gebhart/patrepeval huggingface dataset:
Synapsin I Is an Oligomannose-Carrying Glycoprotein, Acts As an Oligomannose-Binding Lectin, and Promotes Neurite Outgrowth and Neuronal Survival When Released via Glia-Derived Exosomes (2011)

Oligomannosidic glycans play important roles in nervous system development and function. By performing a phage display screening with oligomannose-specific antibodies, we identified an oligomannose-mimicking peptide that was functionally active in modulating neurite outgrowth and neuron-astrocyte adhesion. Using the oligomannose-mimicking peptide in crosslinking experiments, synapsin I was identified as a novel oligomannose-binding protein in mouse brain. Further analyses not only verified that synapsin I is an oligomannose-binding lectin, but also indicated that it is a glycoprotein carrying oligomannose and Lewis(x). We also found that synapsin I is expressed in glia-enriched cultures and is released from glial cells via exosomes. Incubation of glial-derived exosomes in the presence of high KCl concentrations or subjecting glial cell cultures to either oxygen/glucose deprivation or hydrogen peroxide resulted in release of synapsin I from exosomes. Application of synapsin I promoted neurite outgrowth from hippocampal neurons and increased survival of cortical neurons upon hydrogen peroxide treatment or oxygen/glucose deprivation. Coculture experiments using wild-type hippocampal neurons and wild-type or synapsin-deficient glial cells showed enhanced neurite outgrowth when synapsin was expressed by glial cells. Synapsin-induced neurite outgrowth was dependent on oligomannose on synapsin I and the neural cell adhesion molecule NCAM at the neuronal cell surface. The data indicate that, under conditions of high neuronal activity and/or oxidative stress, synapsin can be released from glial-derived exosomes and promotes neurite outgrowth and neuronal survival by modulating the interactions between glia and neurons.
Effect of Human IgG Antiphospholipid Antibodies on an In Vivo Thrombosis Model in Mice (1994)

High levels of IgG antiphospholipid antibodies (aPL) have been associated with clinical thrombosis. It is uncertain however whether these antibodies play a direct role in thrombosis or are merely epiphenomena. To investigate whether antiphospholipid antibodies might play a role in thrombosis, we utilized a novel mouse model in which the dynamics of in vivo thrombosis can be studied. CD1 mice (26-30 g) were passively immunized with 25 mg of human IgG from a patient with the Antiphospholipid Syndrome (IgG-APS) (n = 17), IgG from normal pooled sera (IgG-NHS) (n = 9), or saline solution (n = 12), followed by 40 mg of the same preparations at 48 h. At 72 h, levels of human aPL antibodies, detected using the anticardiolipin ELISA test (aCL ELISA test), in mice immunized with IgG-APS, were 50-100 GPL units. Each animal was anesthetized, femoral vein minimally mobilized and subjected to a standardized "pinch" injury to induce thrombosis. The vessel was transilluminated using acrylic optical fibers connected to a light source, and clot formation and dissolution were visualized by a standard surgical microscope equipped with a video camera, video recorder, and computer assisted analysis system. Results showed that average clot size was significantly larger in mice immunized with IgG-APS compared to those treated with saline (p < 0.037). In addition, the thrombus persisted longer in a significantly higher number of mice immunized with IgG-APS (10/17) compared to mice immunized with IgG-NHS (1/9) or saline (2/12) (p < 0.02).(ABSTRACT TRUNCATED AT 250 WORDS)
Response to Iron Deprivation in Saccharomyces cerevisiae (2007)

Iron is an essential nutrient for almost every organism because iron cofactors, such as heme and iron-sulfur clusters (ISC), are required for the activity of numerous cellular enzymes involved in a wide range of cellular processes. Although iron is a very abundant metal in the earth's crust, it has
Cross‐Sectional Anthropometric Study of the External Ear (2007)

This cross-sectional anthropometric study was aimed at estimating expansion of the external ear during adult life, in order to evaluate the extent to which anatomical features appearing in earprints may vary with time. A review of the literature was provided. Data extracted from photographed ears of 1353 subjects were analyzed. The effect of age on auricle length, earlobe length, and auricle width was explored using univariate analyses of variance. The regression coefficients of age on these dimensions were, respectively, 0.178, 0.115, and 0.073 mm/yr for males, and 0.162, 0.100, and 0.073 mm/year for females (p=0.000). Regression coefficients of age corrected for stature were assumed to be less accurate. Anthelix prominence and helix width were analyzed using data of 175 subjects, and appeared unaffected by age. As lobe expansion appeared to exceed the estimated cartilage expansion, it was assumed that particularly the imprint of the lobe would be less stable with time.
The fibronectin type III domain as a scaffold for novel binding proteins (1998)

The fibronectin type III domain (FN3) is a small autonomous folding unit which occurs in many animal proteins involving in ligand binding. The beta-sandwich structure of FN3 closely resembles that of immunoglobulin domains. We have prepared a phage display library of FN3 in which residues in two surface loops were randomized. We have selected mutant FN3s which bind to a test ligand, ubiquitin, with significant affinities, while the wild-type FN3 shows no measurable affinity. A dominant clone was expressed as a soluble protein and its properties were investigated in detail. Heteronuclear NMR characterization revealed that the selected mutant protein retains the global fold of FN3. It also has a modest conformational stability despite mutations at 12 out of 94 residues. These results clearly show the potential of FN3 as a scaffold for engineering novel binding proteins.
An automated method for least cost distribution planning (1990)

A method of planning changes to a distribution system to meet load projections by minimizing the cost of these changes while ensuring that the system meets required constraints is described. A computer program uses the method of simulated annealing to evaluate various configurations and to derive the optimal solution. The program evaluates options normally considered in a distribution planning study, such as reconductoring sections of feeders and switching sections of one feeder to another feeder. At each step of the optimization process the program performs a load-flow to find the total losses and to check constraints. The objective function to be optimized is the cost of the changes added to the cost of the losses. Several examples demonstrate the effectiveness of this program as a distribution planning tool.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
What limits working memory capacity? Evidence for modality-specific sources to the simultaneous storage of visual and auditory arrays. (2011)

There is considerable debate on whether working memory (WM) storage is mediated by distinct subsystems for auditory and visual stimuli (Baddeley, 1986) or whether it is constrained by a single, central capacity-limited system (Cowan, 2006). Recent studies have addressed this issue by measuring the dual-task cost during the concurrent storage of auditory and visual arrays (e.g., Cocchini, Logie, Della Sala, MacPherson, & Baddeley, 2002; Fougnie & Marois, 2006; Saults & Cowan, 2007). However, studies have yielded widely different dual-task costs, which have been taken to support both modality-specific and central capacity-limit accounts of WM storage. Here, we demonstrate that the controversies regarding such costs mostly stem from how these costs are measured. Measures that compare combined dual-task capacity with the higher single-task capacity support a single, central WM store when there is a large disparity between the single-task capacities (Experiment 1) but not when the single-task capacities are well equated (Experiment 2). In contrast, measures of the dual-task cost that normalize for differences in single-task capacity reveal evidence for modality-specific stores, regardless of single-task performance. Moreover, these normalized measures indicate that dual-task cost is much smaller if the tasks do not involve maintaining bound feature representations in WM (Experiment 3). Taken together, these experiments not only resolve a discrepancy in the field and clarify how to assess the dual-task cost but also indicate that WM capacity can be constrained both by modality-specific and modality-independent sources of information processing.
Immunomodulatory agents lenalidomide and pomalidomide co‐stimulate T cells by inducing degradation of T cell repressors I karos and A iolos via modulation of the E 3 ubiquitin ligase complex CRL 4 CRBN (2013)

Cereblon (CRBN), the molecular target of lenalidomide and pomalidomide, is a substrate receptor of the cullin ring E3 ubiquitin ligase complex, CRL4(CRBN) . T cell co-stimulation by lenalidomide or pomalidomide is cereblon dependent: however, the CRL4(CRBN) substrates responsible for T cell co-stimulation have yet to be identified. Here we demonstrate that interaction of the transcription factors Ikaros (IKZF1, encoded by the IKZF1 gene) and Aiolos (IKZF3, encoded by the IKZF3 gene) with CRL4(CRBN) is induced by lenalidomide or pomalidomide. Each agent promotes Aiolos and Ikaros binding to CRL4(CRBN) with enhanced ubiquitination leading to cereblon-dependent proteosomal degradation in T lymphocytes. We confirm that Aiolos and Ikaros are transcriptional repressors of interleukin-2 expression. The findings link lenalidomide- or pomalidomide-induced degradation of these transcriptional suppressors to well documented T cell activation. Importantly, Aiolos could serve as a proximal pharmacodynamic marker for lenalidomide and pomalidomide, as healthy human subjects administered lenalidomide demonstrated Aiolos degradation in their peripheral T cells. In conclusion, we present a molecular model in which drug binding to cereblon results in the interaction of Ikaros and Aiolos to CRL4(CRBN) , leading to their ubiquitination, subsequent proteasomal degradation and T cell activation.
Chromosomal assignment of seventeen porcine microsatellites and genes by use of a somatic cell hybrid mapping panel (1995)

Swine-specific sequence tagged (microsatellite) sites, STS and STMS, were assigned chromosomally by polymerase chain reaction analysis of a somatic cell hybrid panel. This study confirms the localization from genetic mapping of seven anonymous microsatellites and the genes ANPEP, ATP2, CGA, DAGK, FSHB, IFNG, IGF1, IL1B and SPP1. New assignment for the gene BNP1 to chromosome 6 is reported. The confirmed and the new assignments extend the information of the previously established linkage maps and provide framework loci on which to order additional informative markers.
Treatment Monitoring by 18F-FDG PET/CT in Patients with Sarcomas: Interobserver Variability of Quantitative Parameters in Treatment-Induced Changes in Histopathologically Responding and Nonresponding Tumors (2008)

SUVmax and SUVpeak provided the most robust measurements of tumor glucose metabolism in sarcomas. Delineation of the whole-tumor volume by semiautomatic thresholding did not decrease the variability of SUV measurements. TBRs were significantly more observer-dependent than were absolute SUVs. These findings should be considered for standardization of clinical (18)F-FDG PET/CT trials.
Incomplete Recovery of Prescription Opioids in Urine using Enzymatic Hydrolysis of Glucuronide Metabolites (2006)

Confirmation of opioids in urine samples of clinical patients requires liberation of opioids from their glucuronide conjugates. Both acid hydrolysis and enzyme hydrolysis using beta-glucuronidase from various sources have been reported, with the latter approach prevailing in most clinical toxicology laboratories. The goal of this study was to compare the efficiency of acid versus different enzyme hydrolysis methods in recovering morphine and common semisynthetic opioids from glucuronide standards and 78 patient urine samples that were screened positive for opioids as a class. Specimens were analyzed with a validated gas chromatography-mass spectrometry (GC-MS) procedure. With the exception of oxycodone, the results indicated that the majority of opioids tested were extensively glucuronide-conjugated in urine. Significantly, acid hydrolysis liberated > 90% of morphine and hydromorphone from their glucuronide standards but enzyme hydrolysis had lower and variable efficiency, depending on the opiate type and the enzyme source. In patient specimens, much higher concentrations of free codeine, morphine, hydromorphone, and oxymorphone were obtained with acid hydrolysis than with various enzyme methods. Incomplete hydrolysis using beta-glucuronidase could lead to false-negative results for many opioids when urine is tested for drugs of abuse. We conclude that acid hydrolysis is the method of choice for GC-MS confirmation of urine opioids.
Tracking Human Speech Events Using a Particle Filter (2006)

A method of detecting and tracking moving human speech events by integrating audio and video signals using a particle filter is proposed and evaluated. Using the particle filter, location, on/off status, and human/non-human determination can be estimated simultaneously for multiple sound sources. Experiments demonstrate that the proposed method performs well for the data obtained in an ordinary meeting room using a microphone array and a monocular camera.
Sildenafil, a novel effective oral therapy for male erectile dysfunction (1996)

These results show that sildenafil is a well tolerated and effective oral therapy for male erectile dysfunction with no established organic cause and may represent a new class of peripherally acting drug for the treatment of this condition.
Comparison of the metastatic properties of B16 melanoma clones isolated from cultured cell lines, subcutaneous tumors, and individual lung metastases. (1982)

Tumors produced by s.c. injection of uncloned B16 melanoma cell lines contain clonal tumor cell subpopulations with widely differing metastatic properties, including clones that are nonmetastatic. Similar metastatic heterogeneity exists in clones isolated from the same cell lines cultured in vitro. In B16 melanoma sublines (B16-BL6, B16-BV8, and B16-BP8) selected for enhanced invasive and metastatic behavior, the proportion of clones with high metastatic capacity is increased relative to the parent cell line. The cellular composition of metastases produced by s.c. or i.v. injection of the uncloned parent cell line has also been examined. Some metastases are populated by clones with indistinguishable metastatic properties (intralesional clonal homogeneity) while others yield clones with different metastatic properties (intralesional clonal heterogeneity). The range of clonal diversity in heterogeneous metastases is, however, substantially less than in the parent line. The number of metastases yielding clones with heterogeneous metastatic phenotypes is higher for "spontaneous" metastases arising from s.c. tumors than in "experimental" metastases produced by i.v. injection of single-cell suspensions. Studies using B16 cells bearing specific biochemical markers indicate that clonally homogeneous metastases are of monoclonal origin and that metastases populated by clones with heterogeneous metastatic phenotypes are of polyclonal origin.
Trigger Factor Retards Protein Export in Escherichia coli (2002)

Trigger factor (TF) is a ribosome-associated protein that interacts with a wide variety of nascent polypeptides in Escherichia coli. Previous studies have indicated that TF cooperates with DnaK to facilitate protein folding, but the basis of this cooperation is unclear. In this study we monitored protein export in E. coli that lack or overproduce TF to obtain further insights into its function. Whereas inactivation of genes encoding most molecular chaperones (including dnaK) impairs protein export, inactivation of the TF gene accelerated protein export and suppressed the need for targeting factors to maintain the translocation competence of presecretory proteins. Furthermore, overproduction of TF (but not DnaK) markedly retarded protein export. Manipulation of TF levels produced similar effects on the export of a cytosolic enzyme fused to a signal peptide. The data strongly suggest that TF has a unique ability to sequester nascent polypeptides for a relatively prolonged period. Based on our results, we propose that TF and DnaK promote protein folding by distinct (but complementary) mechanisms.
Biogenesis of Mitochondria (1988)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
Is High Extracellular Glutamate the Key to Excitotoxicity in Traumatic Brain Injury? (1997)

Traumatic brain injury (TBI) increases extracellular levels of the excitatory amino acid glutamate and aspartate, and N-methyl-D aspartate (NMDA)-receptor antagonists protect against experimental TBI. These two findings have led to the prevalent hypothesis that excitatory amino acid efflux is a major contributor to the development of neuronal damage subsequent to traumatic injury. However, as with stroke, the hypothesis that high extracellular glutamate is the key to excitotoxicity in TBI conflicts with important data. For example, the initial increase in extracellular glutamate is cleared within 5 min after moderate TBI, whereas antagonists of glutamate receptors and the so- called presynaptic glutamate release inhibitors remain effective when administered 30 min after insult. In this article, we argue that the current concept of excitotoxicity in TBI, centered on high extracellular glutamate, does not withstand scientific scrutiny. As alternatives to explain the beneficial actions of glutamate antagonists in experimental TBI, we propose abnormalities of glutamatergic neurotransmission, such as deficient Mg2+ block of NMDA-receptor ionophore complexes, and phenomena such as spreading depression, which requires activation of glutamate receptors and is detrimental to neurons in damaged/vulnerable brain regions. Finally, we introduce the notion that beneficial effects of glutamate receptor antagonists in experimental models of neurological disorders do not necessarily imply the occurrence of excitotoxic processes. Indeed, glutamate-receptor blockade may be protective by reducing the energy demand required to counterbalance Na+ influx associated with glutamatergic synaptic transmission. In other words, glutamate receptor antagonists (and blockers of voltage-gated Na+-channels) may help nervous tissue to cope with increased permeability of the cellular membrane to ions and reduced efficacy of Na+ extrusion, and thus prevent the decay of transmembrane ionic concentrations gradients.
Merging C–H Bond Functionalization with Amide Alcoholysis: En Route to 2-Aminopyridines (2016)

A new route for the synthesis of 2-aminopyridines has been developed that merges C–H functionalization with amide alcoholysis. The key component of this method is the ability of a quinazolinone to template the chemo- and regioselective construction of a latent pyridine ring via site-selective olefinic C–H bond functionalization under Ru(II) catalysis. Thus, highly substituted 2-aminopyridines were prepared in good yield. Mechanistic studies provide insight into the mechanism of the key oxidative C–H activation/annulation process.
Expression of gamma interferon by simian immunodeficiency virus increases attenuation and reduces postchallenge virus load in vaccinated rhesus macaques (1997)

Simian immunodeficiency virus (SIV) infection of macaques is a model for human immunodeficiency virus (HIV) infection. We have previously reported the construction and characterization of an SIV vector with a deletion in the nef gene (SIV(delta nef)) and expressing gamma interferon (SIV(HyIFN)) (L. Giavedoni and T. Yilma, J. Virol. 70:2247-2251, 1996). We now show that rhesus macaques vaccinated with SIV(HyIFN) have a lower viral load than a group similarly immunized with SIV(delta nef). Viral loads remained low in the SIV(HyIFN)-vaccinated group even though SIV expressing gamma interferon could not be isolated after 6 weeks postimmunization in these animals. All immunized and two naive control macaques became infected when challenged with virulent SIV(mac251), at 25 weeks postvaccination. In contrast to the two naive controls that died by 12 and 18 weeks postchallenge, all vaccinated animals remained healthy for more than 32 weeks. In addition, postchallenge cell-associated virus load was significantly lower in SIV(HyIFN)-immunized animals than in the group vaccinated with SIV(delta nef). These findings indicate that cytokine-expressing viruses can provide a novel approach for development of safe and efficacious live attenuated vaccines for AIDS.
BlindAid: Virtual environment system for self-reliant trip planning and orientation and mobility training (2010)

BlindAid is a virtual environment (VE) system that enables blind people to more easily learn about new environments on their own. The system is implemented on a desktop personal computer with a Phantom® haptic interface and three-dimensional spatialized audio. In addition to providing blind users with non-visual stimuli similar to what they will depend on in the actual environment, the system is designed to enhance and accelerate the user's understanding of the unknown environment by giving him/her the ability to interact with the VE in ways that are not possible in the real world. The BlindAid system was developed and evaluated as part of an experimental study related to how people who are blind build cognitive maps of their physical environment and how recent advances in VE technology might support orientation and mobility (O&M) training. The current system is able to provide a visual display and record the user's actions in the VE for later review by researchers and O&M instructors. The paper focuses on the technical development of the system with some results from an initial evaluation by four blind volunteers.
Cooperative Catalyst Effects in Palladium-Mediated Cyanation Reactions of Aryl Halides and Triflates (1998)

Substoichiometric quantities of copper or zinc species dramatically improve both conversion rate and efficiency of Pd(0)-catalyzed cyanation reactions. The optimum reaction conditions involve the use of a nitrile solvent, NaCN, and a catalyst system employing the combination of cuprous iodide with tetrakis(triphenylphosphine)palladium(0), [Pd(PPh3)4]. Beneficial effects were observed for the conversion of aryl halides, aryl triflates, and a vinyl bromide to the corresponding nitriles. The process was demonstrated on preparative scale with a broad range of aromatic and heteroaromatic substrates containing diverse functionality. A dual catalytic cycle is proposed to explain the profound influences of the cocatalyst system.