gebhart/patrepeval huggingface dataset:
Coherent Acoustic Phonons in a Semiconductor Quantum Dot (1997)

Coherent acoustic phonons in PbS quantum dots are observed using femtosecond optical techniques. This is the first observation of coherent acoustic phonons in a semiconductor quantum dot; the phonons are generated through the deformation-potential coupling to the quantum-dot exciton. The acoustic modes are weakly damped, and we also find extremely weak coupling ( $S\ensuremath{\sim}0.01$) to the optical modes. These conclusions have important consequences for the vibronic nature of the exciton transition in the quantum dot and its dephasing.
A Syndrome of Acute Zinc Loss (1975)

Oral administration of the amino acid histidine to six patients with progressive systemic sclerosis produced anorexia, taste ans smell dysfunction, changes in mentation, and cerebellar dysfunction in each patient; these changes were associated with significant decreases in serum zinc concentration and significant increases in urinary zinc excretion. Administration of zinc ion, even with continued histidine administration, returned each of the signs and symptoms to or toward normal within 8 to 24 hours in each patient at the same time that correction of the serum zinc concentration occurred. The signs and symptoms noted constitute a syndrome related to acute zinc loss.
Crystal Structure of the Human Papillomavirus Type 18 E2 Activation Domain (1999)

The papillomavirus E2 protein regulates viral transcription and DNA replication through interactions with cellular and viral proteins. The amino-terminal activation domain, which represents a protein class whose structural themes are poorly understood, contains key residues that mediate these functional contacts. The crystal structure of a protease-resistant core of the human papillomavirus type 18 E2 activation domain reveals a novel fold creating a cashew-shaped form with a glutamine-rich alpha helix packed against a beta-sheet framework. The protein surface shows extensive overlap of determinants for replication and transcription. The structure broadens the concept of activators to include proteins with potentially malleable, but certainly ordered, structures.
The Roles of Annexins and Types II and X Collagen in Matrix Vesicle-mediated Mineralization of Growth Plate Cartilage (2000)

Annexins II, V, and VI are major components of matrix vesicles (MV), i.e. particles that have the critical role of initiating the mineralization process in skeletal tissues. Furthermore, types II and X collagen are associated with MV, and these interactions mediated by annexin V stimulate Ca(2+) uptake and mineralization of MV. However, the exact roles of annexin II, V, and VI and the interaction between annexin V and types II and X collagen in MV function and initiation of mineralization are not well understood. In this study, we demonstrate that annexin II, V, or VI mediate Ca(2+) influx into phosphatidylserine (PS)-enriched liposomes, liposomes containing lipids extracted from authentic MV, and intact authentic MV. The annexin Ca(2+) channel blocker, K-201, not only inhibited Ca(2+) influx into fura-2-loaded PS-enriched liposomes mediated by annexin II, V, or VI, but also inhibited Ca(2+) uptake by authentic MV. Types II and X collagen only bound to liposomes in the presence of annexin V but not in the presence of annexin II or VI. Binding of these collagens to annexin V stimulated its Ca(2+) channel activities, leading to an increased Ca(2+) influx into the liposomes. These findings indicate that the formation of annexin II, V, and VI Ca(2+) channels in MV together with stimulation of annexin V channel activity by collagen (types II and X) binding can explain how MV are able to rapidly take up Ca(2+) and initiate the formation of the first crystal phase.
Thalamocortical Long-Term Potentiation Becomes Gated after the Early Critical Period in the Auditory Cortex (2013)

Cortical maps in sensory cortices are plastic, changing in response to sensory experience. The cellular site of such plasticity is currently debated. Thalamocortical (TC) projections deliver sensory information to sensory cortices. TC synapses are currently dismissed as a locus of cortical map plasticity because TC synaptic plasticity is thought to be limited to neonates, whereas cortical map plasticity can be induced in both neonates and adults. However, in the auditory cortex (ACx) of adults, cortical map plasticity can be induced if animals attend to a sound or receive sounds paired with activation of cholinergic inputs from the nucleus basalis. We now show that, in the ACx, long-term potentiation (LTP), a major form of synaptic plasticity, is expressed at TC synapses in both young and mature mice but becomes gated with age. Using single-cell electrophysiology, two-photon glutamate uncaging, and optogenetics in TC slices containing the auditory thalamus and ACx, we show that TC LTP is expressed postsynaptically and depends on group I metabotropic glutamate receptors. TC LTP in mature ACx can be unmasked by cortical disinhibition combined with activation of cholinergic inputs from the nucleus basalis. Cholinergic inputs passing through the thalamic radiation activate M1 muscarinic receptors on TC projections and sustain glutamate release at TC synapses via negative regulation of presynaptic adenosine signaling through A1 adenosine receptors. These data indicate that TC LTP in the ACx persists throughout life and therefore can potentially contribute to experience-dependent cortical map plasticity in the ACx in both young and adult animals.
Anergic T cells actively suppress T cell responses via the antigen-presenting cell (1998)

We here show that anergic T cells are active mediators of T cell suppression. In co-culture experiments, we found that anergic T cells, derived from established rat T cell clones and rendered anergic via T cell presentation of the specific antigen (Ag), were active inhibitors of T cell responses. Anergic T cells inhibited not only the responses of T cells with the same Ag specificity as the anergic T cells, but were also capable of efficiently inhibiting polyclonal T cell responses directed to other epitopes. This suppression required close cell-cell contact between antigen-presenting cells (APC), anergic T cells and responder T cells, and only occurred when the epitope recognized by the anergic T cell was present. The suppression was not caused by passive competition for ligands on the APC surface, IL-2 consumption, or cytolysis, and was not mediated by soluble factors derived from anergic T cells that were stimulated with their specific Ag. When responder T cells were added 24 h after co-culturing anergic cells in the presence of Ag and APC, T cell responses were still suppressed, indicating that the suppressive effect was persistently present. However, anergic T cells were not able to suppress responder T cells that had already received a full activation signal. We propose that suppression by anergic T cells is mediated via the APC, either through modulation of the T cell-activating capacity of the APC (APC/T cell interaction), or by inhibition of T cells recognizing their ligand in close proximity on the same APC (T/T cell interaction).
Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content. (1996)

A PCR method for uniform amplification of a mixture of DNA templates differing in GC content is described using the two enzyme approach (Klentaq1 and Pfu DNA polymerase) and a combination of DMSO and betaine. This method was applied to amplify the CGG repeat region from the fragile X region.
Cathepsin B and cystatins: evidence for a role in cancer progression. (1990)

The cysteine proteinase cathepsin B has been implicated in the progression of tumors from a premalignant to a malignant state. Activity of cathepsin B has been shown to be elevated in parallel with malignancy or metastatic potential of human and rodent tumors. These increases in cathepsin B activity correspond in part to increases in mRNA for cathepsin B and in part to reduced regulation by endogenous low Mr cysteine proteinase inhibitors. Most properties of tumor cathepsin B appear to be similar to those of cathepsin B from normal tissues. However, the subcellular distribution of cathepsin B is altered in tumors, resulting in association of cathepsin B with plasma membrane fractions or in release of high Mr forms of cathepsin B into the extracellular milieu. Since cathepsin B can degrade laminin, fibronectin and type IV collagen, we speculate that the presence of cathepsin B at the surface of tumor cells may contribute to the local dissolution of basement membrane observed during tumor cell extravasation. Direct evidence that cathepsin B plays a role in cancer progression awaits studies in which upregulation or downregulation of the expression of cathepsin B and its endogenous inhibitors is found to alter tumorigenesis, metastatic potential, etc.
Middle cerebral artery occlusion in rats studied by magnetic resonance imaging. (1989)

Ischemia due to middle cerebral artery occlusion was studied in 29 rats from 1 to 24 hours after occlusion using magnetic resonance imaging. Images were made before and after the injection of a superparamagnetic iron oxide compound, AMI-25. Subtraction images demonstrated the region of perfusion deficit as early as 1 hour after occlusion, earlier than conventional T2-weighted images. The area of altered perfusion detected by this technique (subtraction imaging after AMI-25 administration) correlated with that demonstrated by iodoantipyrine autoradiography. Since this magnetic resonance technique can be used to serially estimate the location and size of the ischemic area, the technique can be an important adjunct to metabolic studies of focal ischemia using magnetic resonance spectroscopy. The technique may have clinical applications as well.
Methods for siRNA-mediated Reduction of mRNA and Protein Expression in Human Placental Explants, Isolated Primary Cells and Cell Lines (2008)

The use of RNA interference (RNAi) to deplete individual proteins from cells or tissue has revolutionised our ability to characterise gene function. The placenta is an attractive target for studies in which the role of specific proteins can be compared with cell culture models and explanted villous tissue where physiological function can be maintained ex vivo. In this study, we compared a variety of commercially available reagents and approaches to define methods for efficient delivery of siRNA to placental cells. Protocols optimised using fluorescently-labelled siRNA were subsequently tested using siRNA sequences that target placental alkaline phosphatase (PLAP), chosen because of its high abundance in trophoblast. mRNA abundance was assayed using qRT-PCR, and the effect on protein was examined using immunolocalisation. We report that different protocols are required for BeWo choriocarcinoma cells (nucleofection), primary cytotrophoblast cells (lipid-based transfection) and villous tissue explants (nucleofection). The results provide guidelines for optimal siRNA-mediated knockdown in these three models of the human placenta.
Minimizing damage during FIB sample preparation of soft materials (2011)

Summary Although focused ion beam (FIB) microscopy has been used successfully for milling patterns and creating ultra‐thin electron and soft X‐ray transparent sections of polymers and other soft materials, little has been documented regarding FIB‐induced damage of these materials beyond qualitative evaluations of microstructure. In this study, we sought to identify steps in the FIB preparation process that can cause changes in chemical composition and bonding in soft materials. The impact of various parameters in the FIB‐scanning electron microscope (SEM) sample preparation process, such as final milling voltage, temperature, ion beam overlap and mechanical stability of soft samples, was evaluated using two test‐case materials systems: polyacrylamide, a low melting‐point polymer, and Wyodak lignite coal, a refractory organic material. We evaluated changes in carbon bonding in the samples using X‐ray absorption near‐edge structure spectroscopy (XANES) at the carbon K edge and compared these samples with thin sections that had been prepared mechanically using ultramicrotomy. Minor chemical changes were induced in the coal samples during FIB‐SEM preparation, and little effect was observed by changing ion‐beam parameters. However, polyacrylamide was particularly sensitive to irradiation by the electron beam, which drastically altered the chemistry of the sample, with the primary damage occurring as an increase in the amount of aromatic carbon bonding (C=C). Changes in temperature, final milling voltage and beam overlap led to small improvements in the quality of the specimens. We outline a series of best practices for preparing electron and soft X‐ray transparent samples, with respect to preserving chemical structure and mechanical stability of soft materials using the FIB.
Hydrogenation of dimethyl oxalate to ethylene glycol over mesoporous Cu‐MCM‐41 catalysts (2012)

The synthesis and utilization of mesoporous Cu ‐ MCM ‐41 catalysts for hydrogenation of dimethyl oxalate to ethylene glycol is described in this article. Physicochemical properties of these Cu ‐ MCM ‐41 catalysts have been investigated by N 2 ‐physisorption, X ‐ray diffraction, inductively coupled plasma, N 2 O titration, transmission electron microscopy, temperature programmed reduction, F ourier transform infrared spectroscopy, and X ‐ray photoelectron spectroscopy. It was found that the copper loading significantly influenced the pore structure and copper surface area of the catalyst. High catalytic performance is obtained over a 20 Cu ‐ MCM ‐41 catalyst with a full DMO conversion and EG yield of 92% at a LHSV of 3.0 h −1 . The catalytic performance of optimized 20 Cu ‐ MCM ‐41 catalyst could be attributed to the fine copper dispersion and large copper surface areas. © 2013 American Institute of Chemical Engineers AIChE J , 59: 2530–2539, 2013
Full-field time-encoded frequency-domain optical coherence tomography (2006)

Ultrahigh axial resolution surface profiling as well as volumetric optical imaging based on time encoded optical coherence tomography in the frequency domain without any mechanical scanning element is presented. A frequency tuned broad bandwidth titanium sapphire laser is interfaced to an optical microscope (Axioskop 2 MAT, Carl Zeiss Meditec) that is enhanced with an interferometric imaging head. The system is equipped with a 640 x 480 pixel CMOS camera, optimized for the 800 nm wavelength tuning range for transmission and reflection measurements of a microscopic sample. Sample volume information over 1.3 x 1 x 0.2 mm(3) with ~3 mum axial and ~4 mum transverse resolution in tissue is acquired by a single wavelength scan over more than 100 nm optical bandwidth from <760 to >860 nm with 128-2048 equidistant optical frequency steps with an acquisition time of 1 to 50 ms per step. Topography and tomography with a signal to noise ratio of 83 dB is demonstrated on test surfaces and biological specimen respectively. This novel OCT technique promises to enable high speed, three dimensional imaging by employing high frame rate cameras and state of the art tunable lasers in a mechanically stable environment, due to lack of moving components while reducing the intensity on the sample.
Ro 09-1679, A NOVEL THROMBIN INHIBITOR. (1992)

Among the serine proteases involved in thrombosis and hemostasis, thrombin plays a key role in blood coagulation;
Inhibition of breast cancer growth in vivo by antiangiogenesis gene therapy with adenovirus-mediated antisense-VEGF (2001)

Increased expression of VEGF in several types of tumours has been shown to correlate with poor prognosis. We used a replication-deficient adenoviral vector containing antisense VEGF cDNA (Ad5CMV-αVEGF) to down-regulate VEGF expression and increase the efficiency of delivery of the antisense sequence in the human breast cancer cell line MDA231-MB. Transfection of these cells with Ad5CMV-αVEGF in vitro reduced secreted levels of VEGF protein without affecting cell growth. Moreover, injection of the Ad5CMV-αVEGF vector into intramammary xenografts of these cells established in nude mice inhibited tumour growth and reduced the amount of VEGF protein and the density of microvessels in those tumours relative to tumours treated with the control vector Ad5(dl312). Our results showed that antisense VEGF165cDNA was efficiently delivered in vivo via an adenoviral vector and that this treatment significantly inhibited the growth of established experimental breast tumours. The Ad5CMV-αVEGF vector may be useful in targeting the tumour vasculature in the treatment of breast cancer. © 2001 Cancer Research Campaign http://www.bjcancer.com
Low-temperature anti-Stokes luminescence mediated by disorder in semiconductor quantum-well structures (1995)

In low-temperature photoluminescence experiments on II-VI semiconductor quantum wells we find an energy transfer from confined quantum-well states to above-barrier states. The observed anti-Stokes barrier luminescence exhibits a characteristic intensity dependence showing that this transfer is caused by a two-step absorption process involving localized or impurity bound-exciton states in the quantum well. Time-resolved photoluminescence experiments show that the photon for the second intraband absorption step can be provided by the quantum-well luminescence, i.e., the anti-Stokes barrier luminescence is a direct consequence of photon recycling.
The Respiratory Metabolism and Swimming Performance of Young Sockeye Salmon (1964)

The rate of oxygen consumption in young sockeye salmon (Oncorhynchus nerka) was determined for various swimming speeds, including fatigue levels, at temperatures of 5, 10, 15, 20, and 24 °C. A logarithmic increase in oxygen demand with increase in swimming speed characterized each acclimation temperature. Extrapolation to zero activity (standard metabolism) and maximum activity (active metabolism) provided differences of the order of 10 to 12 times the minimum rate.The greatest scope for activity occurred at 15 °C with an average active metabolic rate of 895 mg O 2 /kg/hr for a swimming speed of 4.1 body lengths per second, just maintained for 1 hr. Above 15 °C active metabolism was limited, apparently by oxygen availability.Rate of replacement of oxygen debt following fatigue was determined by tracing the return to a resting state of metabolism, and confirmed by re-tests at fatigue velocities. In most instances the rate declined logarithmically with time; in some there was an initial or secondary slump. Times to recovery (return of spontaneous activity) averaged 3.2 hr, independent of acclimation temperature.Swimming speed–fatigue tests indicated a sustained level of performance at about 200–300 min. Comparison with other fish suggests a marked change in slope of the fatigue curve at about 20 sec. The effect of temperature was greatest on sustained speeds and least on burst speeds.
Isolation and characterization of mutations in the gene encoding an endogenous Bacillus subtilis beta-galactosidase and its regulator (1990)

We have isolated mutations that appear to inactivate the gene (lacA) encoding an endogenous beta-galactosidase activity in Bacillus subtilis and in a closely linked negative regulatory element (lacR). Both genes map to the hisA-thrA region. The lacA mutations may help to avoid some of the problems arising from the use of the Escherichia coli lacZ gene as a reporter gene in B. subtilis.
N-Type Calcium Channels in the Developing Rat Hippocampus: Subunit, Complex, and Regional Expression (1997)

The expression of multiple classes of voltage-dependent calcium channels (VDCCs) allows neurons to tailor calcium signaling to functionally discrete cellular regions. In the developing hippocampus a central issue is whether the expression of VDCC subtypes plays a role in key phases such as migration and synaptogenesis. Using radioligand binding and immunoblotting, we show that some N-type VDCCs exist before birth, consistent with a role in migration; however, most N-VDCC subunit expression is postnatal, coinciding with synaptogenesis. Immunoprecipitation studies indicate that the increased expression of N-VDCCs in early development occurs without subunit switching because there is no change in the fraction of beta3 subunits in the N-VDCC alpha1B-beta3 heteromers. Fluorescence imaging of cell surface N-VDCCs during this period reveals that N-VDCCs are expressed on somata before dendrites and that this expression is asynchronous between different subfields of the hippocampus (CA3-CA4 before CA1-CA2 and dentate gyrus). Our data argue that N-VDCC expression is an important cue in the genesis of synaptic transmission in discrete hippocampal subfields.
Clonal Expansions of Cd8+ T Cells Dominate the T Cell Infiltrate in Active Multiple Sclerosis Lesions as Shown by Micromanipulation and Single Cell Polymerase Chain Reaction (2000)

Clonal composition and T cell receptor (TCR) repertoire of CD4(+) and CD8(+) T cells infiltrating actively demyelinating multiple sclerosis (MS) lesions were determined with unprecedented resolution at the level of single cells. Individual CD4(+) or CD8(+) T cells were isolated from frozen sections of lesional tissue by micromanipulation and subjected to single target amplification of TCR-beta gene rearrangements. This strategy allows the assignment of a TCR variable region (V region) sequence to the particular T cell from which it was amplified. Sequence analysis revealed that in both cases investigated, the majority of CD8(+) T cells belonged to few clones. One of these clones accounted for 35% of CD8(+) T cells in case 1. V region sequence comparison revealed signs of selection for common peptide specificities for some of the CD8(+) T cells in case 1. In both cases, the CD4(+) T cell population was more heterogeneous. Most CD4(+) and CD8(+) clones were represented in perivascular infiltrates as well as among parenchymal T cells. In case 2, two of the CD8(+) clones identified in brain tissue were also detected in peripheral blood. Investigation of the antigenic specificities of expanded clones may help to elucidate their functional properties.
Why was PERV not transmitted during preclinical and clinical xenotransplantation trials and after inoculation of animals? (2018)

Porcine endogenous retroviruses (PERVs) are present in the genome of all pigs, they infect certain human cells and therefore pose a special risk for xenotransplantation using pig cells, tissues and organs. Xenotransplantation is being developed in order to alleviate the reduced availability of human organs. Despite the fact that PERVs are able to infect certain human cells and cells from other species, transmission of PERVs has not been observed when animals (including non-human primates) were inoculated with PERV preparations or during preclinical xenotransplantations. The data indicate that PERVs were not transmitted because they were not released from the transplant or were inhibited by intracellular restriction factors and innate immunity in the recipient. In a single study in guinea pigs, a transient PERV infection and anti-PERV antibodies were described, indicating that in this case at least, the immune system may also have been involved.
Current topics in diabetes research : 4th International Diabetes Conference, Florence, March 18-20, 1992 (1993)

Genetics of type 2 diabetes methods of advanced clinical investigation in diabetes (I) - substrate flux and utilization methods of advanced clinical investigation in diabetes (II) - measurement of insulin resistance and B-cell function methods of advanced clinical investigation in diabetes (III) - diabetic complications methods of advanced clinical investigation in diabetes (IV) - immunity in type 1 diabetes polymetabolic disorders diabetic retinopathy short communications.