gebhart/patrepeval huggingface dataset:
The Neurite Retraction Induced by Lysophosphatidic Acid Increases Alzheimer's Disease-like Tau Phosphorylation (1999)

The bioactive phospholipid lysophosphatidic acid (LPA) causes growth cone collapse and neurite retraction in neuronal cells. These changes are brought about by the action of a cell surface receptor coupled to specific G proteins that control morphology and motility through the action of a group of small GTPases, the Rho family of proteins. Many studies have focused on actin reorganization modulated by Rho-GTPases, but almost no information has been obtained concerning microtubular network reorganization after LPA-induced neurite retraction. In the present study, we demonstrate an increase in site-specific Alzheimer's disease-like Tau phosphorylation during LPA-induced neurite retraction in differentiated SY-SH5Y human neuroblastoma cells. The phosphorylation state of Tau was inferred from its immunoreactivity with antibodies that recognize phosphorylation-sensitive epitopes. The effects of specific kinase inhibitors indicate that this phosphorylation is mediated by glycogen synthase kinase-3 (GSK-3). In support of this idea, we observed an increase of GSK-3 activity upon growth cone collapse. Our results are consistent with the hypothesis that activation of GSK-3 occurs in the Rho pathway and may represent an important link between microtubules and microfilaments dynamics during neuritogenesis and in pathological situations such as Alzheimer's disease.
Gene structure of human apolipoprotein Al (1983)

Apolipoprotein A1 is the major polypeptide of the human plasma high density lipoprotein (HDL). The structure and function of the apo A1 gene are of interest because of the inverse correlation shown between HDL levels and coronary heart disease. We have determined the nucleotide sequence of the apo A1 gene previously isolated. Its coding sequence is interrupted by two introns of 185 and 588 base pairs. As there may be one or more introns in the 5' non coding region, the 5' end of the gene could not be precisely located. The human apo A1 has an unusual propeptide segment very similar to its rat counterpart. The data reported here provide an essential basis for future studies of structural and functional alleles of the apo A1 gene.
Complete characterization of ultrashort pulse sources at 1550 nm (1999)

This paper reviews the use of frequency-resolved optical gating (FROG) to characterize mode-locked lasers producing ultrashort pulses suitable for high-capacity optical communications systems at wavelengths around 1550 nm, Second harmonic generation (SHG) FROG is used to characterize pulses from a passively mode-locked erbium-doped fiber laser, and both single-mode and dual-mode gain-switched semiconductor lasers. The compression of gain-switched pulses in dispersion compensating fiber is also studied using SHG-FROG, allowing optimal compression conditions to be determined without a priori assumptions about pulse characteristics. We also describe a fiber-based FROG geometry exploiting cross-phase modulation and show that it is ideally suited to pulse characterization at optical communications wavelengths. This technique has been used to characterize picosecond pulses with energy as low as 24 pJ, giving results in excellent agreement with SHG-FROG characterization, and without any temporal ambiguity in the retrieved pulse.
Alpha-Keto Acid Dehydrogenase Complexes (1996)

Found in all organisms, the alpha-keto acid dehydrogenase complexes have central roles in cellular metabolism and are major sites of regulation. The understanding of the organization, function and reg
Constrained Kalman filtering using pseudo-measurements (1995)

A novel solution to the problem of applying kinematic inequality constraints to a Kalman filter based radar tracker using pseudo-measurements is presented. The technique is demonstrated by applying height and speed constraints to a Cartesian radar tracking filter. (5 pages)
The treatment of malignant tumors by repeated inoculations of erysipelas. With a report of ten original cases. 1893. (1991)

William Bradley Coley (Fig. I) stemmed from old New England stock. After graduating from Yale in 1884. Coley spent two years in Portland, Oregon, teaching Latin and Greek before entering Harvard Medical School. After completing a competitive examination, he became an intern at the New York Hospital
Immunoreactive apolipoprotein E is a widely distributed cellular protein. Immunohistochemical localization of apolipoprotein E in baboon tissues. (1986)

Apolipoprotein (apo)E is an important protein determinant in cholesterol homeostasis in man. The protein is synthesized by the liver as well as by a number of extrahepatic tissues. In the present study, immunohistochemical techniques were used to identify apoE in specific cells in various baboon organs. In the 11 tissues studied, the following cell types have been found to harbor apoE immunoreactivity: cerebral astrocytes; thyroid follicular cells; alveolar type II pneumocytes; hepatocytes, and Kupffer cells; adrenocortical cells in zona fasciculata and zona reticularis; adrenal medullary cells; some renal tubular epithelia; some pancreatic islet cells; histiocytic macrophages in lymph nodes and the spleen; some gastric mucosal epithelia; and ovarian oocytes. These observations indicate the wide distribution of apoE in many organs and suggest that the protein might perform other important functions such as regulation of local hormonal homeostasis in addition to its role in cholesterol metabolism.
Electrochemical fabrication of ordered Bi2S3nanowire arrays (2001)

We have successfully fabricated ordered, well-crystallized Bi2S3 nanowire arrays embedded in the nanochannels of porous anodic aluminium oxide templates by direct current electrodeposition from a dimethylsulfoxide solution containing BiCl3 and elemental sulfur. X-ray diffraction and selected area electron diffraction investigations demonstrate that the Bi2S3 nanowires have an orthorhombic uniform structure. Electromicroscopy results show that the nanowires are quite ordered with diameters of about 40 nm and lengths up to 5 µm. X-ray energy dispersion analysis indicates that the atomic composition of Bi and S is very close to a 2 : 3 stoichiometry. The optical properties of these nanowires were characterized by optical absorption techniques. These studies reveal that the annealed Bi2S3 nanowires have an optical band edge (direct) of about 1.56 eV.
Pseudosubstrate regulation of the SCF β-TrCP ubiquitin ligase by hnRNP-U (2002)

beta-TrCP/E3RS (E3RS) is the F-box protein that functions as the receptor subunit of the SCF(beta-TrCP) ubiquitin ligase (E3). Surprisingly, although its two recognized substrates, IkappaB(alpha) and beta-catenin, are present in the cytoplasm, we have found that E3RS is located predominantly in the nucleus. Here we report the isolation of the major E3RS-associated protein, hnRNP-U, an abundant nuclear phosphoprotein. This protein occupies E3RS in a specific and stoichiometric manner, stabilizes the E3 component, and is likely responsible for its nuclear localization. hnRNP-U binding was abolished by competition with a pIkappaB(alpha) peptide, or by a specific point mutation in the E3RS WD region, indicating an E3-substrate-type interaction. However, unlike pI(kappa)Balpha, which is targeted by SCF(beta-TrCP) for degradation, the E3-bound hnRNP-U is stable and is, therefore, a pseudosubstrate. Consequently, hnRNP-U engages a highly neddylated active SCF(beta-TrCP), which dissociates in the presence of a high-affinity substrate, resulting in ubiquitination of the latter. Our study points to a novel regulatory mechanism, which secures the localization, stability, substrate binding threshold, and efficacy of a specific protein-ubiquitin ligase.
Affinity Isolation of Transcriptionally Active Murine Erythroleukemia Cell DNA Using a Cleavable Biotinylated Nucleotide Analog (1989)

We have developed an affinity technique to obtain active gene domains from murine erythroleukemia cell nuclei, based on the differential sensitivity of potentially active and inactive chromatin to DNase I. Nuclei isolated from potentially active noninduced cells and transcriptionally active induced MEL cells were treated with DNase I at concentrations which did not digest the beta-globin gene, followed by repair using a typical nick translation reaction during which a cleavable biotinylated nucleotide analog, 5-[N-biotinamido)hexanoamido-ethyl-1,3-dithiopropionyl -3-aminoallyl]-2'- deoxyuridine 5'-triphosphate (Bio-19-SS-dUTP), was inserted into DNA sequences. Following purification and digestion with EcoRI restriction endonuclease, biotinylated sequences were affinity isolated by sequential binding to streptavidin and biotincellulose. The streptavidin/biotin-cellulose complex bound up to 80% of the nick-translated DNA, which comprised a small percentage of the total nuclear DNA. Cleavage of the disulfide bond in the linker arm of the biotinylated nucleotide resulted in elution of virtually all of the affinity isolated sequences. Hybridization analysis of this fraction of DNA revealed up to a 16-fold enrichment for the active beta-globin gene, as compared with DNA which did not bind to the biotincellulose. Conversely, the inactive alpha-fetoprotein gene was barely detectable in affinity isolated DNA from noninduced cells and was 2-fold depleted in samples from induced cells.
Whole-Genome Transcription Profiling Reveals Genes Up-Regulated by Growth on Fucose in the Human Gut Bacterium “Roseburia inulinivorans” (2006)

"Roseburia inulinivorans" is an anaerobic polysaccharide-utilizing firmicute bacterium from the human colon that was identified as a producer of butyric acid during growth on glucose, starch, or inulin. R. inulinivorans A2-194 is also able to grow on the host-derived sugar fucose, following a lag period, producing propionate and propanol as additional fermentation products. A shotgun genomic microarray was constructed and used to investigate the switch in gene expression that is involved in changing from glucose to fucose utilization. This revealed a set of genes coding for fucose utilization, propanediol utilization, and the formation of propionate and propanol that are up-regulated during growth on fucose. These include homologues of genes that are implicated in polyhedral body formation in Salmonella enterica. Dehydration of the intermediate 1,2-propanediol involves an enzyme belonging to the new B12-independent glycerol dehydratase family, in contrast to S. enterica, which relies on a B12-dependent enzyme. A typical gram-positive agr-type quorum-sensing system was also up-regulated in R. inulinivorans during growth on fucose. Despite the lack of genome sequence information for this commensal bacterium, microarray analysis has provided a powerful tool for obtaining new information on its metabolic capabilities.
Preventive Effect of Argatroban on Ellagic Acid-Induced Cerebral Thromboembolism in Rats (1994)

The preventive effect of argatroban, a synthetic thrombin inhibitor, on cerebral infarction was evaluated with ellagic acid (EA)-induced cerebral thromboembolism in rats. Platelet-rich thrombi containing fibrin and EA crystal were formed in the microarteries in the affected hemisphere by the injection of EA suspension into the cerebral arteries. The mortality in saline control was over 80% 6 h after the EA injection. Argatroban decreased the mortality to 0% at a dose of 3 mg/kg/h, and significantly reduced the ischemic area in the affected cerebral hemisphere. Heparin also decreased the mortality to 30% at a dose of 600 U/kg/h, but marked bleeding was observed at the incised wound. These findings suggest that argatroban is a more effective and safer anticoagulant than heparin for the prevention of ischemic damage on cerebral thrombosis.
Rat Models of Traumatic Spinal Cord Injury to Assess Motor Recovery (2007)

Devastating motor, sensory, and autonomic dysfunctions render long-term personal hardships to the survivors of traumatic spinal cord injury (SCI). The suffering also extends to the survivors' families and friends, who endure emotional, physical, and financial burdens in providing for necessary surgeries, care, and rehabilitation. After the primary mechanical SCI, there is a complex secondary injury cascade that leads to the progressive death of otherwise potentially viable axons and cells and that impairs endogenous recovery processes. Investigations of possible cures and of ways to alleviate the hardships of traumatic SCI include those of interventions that attenuate or overcome the secondary injury cascade, enhance the endogenous repair mechanisms, regenerate axons, replace lost cells, and rehabilitate. These investigations have led to the creation of laboratory animal models of the different types of traumatic human SCI and components of the secondary injury cascade. However, no particular model completely addresses all aspects of traumatic SCI. In this article, we describe adult rat SCI models and the motor, and in some cases sensory and autonomic, deficits that each produces. Importantly, as researchers in this area move toward clinical trials to alleviate the hardships of traumatic SCI, there is a need for standardized small and large animal SCI models as well as quantitative behavioral and electrophysiological assessments of their outcomes so that investigators testing various interventions can directly compare their results and correlate them with the molecular, biochemical, and histological alterations.
Effect of intracerebroventricular infusion of epidermal growth factor in rats hemitransected in the nigro-striatal pathway. (1993)

The most recent attempt at surgical treatment of Parkinson's disease is represented by implant of dopaminergic tissue in the striate nuclei. Growth factors have been associated to the neural implants in order to favor successful grafting and functional survival. Among diverse growth factors Epidermal Growth Factor (EGF) is active in vitro on axonal regeneration of dopaminergic cells of the substantia nigra. Our research group has recently assessed the effect of a 35-day delayed intracerebroventricular infusion of EGF on the survival and function of the dopaminergic neurons in rats made hemiparkinsonian by unilateral mechanical transection of rat nigrostriatal pathway. EGF infusion resulted in a two-fold increase in the number of surviving tyrosine hydroxylase (TH)-positive substantia nigra neurons and a significant increase in ipsilateral striatal TH-positive fiber staining compared to controls. In addition there was a persistent enhancement of behavioral recovery, as indicated by a reduction in amphetamine-induced rotations. In the present study EGF is tested at a lower dosage starting administration at the time of lesion. Effects have been assessed by the available functional and biochemical methods. Results confirm that neurotrophic effect of EGF on dopaminergic neurons in the nigro-striatal pathways follow early administration also at low dosage.
Repair of Articular Cartilage Defects with Collagen–Chondrocyte Allografts (1995)

This study was designed to evaluate the potential use of a prototype collagen-chondrocyte allograft in the repair of full-thickness articular cartilage defects. Articular cartilage was harvested from young donor New Zealand White rabbits, enzymatically digested, cultured in monolayer, and passed into a three-dimensional porous type I collagen sponge (American Biomaterials). The composite grafts were incubated for 1 week. (Phase I) Twenty adult NZW rabbits underwent bilateral knee arthrotomies. Three-millimeter full-thickness articular cartilage defects were made in the trochlea of the distal femur. A 4-mm circular punch from the composite cell-seeded grafts was press-fit into the right knee defects. The left knee served as a control (collagen sponge alone or ungrafted defect). Animals were allowed free activity postoperatively and were killed in groups of five at 4, 8, 12, and 24 weeks postoperatively. Defect areas were harvested. Sections were cut at 5-microm thickness and stained with hematoxylin and eosin. The degree as well as quality of healing were assessed and scored with a grading system modified from Salter and O'Driscoll for cartilage repair. (The maximum score was 24 points.) Safranin-O staining as well as polarized light examination of representative sections was undertaken to assess the proteoglycan content and structural characteristics of the repair matrix. (Phase II) An additional 15 NZW rabbits underwent the above procedure but with the addition of fibroblast growth factor (FGF) (100 ng/ml) and insulin (5 microg/ml) to the growth medium of the composite grafts as stimulators of chondrocyte proliferation and proteoglycan synthesis. Control specimens in phase I and II (collagen sponge alone or ungrafted defects) healed with a primarily fibrous or fibrocartilagenous matrix. Defects grafted with cell-seeded collagen sponges demonstrated enhanced healing at all time points examined when compared to controls. There was a strong tendency toward a hyaline appearing matrix with increased Safranin-O staining and birefringence under polarized light more closely resembling the normal native cartilage. Mean histologic score for grafted defects was 18.4 (+/-3.1). Mean scores for collagen sponge alone and ungrafted defects in phase I were 12.7 (+/-4) and 12.7 (+/-3.1) (P<0.01). The addition of FGF and insulin to the growth medium (phase II) resulted in a significantly enhanced repair matrix when compared to the non-FGF-enhanced grafts, with a greater percentage of hyaline appearing tissue at all time points examined (4,8, and 12 weeks). Organization of the chondrocytes was improved at all time points examined as well. Mean histologic score for the FGF-grafted defects was 21.1 (+/-3.0). Mean scores for collagen sponge alone and ungrafted defects in phase II were 14.9 (+/-2.9) and 15.5 (+/-1.9) (p<0.01).
Self-Diffusion Coefficient and Viscosity in Liquids (1955)

The relation between self-diffusion coefficient and viscosity is examined in terms of the early hydrodynamic theory and Eyring's kinetic theory. They differ by a factor of about 6. A detailed consideration of the kinetic theory shows that this factor should have been included in Eyring's derivation of viscosity if a proper meaning is given to the relative velocity involved.
Improving the approximation ability of Volterra series identified with a cross-correlation method (2014)

This paper proposes an improvement in cross-correlation methods derived from the Lee–Schetzen method, in order to obtain a lower mean square error in the output for a wider range of the input variances. In particular, each Wiener kernel is identified with a different input variance and new formulas for conversion from Wiener to Volterra representation are presented.
Brèves notules (1988)

Bertrand Marc. Brèves notules. In: L'Information Grammaticale, N. 38, 1988. pp. 19-20.
Neural Point-and-Click Communication by a Person With Incomplete Locked-In Syndrome (2014)

A goal of brain-computer interface research is to develop fast and reliable means of communication for individuals with paralysis and anarthria. We evaluated the ability of an individual with incomplete locked-in syndrome enrolled in the BrainGate Neural Interface System pilot clinical trial to communicate using neural point-and-click control. A general-purpose interface was developed to provide control of a computer cursor in tandem with one of two on-screen virtual keyboards. The novel BrainGate Radial Keyboard was compared to a standard QWERTY keyboard in a balanced copy-spelling task. The Radial Keyboard yielded a significant improvement in typing accuracy and speed-enabling typing rates over 10 correct characters per minute. The participant used this interface to communicate face-to-face with research staff by using text-to-speech conversion, and remotely using an internet chat application. This study demonstrates the first use of an intracortical brain-computer interface for neural point-and-click communication by an individual with incomplete locked-in syndrome.
Size dependence of exciton fine structure in CdSe quantum dots (1996)

We use photoluminescence excitation and fluorescence line narrowing spectroscopies to examine structure observed in the band-edge absorption feature of CdSe quantum dots. We study eight samples ranging from \ensuremath{\sim}15 to \ensuremath{\sim}50 \AA{} in radius to probe the size dependence of this structure. We compare our results with recent theories, which predict band-edge exciton splittings in CdSe dots due to their internal crystal structure, nonspherical shape, and the exchange interaction between the electron and hole. We find reasonable agreement between our data and theory, supporting the observation of exciton fine structure. \textcopyright{} 1996 The American Physical Society.
Messages in Molecules: Ligand/Cation Coding and Self‐Recognition in a Constitutionally Dynamic System of Heterometallic Double Helicates (2006)

Double helicates are known to exhibit self-recognition characteristics determined by the coordination geometry of the metal involved as well as by the topicity of the ligands. Combining tridentate (terpyridine, T) or bidentate (bipyridine, B) subunits in a tritopic strand affords a set of ligands able to assemble by pairs to form double helicates, homo- or heterostranded, homo- or heterotopic, depending on the coordination properties of the metals involved. The four ligand strands, BBB, TTT, BBT, and TBT form constitutionally dynamic sets of double helicates with the metal ions Cu(I), Cu(II), and Zn(II); these helicates correspond to the correct coding of the BB, BT, and TT pairs for tetra-, penta-, and hexacoordinate Cu(I), Cu(II), and Zn(II) cations, respectively.
Update of the pompe disease mutation database with 60 novel GAA sequence variants and additional studies on the functional effect of 34 previously reported variants (2012)

Pompe disease is an autosomal recessive lysosomal glycogen storage disorder, characterized by progressive muscle weakness. Deficiency of acid α-glucosidase (EC; 3.2.1.20/3) can be caused by numerous pathogenic variants in the GAA gene. The Pompe Disease Mutation Database at http://www.pompecenter.nl aims to list all variants and their effect. This update reports on 94 variants. We examined 35 novel and 34 known mutations by site-directed mutagenesis and transient expression in COS-7 cells or HEK293T cells. Each of these mutations was given a severity rating using a previously published system, based on the level of acid α-glucosidase activity in medium and transfected cells and on the quantity and quality of the different molecular mass species in the posttranslational modification and transport of acid α-glucosidase. This approach enabled to classify 55 missense mutations as pathogenic and 13 as likely nonpathogenic. Based on their nature and the use of in silico analysis (Alamut® software), 12 of the additional 25 novel mutations were predicted to be pathogenic including 4 splicing mutations, 6 mutations leading to frameshift, and 2 point mutations causing stop codons. Seven of the additional mutations were considered nonpathogenic (4 silent and 3 occurring in intron regions), and 6 are still under investigation.