gebhart/patrepeval huggingface dataset:
On Secure and Precise IR-UWB Ranging (2012)

To provide high ranging precision in multipath environments, a ranging protocol should find the first arriving path, rather than the strongest path. We demonstrate a new attack vector that disrupts such precise Time-of-Arrival (ToA) estimation, and allows an adversary to decrease the measured distance by a value in the order of the channel spread (10-20 meters). This attack vector can be used in previously reported physical-communication-layer (PHY) attacks against secure ranging (or distance bounding). Furthermore, it creates a new type of attack based on malicious interference: This attack is much easier to mount than the previously known external PHY attack (distance-decreasing relay) and it can work even if secret preamble codes are used. We evaluate the effectiveness of this attack for a PHY that is particularly well suited for precise ranging in multipath environments: Impulse Radio Ultra-Wideband (IR-UWB). We show, with PHY simulations and experiments, that the attack is effective against a variety of receivers and modulation schemes. Furthermore, we identify and evaluate three types of countermeasures that allow for precise and secure ranging.
Binary Complementary Synthetic-White LED Illuminators (1999)

&lt;div class="htmlview paragraph"&gt;Synthetic-white illuminators for automobiles and other applications were constructed using a plurality of high-intensity light emitting diode (LED) components emitting saturated light with two different complementary hues. This configuration projects an additive color mixture forming white illumination and providing high illuminance, good color rendering, and high contrast. Unique optical components, electronic controls and manufacturing processes were also employed to maximize the advantages of this new lighting technology. The resulting system provides a combination of production-proven benefits previously unavailable in compact, rugged illuminators.&lt;/div&gt;
16S-23S rDNA internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Fusobacterium. (2002)

The 16S-23S rDNA internal transcribed spacer (ITS) regions of all currently defined Fusobacterium species and related taxa such as Leptotrichia buccalis, Sebaldella termitidis and Streptobacillus moniliformans, were analysed to examine inter- and intraspecies as well as subspecies relationships. For the ITS-amplification, a new eubacterial universal primer pair was designed and used. The majority of the Fusobacterium strains, along with L. buccalis showed one major, and two to three weaker, distinct bands (short and long versions) with lengths of 800-830 bp and 1000-1100 bp. Nevertheless, six other patterns were also found within the genus Fusobacterium, demonstrating its heterogeneity. The ITS region was sequenced and found to consist both of conserved motifs, which functioned as a framework for alignment, and of variable sites, which provided high phylogenetic resolution. Analyses of the ITS-DNA sequences and ITS relative length (short version) allowed species and subspecies differentiation in most cases. The results confirmed the strikingly distant relationship between Fusobacterium prausnitzii and the genus Fusobacterium. Fusobacterium nucleatum subspecies, along with Fusobacterium naviforme, Fusobacterium simiae and Fusobacterium periodonticum, formed a cluster with an inherently high potential for diversification. Other clusters were formed by Fusobacterium necrophorum subspecies with Fusobacterium gonidaformans and by Fusobacterium varium with Fusobacterium mortiferum and Fusobacterium ulcerans. Fusobacterium russii as well as Fusobacterium perfoetens formed separate branches. Fusobacterium necrophorum subspp. necrophorum and funduliforme on the one hand, and Fusobacterium varium and Fusobacterium mortiferum on the other, were found to be very similar, even at the high-resolution ITS level.
Synthetic hexa- and heptapeptides that inhibit IL-8 from binding to and activating human blood neutrophils. (1995)

IL-8 is a member of the chemokine alpha subfamily that activates and is chemotactic for neutrophils. In these studies, we have synthesized and characterized a hexapeptide inhibitor of IL-8. This peptide, with an acetylated amino terminus and an amidated carboxyl terminus (Ac-RRWWCR-NH2), inhibited the specific binding of 125I-IL-8 to neutrophils. The inhibition was biphasic and apparent Ki was estimated to be approximately 2.7 microM and 13 microM for two different IL-8 binding sites. The peptide inhibited neutrophil chemotaxis, beta-glucuronidase release from neutrophils, and rabbit skin edema induced by IL-8 with an EC50 of 90 microM, 0.8 microM, respectively. Ac-RRWWCR-NH2 also suppressed the binding of macrophage inflammatory protein (MIP) 2 beta to neutrophils. However, it did not inhibit the binding of MIP-1 alpha, C5a, or leukotriene B4 to neutrophils, chemotaxis induced by FMLP, or beta-glucuronidase release induced by FMLP, C5a, or leukotriene B4. Additional peptides were analyzed to identify a better inhibitor. Inhibition of binding by Ac-rrwwcrc-NH2 synthesized with all D-amino acids was almost four times more potent than Ac-RRWWCR-NH2. Small peptide homologues of the amino-terminal end of IL-8 failed to inhibit IL-8 binding to neutrophils. These studies have identified several peptides that significantly inhibit IL-8 function. Because IL-8 seems to be an important inflammatory mediator of several human illnesses, these peptides may have pharmacologic potential.
A Strategy for Precise and Large Scale Identification of Core Fucosylated Glycoproteins (2009)

Core fucosylation (CF) patterns of some glycoproteins are more sensitive and specific than evaluation of their total respective protein levels for diagnosis of many diseases, such as cancers. Global profiling and quantitative characterization of CF glycoproteins may reveal potent biomarkers for clinical applications. However, current techniques are unable to reveal CF glycoproteins precisely on a large scale. Here we developed a robust strategy that integrates molecular weight cutoff, neutral loss-dependent MS(3), database-independent candidate spectrum filtering, and optimization to effectively identify CF glycoproteins. The rationale for spectrum treatment was innovatively based on computation of the mass distribution in spectra of CF glycopeptides. The efficacy of this strategy was demonstrated by implementation for plasma from healthy subjects and subjects with hepatocellular carcinoma. Over 100 CF glycoproteins and CF sites were identified, and over 10,000 mass spectra of CF glycopeptide were found. The scale of identification results indicates great progress for finding biomarkers with a particular and attractive prospect, and the candidate spectra will be a useful resource for the improvement of database searching methods for glycopeptides.
Senescent cells fail to express cdc2, cycA, and cycB in response to mitogen stimulation. (1991)

Senescent human diploid fibroblasts (HDF) contain no detectable cdc2 mRNA or p34cdc2 protein. Similarly, young quiescent HDF have only low levels of cdc2 mRNA and protein. After serum stimulation, quiescent HDF accumulate increasing amounts of cdc2 mRNA and protein and go through DNA synthesis and mitosis. In contrast, serum-stimulated senescent HDF fail to accumulate detectable amounts of cdc2 mRNA and protein and fail to enter S phase. Mitosis is likewise deficient in senescent cells even when they have been induced to synthesize DNA by simian virus 40 large tumor antigen. Since p34cdc2 or its homologues appear to be required for DNA synthesis and mitosis in eukaryotes, a lack of these molecules in serum-stimulated senescent HDF could be an important reason for their inability to enter S phase or mitosis. Nuclear microinjection of cdc2 DNA into senescent HDF causes rounding up of the cells but no induction of DNA synthesis. Since cyclins A and B are important cofactors of the protein kinase activity of p34cdc2 or its homologues, we analyzed expression of these genes in serum-stimulated senescent HDF and determined that they contain little or no cycA or cycB mRNA. These deficiencies may be relevant to the lack of DNA synthesis and mitosis in senescent HDF.
Initial Clinical Testing of a Holographic Non-Invasive Contact Lens Glucose Sensor (2006)

The holographic contact lens glucose sensor shows promise as a non-invasive home glucose monitor.
Antiinflammatory activity of a COOH‐terminal fragment of the neuropeptide α‐MSH (1989)

The endogenous neuropeptide α‐melanocyte stimulating hormone (α‐MSH 1‐13), previously found to have marked antipyretic activity, inhibits histamine‐induced increases in vasopermeability. The primary antipyretic amino acid message sequence is believed to be the COOH‐terminal trieptide, lysine‐proline‐valine. In recent preliminary research this tripeptide inhibited increases in vasopermeability, raising the possibility that this portion of the α‐MSH molecule has general antiinflammatory activity. To test this idea, the effects of graded doses of α‐MSH [11‐13] on ear swelling induced by picryl chloride in mice were compared with the effects of saline and a large dose of corticosteroid. α‐MSH [11‐13] inhibited swelling in a dose‐related fashion. This result, together with previous findings, suggests that endogenous circulating α‐MSH and its COOH‐terminal fragments may contribute to modulation of physiological responses in host defense. If this is true, it may be possible to develop new peptide drugs or mimetics based on the tripeptide that are useful in treating inflammation.— H iltz , M. E.; L ipton , J. M. Antiinflammatory activity of a COOH‐terminal fragment of the neuropeptide α‐MSH. FASEB J. 3: 2282‐2284; 1989.
Characterization of Two Distinct Monoclonal Antibodies to Paired Helical Filaments: Further Evidence for Fetal‐Type Phosphorylation of the τ in Paired Helical Filaments (1993)

Two monoclonal antibodies C5 and M4 raised against Sarkosyl-insoluble paired helical filaments (PHF) specifically labeled fetal tau, but hardly labeled normal adult tau. C5 immunoreactivity was eliminated by alkaline phosphatase treatment at 37 degrees C, whereas M4 reactivity could be removed only by the treatment at 67 degrees C. Epitope analysis showed that C5 and M4 recognition sites are in residues 386-406 and 198-250, respectively, according to the numbering of the longest human tau isoform. Thus, the phosphorylation sites are located in the amino- and carboxyl-terminal portions of the microtubule-binding region. These two well-characterized monoclonals should be valuable in the identification of a protein kinase(s) that converts normal tau into PHF-tau.
Preparation of La Crosse Virus Hemagglutinating Antigen in BHK-21 Suspension Cell Cultures (1969)

Hemagglutinating and complement-fixing antigens of La Crosse virus (California arbovirus group) were produced in serum-free suspension cultures of BHK-21/13S cells. The appearance and production of these antigens were correlated with the titer of infectious virus. No significant differences in antigen titers were produced by varying virus dose 10-fold. Hemagglutinin appeared 6 to 8 hr after inoculation and reached peak titer in 14 to 22 hr. Both beta-propiolactone and Tween 80-ether treatment inactivated infectious virus in the antigens. Unlyophilized antigen was stable at -60, 5 and 24 C for at least 117 days but not for 1 year. Lyophilized antigen was stable for at least a year, however, at -20 and 5 C. Cell culture-produced antigen was more sensitive than brain-produced antigen in detecting hemagglutination inhibition antibody in human sera.
The importance of nef in the induction of human immunodeficiency virus type 1 replication from primary quiescent CD4 lymphocytes. (1994)

The viral regulatory gene, nef, is unique to the human immunodeficiency viruses (HIV) and their related primate lentiviruses. Expression of the nef gene has been shown to be essential to the maintenance of high levels of virus replication and the development of pathogenesis in the animal model of simian immunodeficiency virus (SIV) infection. In contrast to this in vivo model, the use of standard T cell culture systems to study nef function in vitro has produced a spectrum of contradictory results, and has failed to demonstrate a significant positive influence of nef on viral life cycle. We have developed a cell model to study regulation of HIV-1 replication that we believe reflects more accurately virus-cell interactions as they occur in vivo. Our experimental system used acute virus infection of purified, quiescent CD4 lymphocytes and subsequent induction of viral replication through T cell activation. With this cell model, NL4-3 virus clones with open and mutated nef reading frames were compared for replication competence. The clones with nef mutations showed reproducible and significant reductions in both rates of growth and maximal titers achieved. The degree of reduced replication was dependent on initial virus inoculum and the timing of T cell activation. The influence of nef was highly significant for induction of virus replication from a latent state within resting CD4 cells. Its effect was less apparent for virus infection of fully proliferating CD4 cells. This study demonstrates that nef confers a positive growth advantage to HIV-1 that becomes readily discernable in the primary cell setting of virus induction through T cell activation. The experimental cell model, which we describe here, provides not only a means to study nef function in vitro, but also provides important clues to the function of nef in HIV infection in vivo.
Piezoelectric stimulation by ultrasound facilitates chondrogenesis of mesenchymal stem cells (2020)

A cellular stimulation device utilizing an AT-cut quartz coverslip mounted on an ultrasonic live imaging chamber is developed to investigate the effect of piezoelectric stimulation. Two types of chambers deliver ultrasound at intensities ranging from 1 to 20 mW/cm<sup>2</sup> to mesenchymal stem cells (MSCs) seeded on the quartz coverslip. The quartz coverslip imposes additionally localized electric charges as it vibrates with the stimulation. The device was applied to explore whether piezoelectric stimulation can facilitate chondrogenesis of MSCs. The results suggest piezoelectric stimulation drove clustering of MSCs and consequently facilitated chondrogenesis of MSCs without the use of differentiation media.
Substitution of foreign protein sequences into a chimeric toxin composed of transforming growth factor alpha and Pseudomonas exotoxin. (1991)

TGF alpha-PE40 is a chimeric toxin made by replacing domain Ia of Pseudomonas exotoxin (PE) with transforming growth factor alpha (TGF alpha). We have now replaced a portion of domain Ib of PE with different polypeptides or an extra domain III of PE in transforming growth factor alpha-PE40 and maintained cell killing. Thus, TGF alpha-PE40 can be used to transport foreign protein sequences into the cytosol of cells.
CD59 molecule: A second ligand for CD2 in T cell adhesion (1992)

The T cell surface molecule CD2 forms, with its counter-receptor CD58 (LFA-3), a powerful adhesion/activation pathway. There is some evidence that CD2 might bind more than a single ligand. Chinese hamster ovary cells (CHO) expressing human CD59 after cDNA transfection (CD59+CHO) form rosettes with human T cells; these rosettes are inhibited in a dose-dependent fashion by the CD59 monoclonal antibody (mAb) H19 and by the CD2 mAb O275 known to block natural rosettes, but not by the CD2R mAb D66, a poor rosette blocker. CD2+CHO transfectants form rosettes with human erythrocytes; these rosettes are inhibited by the CD59 mAb H19 in addition to CD2 mAb O275 and CD58 mAb; murine thymoma cells expressing human CD2 form rosettes with CD59+CHO cells that again are blocked by CD59 H19 and by CD2 O275 mAb. In a marked contrast with H19, two others CD59 mAb, YTH 53.1 and MEM 43, which react with a different epitope on CD59, led to a 50%-70% increase of the number of cells forming rosettes. In addition to rosette experiments, the binding of 125I-labeled CD59 molecules to CD2+CHO cells was specifically inhibited by unlabeled CD59 molecule and CD2 mAb. Furthermore, the binding of CD59 molecules to resting T cells induced expression of CD2R epitopes. These results directly show that CD2 binds CD59 and that subtle molecular changes occur upon binding.
Synthesis of Site-Specific Radiolabeled Antibodies for Radioimmunotherapy via Genetic Code Expansion (2016)

Radioimmunotherapy (RIT) delivers radioisotopes to antigen-expressing cells via monoantibodies for the imaging of lesions or medical therapy. The chelates are typically conjugated to the antibody through cysteine or lysine residues, resulting in heterogeneous chelate-to-antibody ratios and various conjugation sites. To overcome this heterogeneity, we have developed an approach for site-specific radiolabeling of antibodies by combination of genetic code expansion and click chemistry. As a proof-of-concept study, model systems including anti-CD20 antibody rituximab, positron-emitting isotope <sup>64</sup>Cu, and a newly synthesized bifunctional linker (4-dibenzocyclooctynol-1,4,7,10-tetraazacyclotetradecane-1,4,7,10-tetraacetic acid, DIBO-DOTA) were used. The approach consists of three steps: (1) site-specific incorporation of an azido group-bearing amino acid (NEAK) via the genetic code expansion technique at the defined sites of the antibody as a "chemical handle"; (2) site-specific and quantitative conjugation of bifunctional linkers with the antibodies under a mild condition; and (3) radiolabeling of the chelate-modified antibodies with the appropriate isotope. We used heavy-chain A122NEAK rituximab as proof-of-concept and obtained a homogeneous radioconjugate with precisely two chelates per antibody, incorporated only at the chosen sites. The conjugation did not alter the binding and pharmacokinetics of the rituximab, as indicated by in vitro assays and in vivo PET imaging. We believe our research is a good supplement to the genetic code expansion technique for the development of novel radioimmunoconjugates.
A Potentiometric Study of the Interaction of Zr(IV) and O(II) Ions in the LiCl-KCl Eutectic Molten Salt (2004)

International audience
Interpretation of the Electrocardiogram of Young Athletes (2011)

Although no detailed guidance for the interpretation of the athlete’s ECG exists, many physicians will be called on to interpret an athlete’s ECG.A principal obstacle to such interpretation is the difficulty in distinguishing abnormal patterns from physiological effects of training. Many clinical and ECG findings that may be a cause of concern in the general population are normal for athletes. In addition, the test characteristics of the ECG for different findings vary according to age, sex, ethnicity, sport, and level of training. In particular, different challenges exist for younger athletes because of the evolution of the ECG with age. This is further complicated by historical inconsistencies in the definition of ECG abnormalities and the uncertainty about criteria for final diagnosis of several diseases in secondary testing. Finally, low disease prevalence limits the positive predictive value of many ECG criteria, even for those with otherwise favorable sensitivity and specificity. Although this document focuses in large part on the diagnostic gray area presented by ECG screening, we have where possible included suggestions for secondary testing strategies. Current recommendations for patients diagnosed with cardiomyopathy or channelopathy are clearly against participation in high-level or competitive exercise.
Coordinating Persistent Infection (2004)

In patients with cystic fibrosis, chronic infection with the pathogen Pseudomonas aeruginosa is the primary cause of death. During the course of long-lasting infections, bacteria respond to their environment, first expressing a set of genes for infection and initial colonization and later expressing components that favor the formation of biofilms that allow aggregation and protection from host defenses. Goodman et al. screened for two-component system proteins (histidine kinase sensors or phosphate receiver response regulators) that might participate in control of the early or late gene expression programs. They isolated a gene named retS (for regulator of exopolysaccharide and type III secretion). Transcriptional profiling showed that expression of retS enhanced expression of genes encoding virulence factors and decreased expression of genes that enhance synthesis of exopolysaccharides: cell surface components that support the formation of biofilms. The RetS protein has an unusual structure: It contains two dissimilar response regulator receiver domains and lacks a histidine phosphotransfer domain. The authors propose that one or both of the receiver domains may respond to phosphorylation by proteins other than RetS itself, thus allowing RetS to coordinate multiple inputs in the phenotypic response. — LBR
Biosynthesis of Isoprenoids. Purification and Properties of IspG Protein from Escherichia coli (2005)

[Structure: see text]. The IspG protein is known to catalyze the transformation of 2-C-methyl-d-erythritol 2,4-cyclodiphosphate into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the nonmevalonate pathway of isoprenoid biosynthesis. We have found that the apparent IspG activity in the cell extracts of recombinant Escherichia coli cells as observed by a radiochemical assay can be enhanced severalfold by coexpression of the isc operon which is involved in the assembly of iron-sulfur clusters. The recombinant protein was isolated by affinity chromatography under anaerobic conditions. With a mixture of flavodoxin, flavodoxin reductase, and NADPH as the reducing agent, stringent assay methods based on photometry or on 13C NMR detection of multiply 13C-labeled substrate/product ratios afforded catalytic activities greater than 60 nmol mg(-1) min(-1) for the protein "as isolated" (i.e., without reconstitution of any kind). Lower apparent activities were found using photoreduced deazaflavin as an artifactual electron donor, whereas dithionite was unable to serve as an artificial electron donor. The apparent Michaelis constant for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate was 700 microM. The enzyme was inactivated by EDTA and could be reactivated by Mn2+. The pH optimum was at 9.0. The protein contained 2.4 iron ions and 4.4 sulfide ions per subunit. The replacement of any of the three conserved cysteine residues afforded mutant proteins which were devoid of catalytic activity and contained less than 6% of Fe2+ and less than 23% of S2- as compared to the wild-type protein. Sequence comparison indicates that putative IspG proteins of plants, the apicomplexan protozoan Plasmodium falciparum, and bacteria from the Bacteroidetes/Chlorobi group contain an insert of about 170-320 amino acid residues as compared with eubacterial enzymes.