gebhart/patrepeval huggingface dataset:
Pyogenic Bacterial Infections in Humans with IRAK-4 Deficiency (2003)

Members of the Toll-like receptor (TLR) and interleukin-1 receptor (IL-1R) superfamily share an intracytoplasmic Toll-IL-1 receptor (TIR) domain, which mediates recruitment of the interleukin-1 receptor-associated kinase (IRAK) complex via TIR-containing adapter molecules. We describe three unrelated children with inherited IRAK-4 deficiency. Their blood and fibroblast cells did not activate nuclear factor kappaB and mitogen-activated protein kinase (MAPK) and failed to induce downstream cytokines in response to any of the known ligands of TIR-bearing receptors. The otherwise healthy children developed infections caused by pyogenic bacteria. These findings suggest that, in humans, the TIR-IRAK signaling pathway is crucial for protective immunity against specific bacteria but is redundant against most other microorganisms.
Strong expression of the neuronal transcription factor FOXP2 is linked to an increased risk of early PSA recurrence in ERG fusion-negative cancers (2013)

These data demonstrate that similar high FOXP2 protein levels as in normal prostate epithelium exert a 'paradoxical' oncogenic role in 'non fusion-type' prostate cancer. It may be speculated that interaction of FOXP2 with members of pathways that are specifically activated in 'non fusion-type' cancers may be responsible for this phenomenon.
Structural Intermediates in the Reactions of Antigenic Peptides with MHC Molecules (1989)

Molecular complexes of class I and class II major histocompatibility complex (MHC) molecules and antigenic peptides are recognized by specific cytotoxic and helper lymphocytes (Schwartz 1985; Townsend and Bodmer 1989). Class II MHC/peptide complexes reconstituted in planar lipid bilayers are recognized by specific T-helper cells (Watts et al. 1984,1985). That is, specific antigenic peptides bind to affinity-purified class II MHC molecules in lipid membranes, the resulting MHC/peptide complexes have long lifetimes (Watts and McConnell 1986), and even after extensive washing, such MHC/peptide complexes trigger specific T-helper cells to release interleukin-2. However, there are major questions as to the mechanism by which exogenous peptides bind to MHC molecules in bilayer membranes. Such questions are raised by the difficulty of preparing MHC/peptide complexes of defined stoichiometry, with many preparations only showing 5–10% binding of added peptide (Watts and McConnell 1986; Sadegh-Nasseri and McConnell 1989). This raises the issue of the possible role...
In vitro and ex vivo effects of cyclosporin A on phagocytic host defenses against Aspergillus fumigatus (1994)

Because cyclosporin A (CsA) is extensively used as an immunosuppressive agent, its effects on phagocytic defenses against Aspergillus fumigatus were studied in vitro and ex vivo. After incubation with 10 to 250 ng of CsA per ml at 37 degrees C for 60 min, polymorphonuclear leukocytes (PMNs) exhibited unaltered superoxide anion (O2-) production in response to phorbol myristate acetate and N-formylmethionyl leucyl phenylalanine, whereas > or = 500 ng/ml significantly suppressed it (P < 0.01). Moreover, at < 250 ng of CsA per ml, PMNs exhibited no change in their capacity to damage unopsonized hyphae of A. fumigatus compared with controls, whereas at > or = 250 ng/ml, CsA suppressed the function (P < 0.01). Although neither CsA (250 ng/ml) nor hydrocortisone (10 micrograms/ml) suppressed PMN O2- production in response to phorbol myristate acetate and N-formylmethionyl leucyl phenylalanine, combination of the two agents reduced the function compared with that at the baseline (P < 0.05). Incubation of monocytes with 100 ng of CsA per ml for 1 or 2 days suppressed their antihyphal activity. No essential change in phagocytic activity of monocyte-derived macrophages (MDMs) against A. fumigatus conidia, tested as the percentage of phagocytosing MDMs and average number of MDM-associated conidia, was detected after 2 or 4 days of incubation with 10 to 1,000 ng of CsA per ml. Furthermore, in rabbits treated with CsA (up to 20 mg/kg of body weight per day intravenously for 7 days), neither O2- production and hyphal damage caused by PMNs or monocytes against hyphae nor phagocytosis of conidia by pulmonary alveolar macrophages was significantly suppressed. Thus, these results demonstrated that CsA within therapeutically relevant concentrations does not suppress antifungal activity of phagocytes except that of circulating monocytes. However, it may induce significant immunosuppression of phagocytes' antifungal function at relatively high concentrations in vitro, especially when combined with corticosteroids.
Obstacle detection in highway environment by colour CCD camera and image processing prototype installed in a vehicle (2005)

This paper deals with a demonstrator which has been developed at THOMSON-CSF/LER in cooperation with French car manufacturers (RENAULT and PSA Research Divisions) during the PROMETHEUS Programme. The vehicle is equipped with a video camera and image processing and visualization hardware. This system has been realized to demonstrate the important role that can be played by electronics, image and information processing to improve security in the vehicle traffic domain.
Antimicrobial effect of acidified nitrite on gut pathogens: importance of dietary nitrate in host defense (1996)

Dietary intake of nitrate generates salivary nitrite, which is acidified in the stomach, leading to a number of reactive intermediates of nitrogen, among which are the potentially carcinogenic N-nitrosamines. Acidified nitrite, however, also has antimicrobial activity which coincides with the formation of nitric oxide. The present study examines the antimicrobial effect in vitro of acidified nitrite on Salmonella enteritidis, Salmonella typhimurium, Yersinia enterocolitica, Shigella sonnei, and Escherichia coli O157. First-order regression plots showed a linear inverse relationship of log-transformed proton and nitrite concentrations with MICs and MBCs after 30 min, 2 h, and 24 h of exposure (P < 0.001 for all antibacterial activities). Susceptibility to the acidified nitrate solutions ranked as follows: Y. enterocolitica > S. enteritidis > S. typhimurium = Shigella sonnei > E. coli O157 (P < 0.05). Addition of SCN-, but not that of CI-, increased the antibacterial activity (paired t testing, P < 0.001). Generation of salivary nitrite from dietary nitrate may provide significant protection against gut pathogens in humans.
Searching for a Neurobiological Basis for Self-Medication Theory in ADHD Comorbid With Substance Use Disorders (2013)

The ADHD + SUD group had lower striatal DAT density in comparison with ADHD without SUD. It is possible to speculate that the use of cannabis and cocaine is responsible for the lower striatal DAT density in this group which would help in understanding the neurobiological basis for the self-medication theory in ADHD adolescents.
Stage-specific increases in cathepsin B messenger RNA content in human colorectal carcinoma. (1991)

Cathepsin B mRNA levels and banding patterns were characterized in human colorectal mucosa and carcinoma tissues from patients with tumors of different Dukes' stages. Quantitation of mRNA content using slot blot hybridization demonstrated an increase in cathepsin B message in seven of eight tumor tissues with an average increase of 3.5-fold over patient-matched control mucosa samples. This tumor-specific increase in cathepsin B mRNA confirms and extends our previous observation that cathepsin B enzyme specific activity levels are significantly elevated in colorectal carcinomas. In fact, the increase in mRNA levels is greater and more consistent than the observed increase in enzyme activity, suggesting that posttranscriptional or posttranslational regulation of cathepsin B expression occurs in colorectal tumors. The mRNA data also support our earlier observation that cathepsin B enzyme activity levels are inversely correlated with Dukes' stage. The tumor-specific increase in cathepsin B mRNA content is almost 4 times greater in earlier stage (Dukes' A and B) tumors than in later stage (Dukes' C and D) tumors. Thus, increased cathepsin B gene expression is particularly characteristic of tumors which are in the process of invading the bowel wall or local tissues compared with tumors which have already spread to more distant sites. Northern blot data on cancer/normal pairs indicate that the increase in cathepsin B mRNA in colorectal carcinoma is due primarily to changes in the amount of the 2.2- and 4.0-kilobase transcripts which are seen in control tissue. However, low levels of two additional cathepsin B mRNA transcripts (1.5 and 3 kilobases in size) were also observed in tumor tissue.
Target RNA capture and cleavage by the Cmr type III-B CRISPR–Cas effector complex (2014)

The effector complex of the Cmr/type III-B CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated) system cleaves RNAs recognized by the CRISPR RNA (crRNA) of the complex and includes six protein subunits of unknown functions. Using reconstituted Pyrococcus furiosus Cmr complexes, we found that each of the six Cmr proteins plays a critical role in either crRNA interaction or target RNA capture. Cmr2, Cmr3, Cmr4, and Cmr5 are all required for formation of a crRNA-containing complex detected by native gel electrophoresis, and the conserved 5' repeat sequence tag and 5'-OH group of the crRNA are essential for the interaction. Interestingly, capture of the complementary target RNA additionally requires both Cmr1 and Cmr6. In detailed functional studies, we determined that P. furiosus Cmr complexes cleave target RNAs at 6-nucleotide (nt) intervals in the region of complementarity, beginning 5 nt downstream from the crRNA tag and continuing to within ∼14 nt of the 3' end of the crRNA. Our findings indicate that Cmr3 recognizes the signature crRNA tag sequence (and depends on protein-protein interactions with Cmr2, Cmr4, and Cmr5), each Cmr4 subunit mediates a target RNA cleavage, and Cmr1 and Cmr6 mediate an essential interaction between the 3' region of the crRNA and the target RNA.
Ultrahigh-throughput screening in drop-based microfluidics for directed evolution (2010)

The explosive growth in our knowledge of genomes, proteomes, and metabolomes is driving ever-increasing fundamental understanding of the biochemistry of life, enabling qualitatively new studies of complex biological systems and their evolution. This knowledge also drives modern biotechnologies, such as molecular engineering and synthetic biology, which have enormous potential to address urgent problems, including developing potent new drugs and providing environmentally friendly energy. Many of these studies, however, are ultimately limited by their need for even-higher-throughput measurements of biochemical reactions. We present a general ultrahigh-throughput screening platform using drop-based microfluidics that overcomes these limitations and revolutionizes both the scale and speed of screening. We use aqueous drops dispersed in oil as picoliter-volume reaction vessels and screen them at rates of thousands per second. To demonstrate its power, we apply the system to directed evolution, identifying new mutants of the enzyme horseradish peroxidase exhibiting catalytic rates more than 10 times faster than their parent, which is already a very efficient enzyme. We exploit the ultrahigh throughput to use an initial purifying selection that removes inactive mutants; we identify approximately 100 variants comparable in activity to the parent from an initial population of approximately 10(7). After a second generation of mutagenesis and high-stringency screening, we identify several significantly improved mutants, some approaching diffusion-limited efficiency. In total, we screen approximately 10(8) individual enzyme reactions in only 10 h, using < 150 microL of total reagent volume; compared to state-of-the-art robotic screening systems, we perform the entire assay with a 1,000-fold increase in speed and a 1-million-fold reduction in cost.
Directional Adhesive Structures for Controlled Climbing on Smooth Vertical Surfaces (2007)

Recent biological research suggests that reliable, agile climbing on smooth vertical surfaces requires controllable adhesion. In nature, geckos control adhesion by properly loading the compliant adhesive structures on their toes. These strongly anisotropic dry adhesive structures produce large frictional and adhesive forces when subjected to certain force/motion trajectories. Smooth detachment is obtained by simply reversing these trajectories. Each toe's hierarchical structure facilitates intimate conformation to the climbing surface resulting in a balanced stress distribution across the entire adhesive area. By controlling the internal forces among feet, the gecko can achieve the loading conditions necessary to generate the desired amount of adhesion. The same principles have been applied to the design and manufacture of feet for a climbing robot. The manufacturing process of these Directional Polymer Stalks is detailed along with test results comparing them to conventional adhesives.
Review of the Comparative Susceptibility of Microbial Species to Photoinactivation Using 380–480 nm Violet‐Blue Light (2018)

Antimicrobial violet-blue light is an emerging technology designed for enhanced clinical decontamination and treatment applications, due to its safety, efficacy and ease of use. This systematized review was designed to compile the current knowledge on the antimicrobial efficacy of 380-480 nm light on a range of health care and food-related pathogens including vegetative bacteria, bacterial endospores, fungi and viruses. Data were compiled from 79 studies, with the majority focussing on wavelengths in the region of 405 nm. Analysis indicated that Gram-positive and Gram-negative vegetative bacteria are the most susceptible organisms, while bacterial endospores, viruses and bacteriophage are the least. Evaluation of the dose required for a 1 log<sub>10</sub> reduction of key bacteria compared to population, irradiance and wavelength indicated that microbial titer and light intensity had little effect on the dose of 405 nm light required; however, linear analysis indicated organisms exposed to longer wavelengths of violet-blue light may require greater doses for inactivation. Additional research is required to ensure this technology can be used effectively, including: investigating inactivation of multidrug-resistant organisms, fungi, viruses and protozoa; further knowledge about the photodynamic inactivation mechanism of action; the potential for microbial resistance; and the establishment of a standardized exposure methodology.
Disruption of Decrements in Conditioned Stimulus Processing by Selective Removal of Hippocampal Cholinergic Input (1997)

The attention directed to environmental stimuli can be modified by experience. For example, preexposure of a conditioned stimulus (CS) in the absence of reinforcement can retard subsequent conditioning of that stimulus when it is paired directly with an unconditioned stimulus, a phenomenon referred to as latent inhibition. Similarly, consistent pairings of a CS with another event can slow the acquisition of new information about that CS. Such phenomena suggest that reductions in the processing of CSs occur when they are made behaviorally irrelevant or consistent predictors of other events. On the basis of the observation that hippocampal lesions prevented such reductions in CS processing, we hypothesized that damage to basal forebrain cholinergic neurons that project to the hippocampus, using microinjections of the selective immunotoxin 192 IgG-saporin into the medial septum/vertical limb of the diagonal band (MS/VDB), also would disrupt normal reductions in CS processing. Lesions of hippocampal cholinergic input disrupted decreases in CS processing, manifested in both an absence of latent inhibition and a lack of reduced processing of a CS that had been a consistent predictor of another CS. These results indicate that cholinergic neurons in the MS/VDB play a role in the regulation of CS processing. Furthermore, these findings (in conjunction with previous findings) implicate both rostral (hippocampal-projecting) and caudal (cortical-projecting) regions of the basal forebrain cholinergic system in the modulation of attention.
A General Method for Constraining Short Peptides to an α-Helical Conformation (1997)

A method for constraining short peptides (<20 residues) of arbitrary sequence to an α-helical conformation (∼100% helical in H2O at 25 °C) is presented. Glutamine residues at positions i and i + 7 of the peptides were tethered with an alkanediyl chain between the side chain nitrogen atoms. Peptides containing this tether were readily synthesized on the solid phase by amide formation between an α,ω-diaminoalkane and the side chain carboxylates of glutamate residues. The resulting cyclic peptides were studied by NMR and CD and were found to adopt an α-helical conformation in aqueous solution. The α-helix was thermally stable to ≥40 °C. Corresponding untethered control peptides with N-methylglutamine at the i and i + 7 positions lacked helicity under the same conditions. Analogous peptides were also prepared for comparison using the thiolysine cross-linking method described previously [Jackson, D. Y.; King, D. S.; Chmielewski, J.; Singh, S.; Schultz, P. G. J. Am. Chem. Soc. 1991, 113, 9391−9392].
Optical band gaps and composition dependence of hafnium–aluminate thin films grown by atomic layer chemical vapor deposition (2005)

We report the optical properties of unannealed hafnium–aluminate (HfAlO) films grown by atomic layer chemical vapor deposition (ALCVD) and correlate them with the aluminum contents in the films. Vacuum ultraviolet spectroscopic ellipsometry (VUV-SE), high-resolution transmission electron microscopy (HRTEM), channeling Rutherford backscattering spectrometry (RBS), and resonant nuclear reaction analysis (NRA) were employed to characterize these films. In the analyses of ellipsometry data, a double Tauc–Lorentz dispersion produces a best fit to the experimental VUV-SE data. As a result, the determined complex pseudodielectric ⟨ε⟩ functions of the films clearly exhibit a dependency on the aluminum densities measured by RBS and NRA. We show that the optical fundamental band gap Eg shifts from 5.56±0.05eV for HfO2 to 5.92±0.05eV for HfAlO. The latter was grown by using an equal number of pulses of H2O∕HfCl4 and H2O∕TMA (trimethylaluminum) precursors in each deposition cycle for HfO2 and Al2O3, respectively. The shift of Eg to higher photon energies with increasing aluminum content indicates that intermixing of HfO2 and Al2O3 occurred during the ALCVD growth process. We found that Eg varies linearly with the mole fraction x of Al2O3 in the alloy (HfO2)x(Al2O3)1−x, but has a parabolic dependency with the aluminum density. We also observed a consistent decrease in the magnitudes of the real ⟨ε1⟩ and imaginary ⟨ε2⟩ part of ⟨ε⟩ of HfAlO films with respect to those of HfO2 as the Al density increased. The absence of the ≈5.7eV peak in the ⟨ε⟩ spectrum, which was previously reported for polycrystalline HfO2 films, indicates that these films are amorphous as confirmed by their HRTEM images.
Short-chain analogs of luteinizing hormone-releasing hormone containing cytotoxic moieties. (1992)

Five hexapeptide and heptapeptide analogs of luteinizing hormone-releasing hormone (LH-RH) were synthesized for use as carriers for cytotoxic compounds. These short analogs were expected to enhance target selectivity of the antineoplastic agents linked to them. Native LH-RH-(3-9) and LH-RH-(4-9) containing D-lysine and D-ornithine at position 6 were amidated with ethylamine and acylated on the N terminus. The receptor-binding affinity of one hexapeptide carrier AJ-41 (Ac-Ser-Tyr-D-Lys-Leu-Arg-Pro-NH-Et) to human breast cancer cell membranes was similar to that of [D-Trp6]LH-RH. Alkylating nitrogen mustards (melphalan, Ac-melphalan), anthraquinone derivatives including anticancer antibiotic doxorubicin, antimetabolite (methotrexate), and cisplatin-like platinum complex were linked to these peptides through their omega-amino group at position 6. The hybrid molecules showed no LH-RH agonistic activity in vitro and in vivo but had nontypical antagonistic effects on pituitary cells in vitro at the doses tested. These analogs showed a wide range of receptor-binding affinities to rat pituitaries and cell membranes of human breast cancer and rat Dunning prostate cancer. Several of these conjugates exerted some cytotoxic effects on MCF-7 breast cancer cell line.
Clinical Signs and Symptoms Predicting Influenza Infection (2000)

When influenza is circulating within the community, patients with an influenza-like illness who have both cough and fever within 48 hours of symptom onset are likely to have influenza and the administration of influenza antiviral therapy may be appropriate to consider. Arch Intern Med. 2000;160:3243-3247.
Ligand Cross-reactivity within the Protease-activated Receptor Family (1996)

Recently, a second member of the protease-activated receptor (PAR) family, named PAR-2, has been identified. Similar to the thrombin receptor, PAR-2 appears to be activated by proteolytic-mediated exposure of a "tethered ligand" sequence and can also be activated by the corresponding synthetic peptides. Similarities in the amino acid sequence of the receptors' tethered ligand sequences suggest that their respective agonist peptides might not be absolutely specific for their particular receptors. To test this, the receptor specificity of each agonist has been determined by measuring the responses of Xenopus oocytes expressing the thrombin receptor or PAR-2 to agonist peptides or enzymes. Thrombin receptors responded to thrombin, the human thrombin receptor-activating peptide SFLLRNP-NH2 (TRAP) (EC50 = 0.1 microM), and Xenopus TRAP, TFRIFD-NH2 (EC50 = 1 microM), but did not show any increase in calcium efflux over control levels with trypsin (50 nM) or PAR-2 agonist peptides (100 microM). Human and murine PAR-2 receptors responded comparably to human and murine PAR-2 agonist peptides (SLIGKVD and SLIGRL, respectively) (EC50 = 0.5-2.0 microM) and trypsin, but not to thrombin. PAR-2 was also found to be responsive to TRAP (EC50 = 1 microM) but was unresponsive to Xenopus TRAP (50 microM). Responses to additional peptide agonist analogs suggest that an amino-terminal serine is critical for PAR-2 agonist activity.
Three lymphoid-specific factors account for all junctional diversity characteristic of somatic assembly of T-cell receptor and immunoglobulin genes. (1992)

The somatic diversity immunoglobulin and T-cell receptor diversity is largely provided by the junctional variation created during site-specific rearrangement of separately encoded gene segments. Using a transient transfection assay, we demonstrate that the recombination activating genes Rag1 and Rag2 direct site-specific rearrangement on an artificial substrate in poorly differentiated as well as in differentiated nonlymphoid cell lines. In addition to a high frequency of precise recombination events, coding joints show deletions and more rarely P-nucleotide insertions, reminiscent of immunoglobulin and T-cell receptor junctions found in fetal tissues. N-region insertions, which are characteristic of adult junctional diversity, are obtained at high frequency upon transfection of a terminal deoxynucleotidyltransferase expression vector together with Rag1 and Rag2. These results show that only three lymphoid-specific factors are needed to generate all types of junctional diversity observed during lymphoid development.