gebhart/patrepeval huggingface dataset:
Polymeric nanoparticles for the drug delivery to the central nervous system (2008)

Polymeric Np have been shown to be promising carriers for CNS drug delivery due to their potential both in encapsulating drugs, hence protecting them from excretion and metabolism, and in delivering active agents across the blood-brain barrier without inflicting any damage to the barrier. Different polymers have been used and different strategies have been applied; among these, the use of specific ligands to enhance the specificity of drugs delivered to the CNS has recently been considered. At present, clinical trials are being conducted appeared for the use of these drug carriers but none related to the treatment of CNS diseases.
Apoptosis signalling by 4-hydroxynonenal: a role for JNK–c-Jun/AP-1 pathway (2007)

4-Hydroxynonenal (HNE) is one of the most abundant aldehyde components of ox-LDL and it exerts various effects on intracellular and extracellular signaling cascades. In this mini-review, a brief synopsis of HNE-modulated signaling pathways will be presented mainly focused on cell death, including recent studies from our laboratory. The results of a number of studies demonstrate the ability of HNE to induce apoptosis and ROS formation in a dose-dependent manner. Several signaling pathways have been shown to be modulated by HNE, including MAP kinases, PKC isoforms, cell-cycle regulators, receptor tyrosine kinases and caspases. In order to get insight into the mechanisms of apoptotic response by HNE, MAP kinase and caspase activation pathways have been studied in 3T3 fibroblasts; HNE induced early activation of JNK and p38 proteins but down-regulated the basal activity of ERK-1/2. We have shown that HNE-induced release of cytochrome c from mitochondria, caspase-9 and caspase-3 activation. Activation of AP-1 along with increased c-Jun and phospho-c-Jun levels could be inhibited by pretreatment of cells with certain molecules such as resveratrol. Additionally, overexpression of dominant negative c-Jun and JNK1 in 3T3 fibroblasts prevented HNE-induced apoptosis, which indicated a role for JNK-c-Jun/AP-1 pathway. JNK-dependent induction of c-Jun/AP-1 activation data in the literature indicates a critical potential role for JNK in the cellular response against toxic products of lipid peroxidation.
Addressing hard classical problems with Adiabatically Assisted Variational Quantum Eigensolvers (2018)

We present a hybrid classical-quantum algorithm to solve optimization problems in current quantum computers, whose basic idea is to assist variational quantum eigensolvers (VQE) with adiabatic change of the Hamiltonian. The rational for this new algorithm is to circumvent the problem of facing very small gradients in the classical optimization piece of a VQE, while being able to run in current hardware efficient devices. A discrete concatenation of VQEs adapted to interpolating Hamiltonians provides a method to keep the quantum state always close to a path faithfully directed to find the final solution. We benchmark this Adiabatically Assisted Variational Quantum Eigensolver (AAVQE) on quantum Hamiltonians and hard classical problems, for which our approach shows fast convergence.
2-Amino-3,4-dihydroquinazolines as Inhibitors of BACE-1 (β-Site APP Cleaving Enzyme):  Use of Structure Based Design to Convert a Micromolar Hit into a Nanomolar Lead (2007)

A new aspartic protease inhibitory chemotype bearing a 2-amino-3,4-dihydroquinazoline ring was identified by high-throughput screening for the inhibition of BACE-1. X-ray crystallography revealed that the exocyclic amino group participated in a hydrogen bonding array with the two catalytic aspartic acids of BACE-1 (Asp(32), Asp(228)). BACE-1 inhibitory potency was increased (0.9 microM to 11 nM K(i)) by substitution into the unoccupied S(1)' pocket.
Synthesis of new tetrazines functionalized with photoactive and electroactive groups (2012)

Au cours de cette thèse, nous avons préparé différents classes de dérives de la s-tétrazine et étudies leurs propriétés de électrochimiques et de fluorescence. Dans la première partie, nous présentons une étude bibliographique de la tétrazine, principalement centre sur sa synthèse et ses propriétés. Dans le second chapitre, nous introduirons des nouveaux récepteurs de paires d ions basés sur des bis-tétrazines. Ces récepteurs utilisent des interactions de type pi-anion, qui ont été rarement observées en solution, pour effectuer la reconnaissance. La complexation de ces récepteurs avec des sels d halogénure d ammonium (C8H17NH3Br et C8H17NH3I) a été démontrée par RMN et fluorescence. Il est démontré que le récepteur 82 forme des complexes plus stables avec les ammoniums que ces équivalents 80 et 81 à chaine plus courte. De plus, tous ces récepteurs présentent une sélectivité inattendue envers les halogènes suivant l ordre : I-&gt;Br-&gt;Cl-. Enfin, une réaction secondaire a été mise en évidence par spectroscopie d absorption qui conduit a la formation de Br2 ou I2. Un mécanisme probable pour cette réaction est propose au vu de tous les résultats spectroscopiques. Dans le troisième partie, de nombreux dérivés de la tétrazine portant des substituants de nature diverse ont été obtenus afin de mieux comprendre les propriétés physico-chimiques de cet aromatique. Il apparait clairement que les propriétés électrochimiques ne dépendent pas de la taille mais seulement de l électronégativité du substituant. De plus, des groupes électrodonneurs conduisent à une inhibition de la fluorescence même s ils ne sont pas directement liés. Une nouvelle classe de dérives de la s-tétrazine a été obtenue grâce à une nouvelle réaction des chlorotétrazines. Cette réaction conduit a l obtention de dérivés non symétriques portant un hétéroatome et une chaine alkyle qui seront utiles pour de développements futurs. Dans la dernière partie, nous présentons de nouvelles dyades a base de tétrazine présentant une brillance améliorée. Ces dyades sont basées sur un transfert d énergie entre un donneur (benzimidazole ou naphtalimide) et un accepteur (la tétrazine). Elles présentent des bons rendements quantiques de fluorescence, des durées de vie allongées et des brillances améliorées. L un de ces dérivés a été utilisé pour fabriquer une cellule fluorescente à trois couleurs contrôlable par électrochimie.
General Sonochemical Method for the Preparation of Nanophasic Selenides:  Synthesis of ZnSe Nanoparticles (1999)

ZnSe nanoparticles of about 3 nm in size have been prepared by the sonochemical irradiation of an aqueous solution of selenourea and zinc acetate under argon. The ZnSe nanoparticles were characterized using techniques such as transmission electron microscopy, X-ray diffraction, absorption spectroscopy, differential scanning calorimetry, transmission and diffuse reflection spectroscopy, photoluminescence spectroscopy, and energy-dispersive X-ray analysis. The mechanism of the sonochemical irradiation is discussed. This sonochemical method was found to be a general method for the preparation of other selenides as well.
Kinetic Characterization of a Monomeric Unconventional Myosin V Construct (1999)

An expressed, monomeric murine myosin V construct composed of the motor domain and two calmodulin-binding IQ motifs (MD(2IQ)) was used to assess the regulatory and kinetic properties of this unconventional myosin. In EGTA, the actin-activated ATPase activity of MD(2IQ) was 7.4 +/- 1.6 s(-1) with a K(app) of approximately 1 microM (37 degrees C), and the velocity of actin movement was approximately 0.3 micrometer/s (30 degrees C). Calcium inhibited both of these activities, but the addition of calmodulin restored the values to approximately 70% of control, indicating that calmodulin dissociation caused inhibition. In contrast to myosin II, MD(2IQ) is highly associated with actin at physiological ionic strength in the presence of ATP, but the motor is in a weakly bound conformation based on the pyrene-actin signal. The rate of dissociation of acto-MD(2IQ) by ATP is fast (>850 s(-1)), and ATP hydrolysis occurs at approximately 200 s(-1). The affinity of acto-MD(2IQ) for ADP is somewhat higher than that of smooth S1, and ADP dissociates more slowly. Actin does not cause a large increase in the rate of ADP release, nor does the presence of ADP appreciably alter the affinity of MD(2IQ) for actin. These kinetic data suggest that monomeric myosin V is not processive.
X-ray Structure and Ligand Binding Study of a Moth Chemosensory Protein (2002)

Chemosensory proteins (CSPs) are believed to be involved in chemical communication and perception. Such proteins, of M(r) 13,000, have been isolated from several sensory organs of a wide range of insect species. Several CSPs have been identified in the antennae and proboscis of the moth Mamestra brassicae. One of them, CSPMbraA6, a 112-amino acid antennal protein, has been expressed in large quantities and is soluble in the Escherichia coli periplasm. X-ray structure determination has been performed in parallel with ligand binding assays using tryptophan fluorescence quenching. The protein has overall dimensions of 25 x 30 x 32 A and exhibits a novel type of alpha-helical fold with six helices connected by alpha-alpha loops. A narrow channel extends within the protein hydrophobic core. Fluorescence quenching with brominated alkyl alcohols or fatty acids and modeling studies indicates that CSPMbraA6 is able to bind such compounds with C12-18 alkyl chains. These ubiquitous proteins might have the role of extracting hydrophobic linear compounds (pheromones, odors, or fatty acids) dispersed in the phospholipid membrane and transporting them to their receptor.
Body Iron Stores and the Risk of Cancer (1988)

Because of evidence that increased body iron stores are associated with an increased risk of cancer, we examined iron status and cancer risk in the first National Health and Nutrition Examination Survey, a survey of more than 14,000 adults begun in 1971, with follow-up between 1981 and 1984. Among 242 men in whom cancer developed, the mean total iron-binding capacity was significantly lower (61.4 vs. 62.9 mumol per liter; P = 0.01) and transferrin saturation was significantly higher (33.1 vs. 30.7 percent; P = 0.002) than among 3113 men who remained free of cancer. The risk of cancer in men in each quartile of transferrin-saturation level relative to the lowest quartile was 1.00, 1.01, 1.10, and 1.37 (P = 0.02 for trend). The serum albumin level was significantly lower in men in whom cancer developed than in those who remained cancer-free. Among women, those in whom cancer developed did not have significantly lower total iron-binding capacity or higher transferrin saturation than those who remained cancer-free. However, a post hoc examination of 5367 women (203 with cancer) yielded a relative risk of 1.3 (95 percent confidence interval, 0.9 to 1.9) associated with a very high transferrin saturation (greater than or equal to 36.8 percent, a value in the highest quartile among men); in 5228 women with at least six years of follow-up (149 with cancer), the relative risk associated with transferrin saturation above this level was 1.5 (1.0 to 2.2). These results are consistent with the hypothesis that high body iron stores increase the risk of cancer in men. The possibility that a similar association exists in women requires further study.
Identification of serum proteins discriminating colorectal cancer patients and healthy controls using surface-enhanced laser desorption ionisation-time of flight mass spectrometry (2006)

SELDI-TOF MS followed by classification tree pattern analysis is a suitable technique for finding new serum markers for CRC. Biomarkers can be identified and reproducibly detected in independent sample sets with high sensitivities and specificities. Although not specific for CRC, these biomarkers have a potential role in disease and treatment monitoring.
Genetic and physical analysis of double-strand break repair and recombination in Saccharomyces cerevisiae. (1989)

We have investigated HO endonuclease-induced double-strand break (DSB) recombination and repair in a LACZ duplication plasmid in yeast. A 117-bp MATa fragment, embedded in one copy of LACZ, served as a site for initiation of a DSB when HO endonuclease was expressed. The DSB could be repaired using wild-type sequences located on a second, promoterless, copy of LACZ on the same plasmid. In contrast to normal mating-type switching, crossing-over associated with gene conversion occurred at least 50% of the time. The proportion of conversion events accompanied by exchange was greater when the two copies of LACZ were in direct orientation (80%), than when inverted (50%). In addition, the fraction of plasmids lost was significantly greater in the inverted orientation. The kinetics of appearance of intermediates and final products were also monitored. The repair of the DSB is slow, requiring at least an hour from the detection of the HO-cut fragments to completion of repair. Surprisingly, the appearance of the two reciprocal products of crossing over did not occur with the same kinetics. For example, when the two LACZ sequences were in the direct orientation, the HO-induced formation of a large circular deletion product was not accompanied by the appearance of a small circular reciprocal product. We suggest that these differences may reflect two kinetically separable processes, one involving only one cut end and the other resulting from the concerted participation of both ends of the DSB.
Combinational clustering of receptors following stimulation by bacterial products determines lipopolysaccharide responses (2004)

The innate immune system has the capacity to recognize a wide range of pathogens based on conserved PAMPs (pathogen-associated molecular patterns). In the case of bacterial LPS (lipopolysaccharide) recognition, the best studied PAMP, it has been shown that the innate immune system employs at least three cell-surface receptors: CD14, TLR4 (Toll-like receptor 4) and MD-2 protein. CD14 binds LPS from Enterobacteriaceae and then transfers it to MD-2, leading to TLR4 aggregation and signal transduction. LPS analogues such as lipid IVa seem to act as LPS antagonists in human cells, but exhibit LPS mimetic activity in mouse cells. Although TLR4 has been shown to be involved in this species-specific discrimination, the mechanism by which this is achieved has not been elucidated. The questions that remain are how the innate immune system can discriminate between LPS from different bacteria as well as different LPS analogues, and whether or not the structure of LPS affects its interaction with the CD14-TLR4-MD-2 cluster. Is it possible that the 'shape' of LPS induces the formation of different receptor clusters, and thus a different immune response? In the present study, we demonstrate using biochemical as well as fluorescence-imaging techniques that different LPS analogues trigger the recruitment of different receptors within microdomains. The composition of each receptor cluster as well as the number of TLR4 molecules that are recruited within the cluster seem to determine whether an immune response will be induced or inhibited.
Cytokine-induced selective expansion and maturation of erythroid versus myeloid progenitors from purified cord blood precursor cells (1993)

To study the role of different cytokine combinations on the proliferation and differentiation of highly purified primitive progenitor cells, a serum-free liquid culture system was used in combination with phenotypic and functional analysis of the cells produced in culture. CD34+ CD45RAlo CD71lo cells, purified from umbilical cord blood by flow cytometry and cell sorting, were selected for this study because of their high content of clonogenic cells (34%), particularly multipotent progenitors (CFU-MIX, 12% of all cells). Four cytokine combinations were tested: (1) mast cell growth factor (MGF; a c-kit ligand) and interleukin-6 (IL-6); (2) MGF, IL-6, IL-3, and erythropoietin (Epo); (3) MGF, IL-6, granulocyte-macrophage colony-stimulating factor (GM-CSF)/IL-3 fusion protein (FP), macrophage colony-stimulating factor (M-CSF), and granulocyte-CSF (G-CSF); and (4) MGF, IL-6, FP, M-CSF, G-CSF, and Epo. Maximum numbers of erythroid progenitors (BFU-E, up to 55-fold increase) and mature erythroid cells were observed in the presence of MGF, IL-6, IL-3, and Epo, whereas maximum levels of myeloid progenitors (CFU-C, up to 70-fold increase) and mature myeloid cells were found in cultures supplemented with MGF, IL-6, FP, M-CSF, and G-CSF. When MGF, IL-6, FP, M-CSF, G-CSF, and Epo were present, maximum levels of both erythroid and myeloid progenitors and their progeny were observed. These results indicate that specific cytokine combinations can act directly on primitive hematopoietic cells resulting in significant expansion of progenitor cell numbers and influencing their overall patterns of proliferation and differentiation. Furthermore, the observations presented in this study suggest that the cytokine combinations used were unable to bias lineage commitment of multipotent progenitors, but rather had a permissive effect on the development of lineage-restricted clonogenic cells.
A new indole-3-carbinol tetrameric derivative inhibits cyclin-dependent kinase 6 expression, and induces G1 cell cycle arrest in both estrogen-dependent and estrogen-independent breast cancer cell lines. (2003)

Indole-3-carbinol (I3C), autolysis product of glucosinolates present in cruciferous vegetables, has been indicated as a promising agent in preventing the development and progression of breast cancer. I3C has been shown to inhibit the growth of human cancer cells in vitro and possesses anticarcinogenic activity in vivo. Because I3C is unstable and may be converted into many polymeric products in the digestive tract, it is not yet clear whether the biological activity observed can be attributed to I3C or some of its polymeric products. In this study we synthesized a stable I3C cyclic tetrameric derivative and investigated its effects on a panel of human breast cancer cell lines. The I3C tetramer suppressed the growth of both estrogen receptor (ER) -positive (MCF-7, 734B, and BT474) and ER-negative (BT20, MDA-MB-231, and BT539) human breast cancer cell lines, and it was found to induce G(1) cell cycle arrest in a dose-dependent manner without evidence of apoptosis, suggesting a growth arrest via a cytostatic mechanism. At the molecular level, the tetramer inhibited cyclin-dependent kinase (CDK) 6 expression and activity, induced an increase in the level of p27(kip1), and reduced the level of retinoblastoma protein expression. Contrarily to CDK6, the level of CDK4, the other kinase involved in the G(1) phase of the cell cycle, remains unchanged. Interestingly, the tetramer resulted about five times more active than I3C in suppressing the growth of human breast cancer cells. On the whole, our data suggest that the I3C tetrameric derivative is a novel lead inhibitor of breast cancer cell growth that may be a considered a new, promising therapeutic agent for both ER+ and ER- breast cancer.
Hematopoietic Stem Cells with High Proliferative Potential (1982)

THIS STUDY WAS DESIGNED TO APPROACH TWO PRIMARY QUESTIONS CONCERNING HEMATOPOIETIC STEM CELLS (HSC) IN MICE: what is the concentration of HSC with extensive proliferative potential in marrow, and how long can an HSC continue to function in an intact animal? The assay system was the W/W(v) mouse, a mouse with an inherited HSC defect, reflected in a reduction in all myeloid tissue and most particularly in a macrocytic anemia.A single chromosomally marked HSC will reconstitute the defective hematopoietic system of the W/W(v). The concentration of HSC in normal littermate (+/+) marrow was assayed by limiting dilution calculation using cure of W/W(v) as an end point (correction of anemia and erythrocytes' macrocytosis) and found to be approximately 10/10(5). This is significantly less than spleen colony forming cell (CFU-S) concentration: approximately 220/10(5) in +/+ and ranging from 50 to 270/10(5) in various other studies. Blood values were studied at selected intervals for as long as 26 mo. Of 24 initially cured mice, which were observed for at least 2 yr, 75% remained cured. However, of all cured mice, 17 lost the cure, returning to a macrocytic anemic state. Cured mice had normal numbers of nucleated and granulocytic cells per humerus and a normal concentration of CFU-S. However, cure of secondary W/W(v) recipients by this marrow was inefficient compared with the original +/+ marrow. These studies suggest the CFU-S assay over-estimates extensively proliferating HSC or perhaps does not assay such a cell. A single such HSC can not only cure a W/W(v), but can sustain the cure for 2 yr or more, despite a relative deficit of cells capable of curing other W/W(v). However, the duration of sustained cure may be finite.
Rhizosphere Response as a Factor in Competition Among Three Serogroups of Indigenous Rhizobium japonicum for Nodulation of Field-Grown Soybeans (1984)

Rhizosphere response was studied as a factor in competition among indigenous Rhizobium japonicum serogroups for the nodulation of soybeans under field conditions. R. japonicum serogroups 110, 123, and 138 were found to coexist in a Waukegan field soil where they were determined to be the major nodulating rhizobia in soybean nodules. Competitive relationships among the three serogroups in that soil and in rhizospheres were examined during two growing seasons with several host cultivars with and without inoculation and with a nonlegume. Enumeration of each of the three competitors was carried out on inner rhizosphere and nonrhizosphere soil by immunofluorescence with serogroup-specific fluorescent antibodies. Rhizobia present in early- and late-season nodules were identified by fluorescent antibody analysis. Populations of each serogroup increased gradually in host rhizospheres, not exceeding 10/g of rhizosphere soil during the first few weeks after planting, whereas numbers in fallow soil remained at initial levels (10 to 10/g). The rhizosphere effects were minor in host plants during this period of nodule initiation and were about the same for all three serogroups. Although serogroup 123 gave no evidence of dominance in early host rhizospheres, it clearly dominated in nodule composition, occupying 60 to 100% of the nodules. High densities of all three serogroups were observed in host rhizospheres during flowering. Rhizosphere populations, especially of serogroup 123, were still high during pod fill and seed maturation. The rhizosphere responses of the R. japonicum serogroups were much greater with the soybean cultivars than with oats, but even in host rhizospheres the R. japonicum populations were greatly outnumbered by other bacteria. The success of serogroup 123 in achieving nodulation does not appear to be due to superior colonization of the host rhizosphere.