gebhart/patrepeval huggingface dataset:
Glutamate Transporters and the Excitotoxic Path to Motor Neuron Degeneration in Amyotrophic Lateral Sclerosis (2009)

Responsible for the majority of excitatory activity in the central nervous system (CNS), glutamate interacts with a range of specific receptor and transporter systems to establish a functional synapse. Excessive stimulation of glutamate receptors causes excitotoxicity, a phenomenon implicated in both acute and chronic neurodegenerative diseases [e.g., ischemia, Huntington's disease, and amyotrophic lateral sclerosis (ALS)]. In physiology, excitotoxicity is prevented by rapid binding and clearance of synaptic released glutamate by high-affinity, Na(+)-dependent glutamate transporters and amplified by defects to the glutamate transporter and receptor systems. ALS pathogenetic mechanisms are not completely understood and characterized, but excitotoxicity has been regarded as one firm mechanism implicated in the disease because of data obtained from ALS patients and animal and cellular models as well as inferred by the documented efficacy of riluzole, a generic antiglutamatergic drug, has in patients. In this article, we critically review the several lines of evidence supporting a role for glutamate-mediated excitotoxicity in the death of motor neurons occurring in ALS, putting a particular emphasis on the impairment of the glutamate-transport system.
Genetic Analysis of Salt-Tolerant Mutants in Arabidopsis thaliana (2000)

Stress caused by the increased salinity of irrigated fields impairs plant growth and is one of the major constraints that limits crop productivity in many important agricultural areas. As a contribution to solving such agronomic problems, we have carried out a large-scale screening for Arabidopsis thaliana mutants induced on different genetic backgrounds by EMS treatment, fast neutron bombardment, or T-DNA insertions. From the 675,500 seeds we screened, 17 mutant lines were isolated, all but one of which yielded 25-70% germination levels on 250 mm NaCl medium, a condition in which their ancestor ecotypes are unable to germinate. Monogenic recessive inheritance of NaCl-tolerant germination was displayed with incomplete penetrance by all the selected mutants, which fell into five complementation groups. These were named SALOBRENO (SAN) and mapped relative to polymorphic microsatellites, the map positions of three of them suggesting that they are novel genes. Strains carrying mutations in the SAN1-SAN4 genes display similar responses to both ionic effects and osmotic pressure, their germination being NaCl and mannitol tolerant but KCl and Na(2)SO(4) sensitive. In addition, NaCl-, KCl-, and mannitol-tolerant as well as abscisic-acid-insensitive germination was displayed by sañ5, whose genetic and molecular characterization indicates that it carries an extremely hypomorphic or null allele of the ABI4 gene, its deduced protein product lacking the APETALA2 DNA binding domain.
Guidelines for the Use of Molecular Biological Methods to Detect Sexually Transmitted Pathogens in Cases of Suspected Sexual Abuse in Children (2012)

Testing for sexually transmitted infections (STIs) in children presents a number of problems for the practitioner that are not usually faced when testing adults for the same infections. The identification of an STI in a child, in addition to medical implications, can have serious legal implications. The presence of an STI is often used to support the presence or allegations of sexual abuse and conversely, the identification of an STI in a child will prompt an investigation of possible abuse. The significance of the identification of a sexually transmitted agent in such children as evidence of possible child sexual abuse varies by pathogen.While culture has historically been used for the detection of STIs in cases of suspected abuse in children, the increasing use of nucleic acid amplification tests (NAATs) in adults and the increasing proliferation of second-generation tests with better sensitivity and specificity has made inroads into the use of such tests in children, especially for diagnostic and treatment purposes. Acceptance by the medicolegal system for sexual abuse cases is still controversial and more test cases will be necessary before definitive use becomes standard practice. In addition, if these assays ever become legally admissible in court, there will be recommendations that more than one NAAT assay be used in order to assure confirmation of the diagnostic result.
Assessment of GFP Tag Position on Protein Localization and Growth Fitness in Yeast (2018)

While protein tags are ubiquitously utilized in molecular biology, they harbor the potential to interfere with functional traits of their fusion counterparts. Systematic evaluation of the effect of protein tags on function would promote accurate use of tags in experimental setups. Here we examine the effect of green fluorescent protein tagging at either the N or C terminus of budding yeast proteins on subcellular localization and functionality. We use a competition-based approach to decipher the relative fitness of two strains tagged on the same protein but on opposite termini and from that infer the correct, physiological localization for each protein and the optimal position for tagging. Our study provides a first of a kind systematic assessment of the effect of tags on the functionality of proteins and provides a step toward broad investigation of protein fusion libraries.
Les spécificites juridiques de l'administration et du pilotage de la recherche (2004)

<titre>The Legal Particularities of Research Administration and Piloting &#8212; the 1982 and 1985 Acts on Research Orientation and Planning of Research </titre> The 15 July 1982 and 23 December 1985 Acts on research orientation and planning aims to are at the origin of the majority of tools for the piloting of public and even private research, of there are of greater legal specificity compared to other administrative tools. At a time when the Minister of Education and Research is planning to present a Research Act to Parliament, it is useful to go back to these texts, which lay the groundwork for the present landscape of French research. All the more so since the recent publication of the legislative part of the code of research unfortunately does not show the coherence of these two laws.
ARIA: A Neuromuscular Junction Neuregulin (1997)

Motor neurons influence the expression and the distribution of acetylcholine receptors in skeletal muscle. Molecules that mediate this carefully choreographed interaction have recently been identified. One of them, ARIA, is a polypeptide purified from chicken brain on the basis of its ability to stimulate the synthesis of muscle acetylcholine receptors. The predicted amino acid sequence suggests that ARIA is synthesized as a transmembrane precursor protein and that it is a member of a family of ligands that activate receptor tyrosine kinases related to the epidermal growth factor receptor. Certain features of the ligand family (the neuregulins) and their receptors (erbBs) are reviewed. Evidence that ARIA plays an important role at developing and mature neuromuscularjunctions is discussed.
“Endogenous adjuvant” activity of the RNA components of lupus autoantigens Sm/RNP and Ro 60 (2006)

We conclude that the RNA components of the Ro 60 (Y1-Y5 RNA) and Sm/RNP (U1 RNA) small ribonucleoproteins act as endogenous adjuvants that could play a role in the pathogenesis of autoimmunity by stimulating DC maturation and IFN-I production.
Amphiphilic Corannulene Derivatives: Synthetic Access and Development of a Structure/Property Relationship in Thermoresponsive Buckybowl Amphiphiles (2017)

Eight new derivatives of corannulene have been synthesized, characterized, and examined for their water solubility and thermally triggered assembly behavior. To achieve this, the hydrophobic corannulene core was attached to the hydrophilic polyethylene glycol arm(s). Here, the substitution pattern as well as the arm length was varied systematically. Furthermore, the hydrophobic/hydrophilic ratio was adjusted by incorporating a phenyl ring at the junction point of the two moieties. A properties study revealed that a proper balance among the number, length, and chemical nature of the arm was required to ensure water solubility and thermoresponsive character. Remarkably, the lower critical solution temperature could be modulated within the range of 30-50 °C simply through adjusting the molecular structure of the assembling building block. This work, therefore, demonstrates synthetic feasibility of a wide range of amphiphilic corannulene derivatives and opportunity for modulation of their thermoresponsive behavior.
Emergence of Early Region 1-Containing Replication-Competent Adenovirus in Stocks of Replication-Defective Adenovirus Recombinants (ΔE1 + ΔE3) During Multiple Passages in 293 Cells (1994)

Early region 1 (E1)-deleted human adenovirus (AV) recombinants have been shown to be powerful tools of gene transfer in vivo and in vitro and are considered for application in human gene therapy. We could detect increasing titers of E1-containing adenovirus in two independent E1 + E3-deleted recombinant AV stocks during multiple passages in 293 cells, most likely due to a recombinant event with the host cell genome. We show the deleterious effects of this E1-containing, mostly replication-competent AV subpopulation in vivo and compare different screening methods of AV stocks for its detection. These considerations are important for the safety of human gene therapy trials.
Sustained activation of SMAD3/SMAD4 by FOXM1 promotes TGF-β–dependent cancer metastasis (2014)

A key feature of TGF-β signaling activation in cancer cells is the sustained activation of SMAD complexes in the nucleus; however, the drivers of SMAD activation are poorly defined. Here, using human and mouse breast cancer cell lines, we found that oncogene forkhead box M1 (FOXM1) interacts with SMAD3 to sustain activation of the SMAD3/SMAD4 complex in the nucleus. FOXM1 prevented the E3 ubiquitin-protein ligase transcriptional intermediary factor 1 γ (TIF1γ) from binding SMAD3 and monoubiquitinating SMAD4, which stabilized the SMAD3/SMAD4 complex. Loss of FOXM1 abolished TGF-β-induced SMAD3/SMAD4 formation. Moreover, the interaction of FOXM1 and SMAD3 promoted TGF-β/SMAD3-mediated transcriptional activity and target gene expression. We found that FOXM1/SMAD3 interaction was required for TGF-β-induced breast cancer invasion, which was the result of SMAD3/SMAD4-dependent upregulation of the transcription factor SLUG. Importantly, the function of FOXM1 in TGF-β-induced invasion was not dependent on FOXM1's transcriptional activity. Knockdown of SMAD3 diminished FOXM1-induced metastasis. Furthermore, FOXM1 levels correlated with activated TGF-β signaling and metastasis in human breast cancer specimens. Together, our data indicate that FOXM1 promotes breast cancer metastasis by increasing nuclear retention of SMAD3 and identify crosstalk between FOXM1 and TGF-β/SMAD3 pathways. This study highlights the critical interaction of FOXM1 and SMAD3 for controlling TGF-β signaling during metastasis.
Extraction of Nucleic Acids from Lyophilized Plant Material (1966)

Four methods for extracting nucleic acids from lyophilized cotton (Gossypium hirsutum L. cv. Stoneville 62) leaves and roots were compared. They were based on the use of: (I) HC10(4); (II) KOH; (III) a mixture of 90% phenol, Tris (hydroxymethyl) aminomethane buffer, and sodium lauryl sulfate; and (IV) NaCl. (I) extracted large amounts of RNA but little DNA and extracted much carbohydrate and protein contaminants. (II) gave a good yield of both RNA and DNA but extracted such large amounts of contaminating material that purification of RNA on an anion exchange column was necessary. (III) extracted only part of the RNA and practically no DNA, but extracted contaminating materials. (IV) resulted in high yields of both RNA and DNA when modified to omit preliminary acid extraction of impurities. The use of cold trichloroacetic acid instead of ethanol, to precipitate NaCl-extracted nucleic acids, separated the nucleic acids from most of the carbohydrate and acid-soluble phosphate contaminants and resulted in good agreement among results by ultraviolet absorbance, pentose tests, and phosphate analysis. This method also resulted in lower protein contents and better ultraviolet absorption spectra than the other methods tested. Nucleic acids were extracted from leaves of 14 other species of plants, in addition to cotton, by this modified NaCl procedure.
Essential role of vif in establishing productive HIV-1 infection in peripheral blood T lymphocytes and monocyte/macrophages. (1994)

The role of vif during the establishment of human immunodeficiency virus type 1 (HIV-1) infection of peripheral blood T lymphocytes and monocyte/macrophages was investigated using vif mutants of three HIV-1 proviral DNAs. Vif was found to be essential for the establishment of productive HIV-1 infection in peripheral blood T lymphocytes after cell-free infection with HXB2 and DFCI-HD, a vpr-positive, vpu-positive, nef-positive derivative of HXB2. A chimeric HIV-1 provirus in which the T-cell line-tropic env sequences in DFCI-HD were replaced with the macrophagetropic env of the ADA strain was constructed for studies on the role of vif during the establishment of HIV-1 infection in primary monocyte/macrophages. These studies showed that vif is also essential for the initiation of productive HIV-1 infection in primary monocyte/macrophage cultures after cell-free virus transmission. The DFCI-HD-ADA virus was shown to replicate in the CD4+ T-cell line Molt 4 clone 8 but not in other T-cell or monocytic cell lines, as previously shown for another macrophagetropic strain YU-2 (1), suggesting that this cell line may be useful for future studies on at least some macrophagetropic strains of HIV-1. The finding that vif is essential for the establishment of productive HIV-1 infection in primary T lymphocytes and monocyte/macrophages suggests that vif may be required for HIV-1 transmission and disease pathogenesis during natural infections and thus may be a good target for prophylactic or therapeutic intervention.
Bioengineered Cardiac Grafts (2000)

Background —The myocardium is unable to regenerate because cardiomyocytes cannot replicate after injury. The heart is therefore an attractive target for tissue engineering to replace infarcted myocardium and enhance cardiac function. We tested the feasibility of bioengineering cardiac tissue within novel 3-dimensional (3D) scaffolds. Methods and Results —We isolated and grew fetal cardiac cells within 3D porous alginate scaffolds. The cell constructs were cultured for 4 days to evaluate viability and morphology before implantation. Light microscopy revealed that within 2 to 3 days in culture, the dissociated cardiac cells form distinctive, multicellular contracting aggregates within the scaffold pores. Seven days after myocardial infarction, rats were randomized to biograft implantation (n=6) or sham-operation (n=6) into the myocardial scar. Echocardiography study was performed before and 65±5 days after implantation to assess left ventricular (LV) remodeling and function. Hearts were harvested 9 weeks after implantation. Visual examination of the biograft revealed intensive neovascularization from the neighboring coronary network. Histological examination revealed the presence of myofibers embedded in collagen fibers and a large number of blood vessels. The specimens showed almost complete disappearance of the scaffold and good integration into the host. Although control animals developed significant LV dilatation accompanied by progressive deterioration in LV contractility, in the biograft-treated rats, attenuation of LV dilatation and no change in LV contractility were observed. Conclusions —Alginate scaffolds provide a conducive environment to facilitate the 3D culturing of cardiac cells. After implantation into the infarcted myocardium, the biografts stimulated intense neovascularization and attenuated LV dilatation and failure in experimental rats compared with controls. This strategy can be used for regeneration and healing of the infarcted myocardium.
Low power systems for wireless microsensors (2002)

Low power wireless sensor networks provide a new monitoring and control capability for civil and military applications in transportation, manufacturing, biomedical, environmental management, and safety and security systems. Wireless microsensor network nodes, operating at average and peak power levels constrained by compact power sources, offer a range of important challenges for low power methods. This paper reports advances in low power systems spanning network design, through power management, low power mixed signal circuits, and highly integrated RF network interfaces. Particular attention is focused on methods for low power RF receiver systems.
Evidence for a relation between inspired gas mixture and the left ventricular contrast achieved with albunex® in a Canine Model (1996)

These findings show an important relationship between the FIO2 and loss of the contrast effect of Albunex. This loss occurs at oxygen concentrations in the therapeutic range, but could be overcome by increasing the dose of Albunex. The mechanism is likely related to an outward nitrogen gradient causing a loss of echogenicity. The clinical implication is that patients on supplemental oxygen may require higher doses of Albunex to achieve optimal opacification.
Expression of Interleukin-1β Converting Enzyme Gene Family and bcl-2 Gene Family in the Rat Brain following Permanent Occlusion of the Middle Cerebral Artery (1997)

Recent investigations have been suggesting that some neuronal subpopulations may die via programmed cell death after focal ischemic injury. To clarify the possible roles of the genes involved in the cell-death program, this study examined the expression of three members of the interleukin-1 beta converting enzyme (Ice) gene family (Ice, Nedd2, and Yama/CPP32) and two members of the bcl-2 gene family (bcl-2 and bcl-x) in the rat brain after permanent occlusion of the middle cerebral artery. Northern blot analysis revealed a transient induction of Nedd2 mRNA 8 h after the ischemic insult (3.8-fold) and an increase in Yama/CPP32 mRNA 16 to 24 h after the insult (5.8-fold at 24 h), whereas the expression of Ice remained constant. The expression of bcl-2 and bcl-x remained constant after the ischemic insult. Taking into account the key role of the Ice gene family in the execution of programmed cell death, the induction of Ice gene family might play a causative role in apoptotic cell death.
Symptoms of Hypoglycaemia and Effects on Mental Performance and Emotions (2007)

This chapter contains sections titled: Introduction Symptoms of Hypoglycaemia Acute Hypoglycaemia and Cognitive Functioning Acute Hypoglycaemia and Emotions Conclusions References
DNase-seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements across the Genome from Mammalian Cells (2010)

INTRODUCTION Identification of active gene regulatory elements is a key to understanding transcriptional control governing biological processes such as cell-type specificity, differentiation, development, proliferation, and response to the environment. Mapping DNase I hypersensitive (HS) sites has historically been a valuable tool for identifying all different types of regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. This method utilizes DNase I to selectively digest nucleosome-depleted DNA (presumably by transcription factors), whereas DNA regions tightly wrapped in nucleosome and higher-order structures are more resistant. The traditional low-throughput method for identifying DNase I HS sites uses Southern blots. Here, we describe the complete and improved protocol for DNase-seq, a high-throughput method that identifies DNase I HS sites across the whole genome by capturing DNase-digested fragments and sequencing them by high-throughput, next-generation sequencing. In a single experiment, DNase-seq can identify most active regulatory regions from potentially any cell type, from any species with a sequenced genome.
Pharmacokinetics and red cell utilization of iron(III) hydroxide–sucrose complex in anaemic patients: a study using positron emission tomography (1999)

The pharmacokinetics of a single intravenous injection of 100 mg iron hydroxide-sucrose complex labelled with a tracer in the form of 52Fe/59Fe was followed in six anaemic patients for a period ranging from 6 to 8 3 h using positron emission tomography (PET). Red cell utilization of the labelled iron was followed for 4 weeks. PET data showed radioactive uptake by the liver, spleen and bone marrow. The uptake by the macrophage-rich spleen demonstrated the reticuloendothelial uptake of this iron preparation, with subsequent effective release of that iron for marrow utilization. Red cell utilization, followed for 4 weeks, ranged from 59% to 97%. The bone marrow influx rate constant was independent of blood iron concentration, indicating non-saturation of the transport system in bone marrow. This implied that higher doses of the iron complex can probably be used in the same setting. A higher influx rate into the marrow compared with the liver seemed to be consistent with higher red cell utilization. This would indicate that early distribution of the injected iron complex may predict the long-term utilization.
Conservation of the hedgehog/patched signaling pathway from flies to mice: induction of a mouse patched gene by Hedgehog. (1996)

The signaling protein Hedgehog (Hh) controls cell fate and polarizes tissues in both flies and vertebrates. In flies, Hh exerts its effects by opposing the function of a novel transmembrane protein, Patched, while also locally inducing patched (ptc) transcription. We have identified a mouse homolog of ptc which in many tissues is transcribed near cells making either Sonic or Indian hedgehog. In addition, ectopic Sonic hedgehog expression in the mouse central nervous system induces ptc transcription. As in flies, mouse ptc transcription appears to be indicative of hedgehog signal reception. The results support the existence of a conserved signaling pathway used for pattern formation in insects and mammals.
Neuroprotection by glial metabotropic glutamate receptors is mediated by transforming growth factor-beta. (1998)

The medium collected from cultured astrocytes transiently exposed to the group-II metabotropic glutamate (mGlu) receptor agonists (2S,1'R, 2'R,3'R)-2-(2,3-dicarboxycyclopropyl)glycine (DCG-IV) or (S)-4-carboxy-3-hydroxyphenylglycine (4C3HPG) is neuroprotective when transferred to mixed cortical cultures challenged with NMDA (). The following data indicate that this particular form of neuroprotection is mediated by transforming growth factor-beta (TGFbeta). (1) TGFbeta1 and -beta2 were highly neuroprotective against NMDA toxicity, and their action was less than additive with that produced by the medium collected from astrocytes treated with DCG-IV or 4C3HPG (GM/DCG-IV or GM/4C3HPG); (2) antibodies that specifically neutralized the actions of TGFbeta1 or -beta2 prevented the neuroprotective activity of DCG-IV or 4C3HPG, as well as the activity of GM/DCG-IV or GM/4C3HPG; and (3) a transient exposure of cultured astrocytes to either DCG-IV or 4C3HPG led to a delayed increase in both intracellular and extracellular levels of TGFbeta. We therefore conclude that a transient activation of group-II mGlu receptors (presumably mGlu3 receptors) in astrocytes leads to an increased formation and release of TGFbeta, which in turn protects neighbor neurons against excitotoxic death. These results offer a new strategy for increasing the local production of neuroprotective factors in the CNS.