gebhart/patrepeval huggingface dataset:
Burst-Mode Femtosecond Pulsed Laser Deposition for Control of Thin Film Morphology and Material Ablation (2009)

We introduce an alternative approach of pulsed laser deposition (PLD) using groups of closely time spaced (20 ns) femtosecond laser pulses, namely burst-mode fs-PLD. This approach enables a broad and continuous tunability over the material morphologies ranging from nanoparticle aggregates to epitaxial thin films with completely droplet-free and atomically smooth surfaces. The tunability of materials is realized by simply tuning laser parameters. An unusual phenomenon of laser-matter interaction is revealed in terms of the breakdown of nanoparticles, the enhancement of plasma ionization, and the decrease of ablation threshold during the burst-mode fs-ablation. A TiO2 film, a wide band gap semiconductor, was deposited with as low as 50 nJ of pulse energy. This approach and the phenomenon are applicable to many other materials.
CD4-Mediated Signals Induce T Cell Dysfunction In Vivo (1999)

Triggering of CD4 coreceptors on both human and murine T cells can suppress TCR/CD3-induced secretion of IL-2. We show here that pretreatment of murine CD4+ T cells with the CD4-specific mAb YTS177 inhibits the CD3-mediated activation of the IL-2 promoter factors NF-AT and AP-1. Ligation of CD4 molecules on T cells leads to a transient stimulation of extracellular signal-regulated kinase (Erk) 2, but not c-Jun N-terminal kinase (JNK) activity. Pretreatment with anti-CD4 mAb impaired anti-CD3-induced Erk2 activation. Costimulation with anti-CD28 overcame the inhibitory effect of anti-CD4 Abs, by induction of JNK activation. The in vivo relevance of these studies was demonstrated by the observation that CD4+ T cells from BALB/c mice injected with nondepleting anti-CD4 mAb were inhibited in their ability to respond to OVA Ag-induced proliferation and IL-2 secretion. Interestingly, in vivo stimulation with anti-CD28 mAb restored IL-2 secretion. Furthermore, animals pretreated with anti-CD4 elicited enhanced IL-4 secretion induced by OVA and CD28. These observations suggest that CD4-specific Abs can inhibit T cell activation by interfering with signal 1 transduced through the TCR, but potentiate those delivered through the costimulatory molecule CD28. These studies have relevance to understanding the mechanism of tolerance induced by nondepleting anti-CD4 mAb used in animal models for allograft studies, autoimmune pathologies, and for immunosuppressive therapies in humans.
A mutant crp allele that differentially activates the operons of the fuc regulon in Escherichia coli (1988)

L-Fucose is used by Escherichia coli through an inducible pathway mediated by a fucP-encoded permease, a fucI-encoded isomerase, a fucK-encoded kinase, and a fucA-encoded aldolase. The adolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Anaerobically, lactaldehyde is converted by a fucO-encoded oxidoreductase to L-1,2-propanediol, which is excreted. The fuc genes belong to a regulon comprising four linked operons: fucO, fucA, fucPIK, and fucR. The positive regulator encoded by fucR responds to fuculose 1-phosphate as the effector. Mutants serially selected for aerobic growth on propanediol became constitutive in fucO and fucA [fucO(Con) fucA(Con)], but noninducible in fucPIK [fucPIK(Non)]. An external suppressor mutation that restored growth on fucose caused constitutive expression of fucPIK. Results from this study indicate that this suppressor mutation occurred in crp, which encodes the cyclic AMP-binding (or receptor) protein. When the suppressor allele (crp-201) was transduced into wild-type strains, the recipient became fucose negative and fucose sensitive (with glycerol as the carbon and energy source) because of impaired expression of fucA. The fucPIK operon became hyperinducible. The growth rate on maltose was significantly reduced, but growth on L-rhamnose, D-galactose, L-arabinose, glycerol, or glycerol 3-phosphate was close to normal. Lysogenization of fuc+ crp-201 cells by a lambda bacteriophage bearing crp+ restored normal growth ability on fucose. In contrast, lysogenization of [fucO(Con)fucA(Con)fucPIK(Non)crp-201] cells by the same phage retarded their growth on fucose.
Specification and implementation of an integrated packet communication facility for an array computer (1983)

Four distinct packet communication requirements for network architectured computer systems are: system control, dataflow data type movement, SIMD, data realignment and movement of high volume data between MIMD configurations when memory sharing is unavailable or too costly. This paper defines and describes a packet switching mechanism which meets each of these requirements. Mechanisms are also defined and described for breaking and restoring SIMD execution structures which are required to complete the implementation of packet switching for SIMD execution. The mechanisms were defined and are described in the context of the Texas reconfigurable array computer (TRAC), but should be in large measure adaptable to other network architectured systems. 8 references.
Homologs of Idoxifene:  Variation of Estrogen Receptor Binding and Calmodulin Antagonism with Chain Length (1996)

A series of homologs of idoxifene [1a, (E)-1-[4-(N-pyrrolidinoethoxy)phenyl]-1-(4-iodophenyl)-2-phenyl-1-butene ] and selected homologs of 4-iodotamoxifen [2a,(E)-1-[4-(N-dimethylamino)-ethoxy]phenyl]-1-(4-iodophenyl)-2-phenyl -1-butene] with the side chain (CH(2))(n) varying in length from n=3 (1b,2b) to n=10(1i,2i) have been synthesized and tested for antagonism of of the calmodulin-dependent activity of cAMP phosphodiesterase and for binding affinity to rat uterine estrogen receptor. Compared with 1a (IC(50) =1.5 microM), the homologs showed a progressive increase in calmodulin antagonism with a maximum inhibition at n=7-9 (1f-h)(IC(50)=0.2 microM), declining at n=10 (1i) to IC(50) =1.6 microM. In the pyrrolidino series, estrogen receptor binding affinity peaked at n=3 (1b, RBA= 23; estradiol = 100), declining by n=10 (1i) to RBA = 0.4, but the homolog n=8 (1g, RBA = 3.5) was still comparable to tamoxifen (RBA = 3.9). A similar pattern of activity was seen for the dimethylamino counterparts. These compounds represent a new class of antiestrogens with potent calmodulin antagonism.
Effect of chronic ipsapirone treatment on the density of 5‐HT1A receptors and 5‐HT1A receptor mRNA in discrete regions of the rat brain (1996)

There is increasing evidence that the 5-hydroxytryptamine (HT)1A partial agonist ipsapirone is an effective anxiolytic/antidepressant agent, although its mechanism of action is not clear. In this study, we investigated the effects of chronic ipsapirone treatment (5 or 10 mg/kg; twice daily, 3 weeks) on 5-HT1A receptor density 8-hydroxy-2-(di-n-propyl amino) tetralin (8O H-DPAT) binding and the level of its mRNA (in situ hybridization) in various regions of the rat (male Wistar 250 g) brain. Receptor density was reduced in the frontal cortex, but did not change significantly in the hippocampus and dorsal raphe nucleus. The level of receptor mRNA was unchanged in each of these brain regions. The present results suggest that the clinical anxiolytic effects of ipsapirone may be mediated partly by postsynaptic action on serotonergic transmission in the frontal cortex, but not in the hippocampus or dorsal raphe nuclei.
Polymicrobial Diseases of Animals and Humans (2014)

Polymicrobial diseases in animals and humans are induced by polyviral infections, polybacterial infections, polymicrobial infections involving viruses and bacteria, polymicrobial infections involving fungi and parasites, and polymicrobial infections as a result of microbe-induced immunosuppression. They are serious diseases whose etiologic agents are sometimes difficult to diagnose and treat. Five common mechanisms of disease pathogenesis exist. First, physical, physiologic, or metabolic abnormalities and stress predispose the host to polymicrobial disease. Second, one organism induces changes in the mucosa that may favor the colonization of others. Third, microorganisms or their products trigger proinflammatory cytokines to increase the severity of disease, reactivate latent infections, or favor the colonization of other microorganisms. Fourth, organisms may share determinants among each other, which give them the ability to damage tissue. Finally, one organism can alter the immune system, which allows the colonization of the host by other microorganisms. Many areas of study in polymicrobial diseases are in their infancy, and the author hopes that this chapter will stimulate interest and work in this evolving field.
Hair Colorants: Chemistry and Toxicology (1998)

Permanent hair colourants semi-permanent hair colourants temporary hair colourants progressive or metallic colourants hair colourants using natural dyestuffs toxicology.
Identification and characterization of the protein antigens of Leptospira interrogans serovar hardjo (1985)

We radiolabeled Leptospira proteins with [35S]methionine. Solubilized extracts of radiolabeled L. interrogans serovar hardjo strain hardjoprajitno were analyzed by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and fluorography. We compared the protein profile obtained in this manner to the protein profiles of various [35S]methionine-labeled Leptospira spp. The profiles of the pathogenic L. interrogans strains were very similar but not identical and exhibited no obvious relationship to those of the two nonpathogenic species. We used solubilized, radiolabeled hardjoprajitno extracts and a sensitive radioimmunoprecipitation procedure to identify protein antigens recognized by immunoglobulin G antibodies present in various rabbit anti-hardjo sera. Homologous hyperimmune rabbit serum efficiently precipitated a large subset of proteins, the majority of which were between 30,000 and 66,500 daltons. Radioimmunoprecipitations with sera prepared against each of four recent hardjo isolates cultured from infected cattle produced similar results. Immunoprecipitations done with various radiolabeled Leptospira extracts and anti-hardjoprajitno serum demonstrated that the pathogenic leptospires possessed a number of cross-reactive major and minor protein antigens. By cell fractionation procedures, we found that most of the major protein antigens were present in the outer envelope. These proteins were exposed on the leptospiral cell surface because intact radiolabeled leptospires bound antibodies directed against them.
Acetylcholine in the orbitofrontal cortex is necessary for the acquisition of a socially transmitted food preference (2005)

The social transmission of food preference task (STFP) has been used to examine the involvement of the hippocampus in learning and memory for a natural odor-odor association. However, cortical involvement in STFP has not been extensively studied. The orbitofrontal cortex (OFC) is important in odor-guided learning, and cholinergic depletion of the entire neocortex results in impairments in STFP. Here we examined the specific role of cholinergic modulation in the OFC by assessing the effect of 192 immunoglobulin G-saporin infusion directly into OFC prior to training on STFP. Cholinergic depletion in the OFC impaired expression of the socially transmitted odor association measured 2 d after training, indicating that cholinergic function in the OFC is essential for this form of associative learning.
A Critical Role for Conserved Residues in the Cleft of HLA-A2 in Presentation of a Nonapeptide to T Cells (1992)

The peptide binding cleft of the class I human histocompatibility antigen, HLA-A2, contains conserved amino acid residues clustered in the two ends of the cleft in pockets A and F as well as polymorphic residues. The function of two conserved tyrosines in the A pocket was investigated by mutating them to phenylalanines and of a conserved tyrosine and threonine in the F pocket by mutating them to phenylalanine and valine, respectively. Presentation of influenza virus peptides and of intact virus to cytolytic T lymphocytes (CTLs) was then examined. The magnitude of the reduction seen by the mutation of the two tyrosines in the A pocket suggests that hydrogen bonds involving them have a critical function in the binding of the NH2-terminal NH3+ of the peptide nonamer and possibly of all bound peptide nonamers. In contrast, the mutations in the F pocket had no effect on CTL recognition.
Reducing the Cost of Session Key Establishment (2009)

Scenarios such as online banking, mobile payment systems, stock trading, selling merchandise, and a host of other applications that need a high level of security have moved from the research domain to real world. Moreover, the nature of clients has been changing from traditional desktops to mobile and handheld devices. Protocols like SSL, SSH are the present standard for establishing secure channels. However, the drawback in these protocols is that both the server and the client need to perform computationally expensive public-key operations for secure channel establishment. In this paper, we present simple constructions that spread the cost of secure channel establishment over several sessions. Our constructions are incrementally deployable and can operate with existing protocols such as SSL and SSH. Experimental results indicate that our constructions are practical and efficient in reducing the computational load at the server as well as the client side.
A positive feedback vector for identification of nucleotide sequences that enhance translation (2005)

In earlier studies, we identified short (6- to 22-nt) sequences that functioned as internal ribosome entry sites (IRESes) and enhanced translation. The size of these IRES elements suggested that they might be prevalent within the messenger population and that individual elements might affect the translation of different groups of mRNAs. To begin to assess the number of different IRES elements in mammalian cells, we have developed a powerful method that uses a positive feedback mechanism to amplify the activities of individual IRES elements. This method uses a vector that encodes a dicistronic mRNA with a reporter gene (Renilla luciferase or the EGFP) as the first cistron and the yeast Gal4/viral protein 16 (VP16) transcription factor as the second cistron. Transcription of this mRNA is driven by a minimal promoter containing four copies of the Gal4 upstream activation sequence. In this method, the presence of an IRES in the intercistronic region facilitates the translation of Gal4/VP16, which binds to the upstream activation sequences and triggers a positive feedback loop that escalates the production of dicistronic mRNA and Gal4/VP16. A corresponding increase in the translation of the first cistron (luciferase or EGFP) is monitored either by measuring luciferase activity or by using FACS. The latter enables IRES-positive cells to be isolated. We present tests of the feedback mechanism by using an IRES module from Gtx homeodomain mRNA and an IRES from hepatitis C virus and demonstrate the utility of this vector system for the screening, identification, and analysis of IRES elements.
A prototype cell for extracting energy from a water salinity difference by means of double layer expansion in nanoporous carbon electrodes (2011)

Electrical energy can be obtained from the controlled mixing of fresh (river) and saline (sea) water. Existing technologies such as pressure retarded osmosis and reverse electrodialysis make use of ion-exchange membranes which must be crossed by either the water or the ions. Recently a new physical principle has been experimentally demonstrated, which allows extraction of electrical energy without making use of membranes, based on the temporary storage of ions inside two porous electrodes kept at different electrical potentials, and the repeatable expansion/contraction of the electrostatic double layers formed inside the electrodes upon changing the salt concentration [D. Brogioli, Phys. Rev. Lett., 2009, 103, 058501]. To make further investigations and to improve the energy recovery, we developed a simple prototype cell of much larger dimensions. Because of the larger dimensions (thus higher currents), testing is more facile, while this design can be the basis for further scaling-up of this technology. In order to reduce the internal resistance of the cell, the electrodes are no longer placed side-by-side, but parallel to one another, separated only by a 250 μm-thick open spacer channel to form a “sandwich”-like flow cell. In a lab-scale experimental stack consisting of 8 such cells (with outer dimensions 6 × 6 × 1 cm3) we extract about 2 J per charging/discharging cycle in 500 mM/1 mM NaCl salt solution, an amount which is 20 times higher per cycle per unit electrode mass than previously obtained. The extracted energy increases with the operating voltage, in line with predictions of the Gouy-Chapman-Stern model for double layer formation.
Mechanoelectric feedback (transduction) in heart: concepts and implications (1996)

It seems that one could regard mechanoelectric feedback in normal heart as an intrinsic regulatory process that modulates normal electromechanical interactions (Fig. 6, left loop). Any physiological mechano-electro-mechano perturbation is self-adjusting and homeostatic. This preserves the status quo, or the heart adapts to form a new electro-mechanoelectric situation. The position in cardiac pathology is different (Fig. 6, right loop), particularly if the disease process produces inhomogeneities. A premature ventricular contraction can be mechanically induced by several of the accepted electrophysiological arrhythmic mechanisms. Thereafter, instantaneous feedback develops within and between regional heterogeneous mechanical conditions. These non-linear recovery processes compound interacting non-linear time courses of recovery of restitution and excitability. Changes in initial loading or mechanical conditions could initiate arrhythmia. Both mechanical and electrical inhomogeneities (also diagrammed in Fig. 5) compound the situation in the intact ventricle. This would enable a milieu of altered excitability, arrhythmogenic current flow and re-entry, to sustain the arrhythmia.
Abnormally Increased Intramuscular Pressure in Human Legs (1998)

Venous stasis of a casted elevated leg is an alternative experimental model to induce abnormally increased intramuscular pressure and neuromuscular dysfunction in the human leg. The venous stasis model may be better than external compression in the study of pathogenesis and pathophysiology of simulated imminent acute compartment syndrome in man.
New frontiers in circulating tumor cell analysis: A reference guide for biomolecular profiling toward translational clinical use (2013)

Circulating tumor cells (CTCs) are now routinely isolated from blood, and measurement of CTC concentrations appears to correlate well with survival in patients with cancer. Interrogation of the molecular profile of CTCs for expression of protein biomarkers, genetic variants and gene expression provides opportunities to use this information to guide personalized treatment, monitor therapy and detect emerging resistance. However, successful application of profiling techniques requires analyses that deliver a reliable and clinically relevant representation of a patient's cancer as it changes with time. Here, we comprehensively review the current knowledge of therapeutically relevant biomarkers in isolated CTCs obtained by fluorescence imaging and genomic profiling approaches. The reviewed data support the notion that molecular profiling of CTCs will provide a reliable representation or surrogate index of tumor burden. Large-scale translational trials, many currently in progress, will provide critical data to progress CTC analysis toward wider clinical use in personalized treatment.
Effect of electric currents on antibacterial effect of chlorhexidine against Entrococcus faecalis biofilm: An in vitro study (2018)

The highest bioelectric effect occurred with the use of high-frequency alternating electric current in the form of an apex locator with CHX as a canal irrigant. <b>Key words:</b>Biofilm, Chlorhexidine, Direct current, Electric current, Enterococcus faecalis.
Chemical structure of urinary dermatan sulfate excreted by a patient with the hunter syndrome. (1980)

The chemical structure of dermatan sulfate (DS) in the urine of a patient the Hunter syndrome was studied through the analysis of disaccharide units which were derived from the urinary DS by digestion with chondroitinase ABC and separated on a Dowex 1 column. The DS was basically composed of repeating disaccharide units of iduronyl N-acetylgalactosamine 4-sulfate. About 90% of the excess sulfate were linked to the iduronate residues as an additional sulfate group in the unit. N-Acetylgalactosamine 6-sulfate and N-acetylgalactosamine 4,6-disulfate residues were minor components. No non-sulfated disaccharide unit was detected in the digestion products. Only sulfoiduronate residue was found as the non-reducing terminal sugar of the DS molecule, consistent with the lack of iduronosulfate sulfatase in this disease.
Antibacterial Components in Bronchoalveolar Lavage Fluid from Healthy Individuals and Sarcoidosis Patients (1999)

Antibacterial peptides and proteins are an integral part of the epithelial defense barrier that provides immediate protection against bacterial invasion. In humans, alpha-defensins are mainly bactericidal effectors in circulating granulocytes, beta-defensin-1 is synthesized in epithelial cells, and LL-37 is produced in granulocytes but is also induced in skin epithelia during inflammation. To investigate the importance of these defense effectors in disease, we analyzed bronchoalveolar lavage fluid (BALF) for bactericidal activity. Antibacterial activity was found in BALF material from healthy individuals and sarcoidosis patients, with enhanced activity in BALF from the patients. The activity was present as several antibacterial components, of which we have so far characterized LL-37, lysozyme, alpha-defensins, and antileukoprotease. In addition, the antibacterial peptide LL-37 was located in alveolar macrophages, bronchial epithelial cells, and bronchial glands, suggesting that it has a defensive role in airway mucosa. In conclusion, the airway epithelium is protected by a complex antibacterial defense system. This is activated in sarcoidosis, and may explain why these patients seldom develop severe respiratory tract infections.
Clostridium difficile—A common and costly colitis (1991)

Clostridium difficile infection manifests as a self-limiting diarrhea, protracted colitis, or toxic pseudomembranous colitis. The incidence of C. difficile in a 514-bed community hospital was studied retrospectively; 155 patients of a total 18,262 admitted during 1988 were identified with C. difficile as an admitting or subsequent diagnosis. The method of diagnosis, mode of therapy, and related costs were analyzed. We have determined that education, with an emphasis on pathogenesis and prevention, is necessary to reduce the incidence in the hospital and the cost to the patient.