (12), one of the ADP receptors on platelets. Metabolic steps that involve cytochrome P450-dependent pathways are required to generate the active metabolite responsible for this in vivo activity. The active moiety is a reactive thiol derivative that targets P2Y (12) on platelets. The interaction is irreversible, accounting for the observation that platelets are definitely antiaggregated, even if no active metabolite is detectable in plasma. The interaction is specific for P2Y (12); other purinoceptors such as P2Y (1) and P2Y (13) are spared. This results in inhibition of the binding of the P2Y (12) agonist 2-methylthio-ADP and the ADP-induced downregulation of adenylyl cyclase. Platelet aggregation is affected not only when triggered by ADP but also by aggregation inducers when used at concentrations requiring released ADP as an amplifier. The efficacy and safety of clopidogrel has been established in several large, randomized, controlled trials. The clopidogrel versus aspirin in patients at risk of ischaemic events (CAPRIE) trial demonstrated the superiority of clopidogrel over acetylsalicylic acid (ASA) in patients at risk of ischemic events, including ischemic stroke, myocardial infarction (MI), and peripheral arterial disease. The clopidogrel in unstable angina to prevent recurrent ischemic events (CURE) trial showed a sustained, incremental benefit when clopidogrel was added to standard therapy (including ASA) in patients with unstable angina and non-Q-wave MI. The clopidogrel for the reduction of events during observation (CREDO) trial demonstrated the benefit of continuing clopidogrel (plus ASA) for 12 months, as opposed to 1 month, after percutaneous coronary intervention. The proven efficacy of clopidogrel, coupled with its favorable safety and tolerability profile, has prompted its evaluation in an extensive, ongoing clinical trial program that will help to further characterize the benefit of clopidogrel in patients with a range of atherothrombotic profiles.
Investigation of the effects of antisense oligodeoxynucleotides to islet amyloid polypeptide mRNA on insulin release, content and expression (1996)

We have investigated the effects of antisense oligodeoxynucleotides (oligos) to islet amyloid polypeptide (IAPP) mRNA on the expression and secretion of IAPP and insulin, in the clonal beta-cell line HIT-T15. Phosphorothioate-modified oligos were cytotoxic compared with phosphodiester (D)-oligos. Of the nine oligos tested using a lipofection reagent, O3, a 30-mer D-oligo complementary to a sequence downstream of the IAPP initiation codon, showed a significant dose-dependent suppression of IAPP mRNA, with a 42% decrease at 7.5 microM, compared with a scrambled (MSO3) control oligo (n = 3, P < 0.01). A subsequent 89% suppression of IAPP release was observed in the 4-h period following antisense treatment (1.78 +/- 0.13 (MSO3) vs 0.19 +/- 0.14 (O3) pmol/10(6) cells per 240 min, n = 7, P < 0.01). A significant increase in insulin mRNA (100 +/- 10% (MSO3) vs 124 +/- 8% (O3), n = 3, P < 0.05) and insulin content (13.0 +/- 0.9 (MSO3) vs 17.4 +/- 1.4 (O3) pmol/10(6) cells, n = 7, P = 0.028) was observed following treatment with O3 at 7.5 microM. O8, a 20-mer D-oligo directed to a region of IAPP mRNA further downstream than O3, also showed a decrease in IAPP mRNA and peptide release and an increase in insulin content. No significant changes were observed in the expression and release of the unrelated beta-cell peptide, neuropeptide Y. We thus show a suppression of synthesis and release of IAPP in HIT-T15 cells using antisense oligos. The associated increase in insulin mRNA and content in these cells after treatment with IAPP antisense oligos is in accord with an inhibitor action of IAPP on insulin availability.
Getting in Touch with Your Friends (2009)

Evolution of complex physical interactions between microbes promotes growth and enables behaviors that neither party can perform alone.