gebhart/patrepeval huggingface dataset:
Multiple binding sites in fibronectin and the staphylococcal fibronectin receptor (1992)

The binding of fibronectin to Staphylococci exhibits the properties of a ligand-receptor interaction and has been proposed to mediate bacterial adherence to host tissues. To localize staphylococcal-binding sites in fibronectin, the protein was subjected to limited proteolysis and, of the generated fragments, Staphylococci appeared to preferentially bind to the N-terminal fragment. Different fibronectin fragments were isolated and tested for their ability to inhibit 125I-fibronectin binding to Staphylococci. The results indicate that only the N-terminal region effectively competed for fibronectin binding. However, when isolated fragments were adsorbed to microtiter wells, we found that two distinct domains, corresponding to the N-terminal fragment and to the heparin-binding peptide mapping close to the C-terminal end of fibronectin, promoted the attachment of both Staphylococcus aureus Newman and coagulase-negative strain of Staphylococcus capitis 651. These same domains were recognized by purified 125I-labeled staphylococcal receptor, either when immobilized on microtiter wells or probed after adsorption onto nitrocellulose membrane. The heparin-binding domain is comprised of type-III-homology repeats 14, 15 and 16. To determine which repeats participate in this interaction, we isolated and tested repeats type III14 and type III16. We found that the major staphylococcal binding site is located in repeat type III14. The staphylococcal receptor bound the N-terminal domain of fibronectin with a KD of 1.8 nM, whereas the dissociation constant of the receptor molecule for the internal heparin-binding domain was 10 nM. Since the fusion protein ZZ-FR, which contains the active sequences of fibronectin receptor (D1-D3) bound only to the N-terminus, it is reasonable to assume that the bacterial receptor may have additional binding sites outside the D domains, capable of interacting with the internal heparin-binding domain of fibronectin.
Antibodies to HLA Class I α1 Domain Trigger Apoptosis of CD40-Activated Human B Lymphocytes (1997)

We analyzed herein whether antibodies to HLA class I α1 domain, which trigger apoptosis of activated T cells, may also control the growth/survival of human B lymphocytes. Addition of monoclonal antibody (MoAb) 90 (mouse IgG1) or YTH862 (rat IgG2b) was found to strongly inhibit the proliferation of CD40-activated total tonsil B cells as well as that of purified naive, germinal center, and memory B-cell subsets. This inhibitory effect was not prevented by addition of B-cell tropic factors, such as interleukin-2 (IL-2), IL-4, and IL-10, and was a result of induced B-cell apoptosis as shown by using a TUNEL assay and DNA electrophoresis. In contrast, engagement of another epitope of the α1 domain, as well as that of the α2 and α3 domains by specific anti-HLA class I MoAbs, failed to inhibit DNA synthesis and to induce apoptosis of CD40-activated B cells. As recently reported for acquisition of sensitivity to Fas (APO-1/CD95) -dependent apoptosis, susceptibility to MoAb90-and YTH862-induced death was restricted to CD40-activated B cells, because resting and anti–IgM-activated B cells did not undergo apoptosis after HLA class I engagement. Moreover, ligation of the B-cell receptor protected CD40-activated B cells from both HLA class I- and Fas-mediated growth inhibition and apoptosis. Taken together, these results show that engagement of the α1 domain of HLA class I induces apoptotic cell death of CD40-activated, but not of antigen-activated B cells, and would, therefore, suggest a possible role for HLA class I molecules in the control of B-cell homeostasis.
HORMONE REPLACEMENT REDUCES VASOCONSTRICTION AND MEAN BLOOD PRESSURE AT REST AND DURING STRESS IN HEALTHY POSTMENOPAUSAL WOMEN (1998)

Light, Kathleen C.; Girdler, Susan S.; West, Sheila G.; Grewen, Karen M.; Steege, John F.; Stanwyck, Catherine L.; Ranc, Jean; Lamothe, Traci L.; Chung, Sunny H.; Brown, Heather; Hinderliter, Alan L. Author Information
Simultaneously quantifying parent drugs and screening for metabolites in plasma pharmacokinetic samples using selected reaction monitoring information‐dependent acquisition on a QTrap instrument (2005)

Bioanalytical support of plasma pharmacokinetic (PK) studies for drug discovery programs primarily involves the quantitative analysis of dosed compounds using liquid chromatography/atmospheric pressure ionization tandem mass spectrometry (LC/MS/MS) operated in selected reaction monitoring (SRM) mode. However, there is a growing need for information on the metabolism of new chemical entities (NCEs), in addition to the time-concentration profiles from these studies. In this paper, we present a novel approach to not only quantify parent drugs with SRM, but also simultaneously screen for metabolites using a hybrid triple quadrupole/linear ion trap (QqQ(LIT)) instrument. This was achieved by incorporating both the conventional SRM-only acquisition of parent compounds and the SRM-triggered information-dependent acquisition (IDA) of potential metabolites within the same scan cycle during the same LC/MS/MS run. Two test compounds were used to demonstrate the applicability of this approach. Plasma samples from PK studies were processed by simple protein precipitation and the supernatant was diluted with water before injection. The fast scanning capability of the linear ion trap allowed for the information-dependent acquisition of metabolite MS/MS spectra (<1 s/scan), in addition to the collection of adequate data points for SRM-only channels. The MS/MS spectra obtained from potential metabolites in post-dose samples correlated well with the spectra of the parent compounds studied, therefore providing additional confirmatory structure information without the need for repetitive analyses. Relative quantitative time-concentration profiles of identified metabolites were also obtained. Furthermore, this articulated SRM+SRM-IDA approach generated equivalent quantitative results for parent compounds to those obtained by conventional SRM-only analysis. This approach has been successfully used to support discovery PK screening programs.
Characterizing phenotypic plasticity: a phase plane analysis (2003)

Flux-balance analysis (FBA) was used to map the optimal metabolic phenotypes expressed by a genotype, under different environments. A finite number of optimal phenotypes were found and they were confined to specific regions in a plane formed by the values of two environmental variables, represented as uptake rates. The analysis was performed for growth on two different carbon sources (acetate and glucose) at various levels of oxygenation. It was determined, that there are a number of distinct optimal metabolic phenotypes expressed under varying carbon-oxygen limitations. These in silico results lead to a mechanistic interpretation of environmental factors on the complex genotype-phenotype relation and characterize the phenotypic plasticity of the organism.
Pancreatic ductal adenocarcinoma: biological hallmarks, current status, and future perspectives of combined modality treatment approaches (2019)

Pancreatic ductal adenocarcinoma (PDAC) is a highly devastating disease with poor prognosis and rising incidence. Late detection and a particularly aggressive biology are the major challenges which determine therapeutic failure. In this review, we present the current status and the recent advances in PDAC treatment together with the biological and immunological hallmarks of this cancer entity. On this basis, we discuss new concepts combining distinct treatment modalities in order to improve therapeutic efficacy and clinical outcome - with a specific focus on protocols involving radio(chemo)therapeutic approaches.
Development of a Novel Virus-Like Particle Vaccine Platform That Mimics the Immature Form of Alphavirus (2017)

ABSTRACT Virus-like particles (VLPs) are noninfectious multiprotein structures that are engineered to self-assemble from viral structural proteins. Here, we developed a novel VLP-based vaccine platform utilizing VLPs from the chikungunya virus. We identified two regions within the envelope protein, a structural component of chikungunya, where foreign antigens can be inserted without compromising VLP structure. Our VLP displays 480 copious copies of an inserted antigen on the VLP surface in a highly symmetric manner and is thus capable of inducing strong immune responses against any inserted antigen. Furthermore, by mimicking the structure of the immature form of the virus, we altered our VLP's in vivo dynamics and enhanced its immunogenicity. We used the circumsporozoite protein (CSP) of the Plasmodium falciparum malaria parasite as an antigen and demonstrated that our VLP-based vaccine elicits strong immune responses against CSP in animals. The sera from immunized monkeys protected mice from malaria infection. Likewise, mice vaccinated with P. yoelii CSP-containing VLPs were protected from an infectious sporozoite challenge. Hence, our uniquely engineered VLP platform can serve as a blueprint for the development of vaccines against other pathogens and diseases.
Monocyte adhesion to endothelium in simian immunodeficiency virus-induced AIDS encephalitis is mediated by vascular cell adhesion molecule-1/alpha 4 beta 1 integrin interactions. (1994)

Because the mechanisms associated with recruitment of monocytes to brain in AIDS encephalitis are unknown, we used tissues from rhesus monkeys infected with simian immunodeficiency virus (SIV) to examine the relative contributions of various adhesion pathways in mediating monocyte adhesion to endothelium from encephalitic brain. Using a modified Stamper and Woodruff tissue adhesion assay, we found that the human monocytic cell lines, THP-1 and U937, and the B cell line, Ramos, preferentially bound to brain vessels from monkeys with AIDS encephalitis. Using a combined tissue adhesion/immunohistochemistry approach, these cells only bound to vessels expressing vascular cell adhesion molecule-1 (VCAM-1). Furthermore, pretreatment of tissues with antibodies to VCAM-1 or cell lines with antibodies to VLA-4 (CD49d) inhibited adhesion by more than 70%. Intercellular adhesion molecule-1 (ICAM-1)/beta 2 integrin interactions were not significant in mediating cell adhesion to the vasculature in encephalitic simian brain using a cell line (JY) capable of binding rhesus monkey ICAM-1. In addition, selectin-mediated interactions did not significantly contribute to cell binding to encephalitic brain as there was no immunohistochemical expression of E-selectin and P-selectin in either normal or encephalitic brain, nor was there a demonstrable adhesive effect from L-selectin using L-selectin-transfected 300.19 cells on simian encephalitic brain. These results demonstrate that using the tissue adhesion assay, THP-1, U937, and Ramos cells bind to vessels in brain from animals with AIDS encephalitis using VCAM-1/alpha 4 beta 1 integrin interactions and suggest that VCAM-1 and VLA-4 may be integral for monocyte recruitment to the central nervous system during the development of AIDS encephalitis.
The Molecular Interaction of CAR and JAML Recruits the Central Cell Signal Transducer PI3K (2010)

Coxsackie and adenovirus receptor (CAR) is the primary cellular receptor for group B coxsackieviruses and most adenovirus serotypes and plays a crucial role in adenoviral gene therapy. Recent discovery of the interaction between junctional adhesion molecule-like protein (JAML) and CAR uncovered important functional roles in immunity, inflammation, and tissue homeostasis. Crystal structures of JAML ectodomain (2.2 angstroms) and its complex with CAR (2.8 angstroms) reveal an unusual immunoglobulin-domain assembly for JAML and a charged interface that confers high specificity. Biochemical and mutagenesis studies illustrate how CAR-mediated clustering of JAML recruits phosphoinositide 3-kinase (P13K) to a JAML intracellular sequence motif as delineated for the alphabeta T cell costimulatory receptor CD28. Thus, CAR and JAML are cell signaling receptors of the immune system with implications for asthma, cancer, and chronic nonhealing wounds.
Efficient detection of single molecules eluting off an optically trapped microsphere (1998)

We demonstrate efficient detection of single fluorescent molecules eluting off a polystyrene microsphere optically trapped in a flowing sheath stream. A 1μm diameter analyte doped microsphere was positioned ∼20 μm upstream of a 16 μm diameter probe laser without significant degradation of the detection signal-to-noise ratio due to scattered laser light and fluorescence from the microsphere. In comparison to more standard capillary sample introduction, the microsphere causes only small perturbations to the sheath fluid flow. The small diameter of the analyte stream eluting from the microsphere results in a greater than 90% detection efficiency for single rhodamine-6G molecules, limited primarily by the photostability of the dye.
Quantitative Assessment of mRNA Cap Analogues as Inhibitors of in Vitro Translation (1999)

Fifty-eight analogues of the 5'-terminal 7-methylguanosine-containing cap of eukaryotic messenger RNA were synthesized and tested for their ability to inhibit in vitro protein synthesis. A new algorithm was developed for extracting KI, the dissociation constant for the cap analogue.eIF4E complex, from protein synthesis data. The results indicated that addition of a methyl group to the N2 of guanine produced more inhibitory compounds, but addition of a second methyl group to N2 decreased the level of inhibition dramatically. Aryl substitution at N7 improved the efficacy of guanine nucleoside monophosphate analogues. Substitution of the aromatic ring at the para position with methyl or NO2 groups abolished this effect, but substitution with Cl or F enhanced it. By contrast, aryl substitution at N7 in nucleoside di- or triphosphate analogues produced only minor effects, both positive and negative. By far the strongest determinants of inhibitory activity for cap analogues were phosphate residues. The beneficial effect of more phosphate residues was related more to anionic charge than to the number of phosphate groups per se. The second nucleotide residue in analogues of the form m7GpppN affected inhibitory activity in the order G > C > U > A, but there was no effect of 2'-O-modification. Opening the first ribose ring of m7GpppG analogues dramatically decreased activity, but alterations at the 2'-position of this ribose had no effect. Non-nucleotide-based cap analogues containing benzimidazole derivatives were inhibitory, though less so than those containing 7-methylguanine.
Urokinase‐mediated posttranscriptional regulation of urokinase‐receptor expression in non small cell lung carcinoma (2003)

The urokinase-type plasminogen activator (uPA) and its cellular receptor (uPAR) are involved in the proteolytic cascade required for tumor cell dissemination and metastasis, and are highly expressed in many human tumors. We have recently reported that uPA, independently of its enzymatic activity, is able to increase the expression of its own receptor in uPAR-transfected kidney cells at a posttranscriptional level. In fact, uPA, upon binding uPAR, modulates the activity and/or the level of a mRNA-stabilizing factor that binds the coding region of uPAR-mRNA. We now investigate the relevance of uPA-mediated posttranscriptional regulation of uPAR expression in non small cell lung carcinoma (NSCLC), in which the up-regulation of uPAR expression is a prognostic marker. We show that uPA is able to increase uPAR expression, both at protein and mRNA levels, in primary cell cultures obtained from tumor and adjacent normal lung tissues of patients affected by NSCLC, thus suggesting that the enzyme can exert its effect in lung cells. We investigated the relationship among the levels of uPA, uPAR and uPAR-mRNA binding protein(s) in NSCLC. Lung tissue analysis of 35 NSCLC patients shows an increase of both uPA and uPAR in tumor tissues, as compared to adjacent normal tissues, in 27 patients (77%); 19 of these 27 patients also show a parallel increase of the level and/or binding activity of a cellular protein capable of binding the coding region of uPAR-mRNA. Therefore, in tumor tissues, a strong correlation is observed among these 3 parameters, uPA, uPAR and the level and/or the activity of a uPAR-mRNA binding protein. We then suggest that uPA regulates uPAR expression in NSCLC at a posttranscriptional level by increasing uPAR-stability through a cellular factor that binds the coding region of uPAR-mRNA.
Sleep, Fatigue, and Medical Training: Setting an Agenda for Optimal Learning and Patient Care (2003)

The difficult issues surrounding discussions of sleep, fatigue, and medical education stem from an ironic biologic truth: physicians share a common physiology with their patients, a physiology that includes an absolute need for sleep and endogenous circadian rhythms governing alertness and performance. We cannot ignore the fact that patients become ill and require medical care at all times of the day and night, but we also cannot escape the fact that providing such care requires that medical professionals, including medical trainees, be awake and functioning at times that are in conflict with their endogenous sleep and circadian physiology. Finally, we cannot avoid the reality that medical education requires long hours in a constrained number of years. Solutions to the problem of sleep and fatigue in medical education will require the active involvement of numerous parties, ranging from trainees themselves to training program directors, hospital administrators, sleep and circadian scientists, and government funding and regulatory agencies. Each of these parties can be informed by previous laboratory and field studies in a variety of operational settings. including medical environments. Education regarding the known effects of sleep. circadian rhythms, and sleep deprivation can help to elevate the general level of discourse and point to potential solutions. Empiric research addressing the effects of sleep loss on patient safety, education outcomes, and resident health is urgently needed: equally important are the development and assessment of innovative countermeasures to maximize performance and learning. Addressing the economic realities of any changes in resident work hours is an essential component of any discussion of these issues. Finally, work-hour regulations may serve as one component of improved sleep and circadian health for medical trainees. but they should not be seen as substitutes for more original solutions that rely less on enforcement and more on collaboration. By working together to address the problems of sleep and fatigue in its own trainees, the medical field can provide a valuable legacy to patients and to future generations of healthcare providers--a legacy or optimal medical education, healthy doctors, and healthy patients.
Detection and determination of lipase (acylglycerol hydrolase) activity from various sources (1983)

Methods for the detection and determination of lipases (acylglycerol hydrolases) and preparation of assays are reviewed including substrates, conditions and screening. Some newer methods for the determination of lipase activity are discussed. Several of these are: (a) titrimetry, (b) colorimetry of Cu soaps of free fatty acids (FFA), (c) colorimetry of chromophores in the acyl chain of FFA or in glycerol, (d) radioassay, (e) gas liquid chromatography, (f) enzymatic treatment of FFA and measurement of the resulting products, and (g) direct immunological determination of the lipase. Examples and sensitivities are given and advantages and disadvantages are described.
Production of stem cells with embryonic characteristics from human umbilical cord blood (2005)

When will embryonic stem cells reach the clinic? The answer is simple -- not soon! To produce large quantities of homogeneous tissue for transplantation, without feeder layers, and with the appropriate recipient's immunological phenotype, is a significant scientific hindrance, although adult stem (ADS) cells provide an alternative, more ethically acceptable, source. The annual global 100 million human birth rate proposes umbilical cord blood (UCB) as the largest untouched stem cell source, with advantages of naive immune status and relatively unshortened telomere length. Here, we report the world's first reproducible production of cells expressing embryonic stem cell markers, - cord-blood-derived embryonic-like stem cells (CBEs). UCB, after elective birth by Caesarean section, has been separated by sequential immunomagnetic removal of nucleate granulocytes, erythrocytes and haemopoietic myeloid/lymphoid progenitors. After 7 days of high density culture in microflasks, (10(5) cells/ml, IMDM, FCS 10%, thrombopoietin 10 ng/ml, flt3-ligand 50 ng/ml, c-kit ligand 20 ng/ml). CBE colonies formed adherent to the substrata; these were maintained for 6 weeks, then were subcultured and continued for a minimum 13 weeks. CBEs were positive for TRA-1-60, TRA-1-81, SSEA-4, SSEA-3 and Oct-4, but not SSEA-1, indicative of restriction in the human stem cell compartment. The CBEs were also microgravity--bioreactor cultured with hepatocyte growth medium (IMDM, FCS 10%, HGF 20 ng/ml, bFGF 10 ng/ml, EGF 10 ng/ml, c-kit ligand 10 ng/ml). After 4 weeks the cells were found to express characteristic hepatic markers, cytokeratin-18, alpha-foetoprotein and albumin. Thus, such CBEs are a viable human alternative from embryonic stem cells for stem cell research, without ethical constraint and with potential for clinical applications.
A room-temperature method for coating a ZnS shell on semiconductor quantum dots (2014)

A room-temperature method based on phase transfer and reaction between Zn<sup>2+</sup> and S<sup>2−</sup> in toluene for coating a ZnS shell on quantum dots.
Les enquêtes sur la victimation et l'insécurité en Europe (2007)

Article téléchargeable sur le site Internet : http://www.gern-cnrs.com/gern/fileadmin/documents/crimprev/newsletters_crimprevinfo/wp7/crimprevinfo_n_05_fr_wp7.pdf
A 15-GHz integrated CMOS switch with 21.5-dBm IP/sub 1dB/ and 1.8-dB insertion loss (2004)

A 15-GHz CMOS switch was fully integrated in a 0.13-/spl mu/m CMOS foundry process. With on-chip LC impedance transformation networks (ITNs), the switch achieves 21.5-dBm input P/sub 1dB/ and 34.5-dBm input IP3. The insertion loss and isolation are 1.8 dB and 17.8 dB. The degradation of insertion loss due to use of ITNs is made negligible by reducing the degradation of insertion loss due to the bond pad capacitances in the switch without ITNs. This is the first CMOS switch operating at 15 GHz with competitive performance as GaAs switches, and requires 3V/1.2V control voltages.