gebhart/patrepeval huggingface dataset:
Pertussis Toxin and Adenylate Cyclase Toxin Provide a One-Two Punch for Establishment of Bordetella pertussis Infection of the Respiratory Tract (2005)

Previously we found that pertussis toxin (PT), an exotoxin virulence factor produced by Bordetella pertussis, plays an important early role in colonization of the respiratory tract by this pathogen, using a mouse intranasal infection model. In this study, we examined the early role played by another exotoxin produced by this pathogen, adenylate cyclase toxin (ACT). By comparing a wild-type strain to a mutant strain (DeltaCYA) with an in-frame deletion of the cyaA gene encoding ACT, we found that the lack of ACT confers a significant peak (day 7) colonization defect (1 to 2 log(10)). In mixed-infection experiments, the DeltaCYA strain was significantly outcompeted by the wild-type strain, and intranasal administration of purified ACT did not increase colonization by DeltaCYA. These data suggest that ACT benefits the bacterial cells that produce it and, unlike PT, does not act as a soluble factor benefiting the entire infecting bacterial population. Comparison of lower respiratory tract infections over the first 4 days after inoculation revealed that the colonization defect of the PT deletion strain was apparent earlier than that of DeltaCYA, suggesting that PT plays an earlier role than ACT in the establishment of B. pertussis infection. Examination of cells in the bronchoalveolar lavage fluid of infected mice revealed that, unlike PT, ACT does not appear to inhibit neutrophil influx to the respiratory tract early after infection but may combat neutrophil activity once influx has occurred.
Genomic correlates of response to CTLA-4 blockade in metastatic melanoma (2015)

Monoclonal antibodies directed against cytotoxic T lymphocyte-associated antigen-4 (CTLA-4), such as ipilimumab, yield considerable clinical benefit for patients with metastatic melanoma by inhibiting immune checkpoint activity, but clinical predictors of response to these therapies remain incompletely characterized. To investigate the roles of tumor-specific neoantigens and alterations in the tumor microenvironment in the response to ipilimumab, we analyzed whole exomes from pretreatment melanoma tumor biopsies and matching germline tissue samples from 110 patients. For 40 of these patients, we also obtained and analyzed transcriptome data from the pretreatment tumor samples. Overall mutational load, neoantigen load, and expression of cytolytic markers in the immune microenvironment were significantly associated with clinical benefit. However, no recurrent neoantigen peptide sequences predicted responder patient populations. Thus, detailed integrated molecular characterization of large patient cohorts may be needed to identify robust determinants of response and resistance to immune checkpoint inhibitors.
Cyclic haemopoiesis at 7‐ or 8‐day intervals (1994)

We report a patient with severe anaemia and cyclic oscillations of reticulocyte and leucocyte counts, as well as serum iron (Fe), unsaturated iron-binding capacity (UIBC), ferritin, C-reactive protein (CRP) levels and temperature, at regular intervals of 7 or 8 d. After treatment with prednisolone, anaemia was corrected and the cyclic oscillations of these parameters ceased; whereas treatment with indomethacin, recombinant granulocyte-colony stimulating factor (G-CSF) and erythropoietin (Epo) were unsuccessful.
Controls of sperm motility (2006)

Spermatozoa must be motile for their journey to the egg. In species that undergo external fertilization, such as sea urchins and fishes, the initiation of sperm motility occurs at spawning and movement is further regulated by factors released by oocytes. In mammals, the swimming ability is progressively acquired by spermatozoa during the epididymal transit even though motility is initiated only after dilution in seminal plasma. Factors from the female genital tract will later on trigger the hyperactivated motility that is needed for sperm penetration of the zona pellucida.
Improving SLP efficiency and extendability by using global attributes and preference filters (2003)

The paper presents two new mechanisms, global attributes and preference filters, that improve the efficiency and extendability of the service location protocol (SLP). Global attributes describe common service properties, which can be used to perform queries across different service types, and can be standardized for service management. Preference filters facilitate processing of search results, such as finding the best match, in SLP servers. They can reduce the amount of data transferred to the client, and better support thin clients with limited resources and capabilities.
An inwardly rectifying K+ channel, Kir4.1, expressed in astrocytes surrounds synapses and blood vessels in brain (2001)

Glial cells express inwardly rectifying K(+) (Kir) channels, which play a critical role in the buffering of extracellular K(+). Kir4.1 is the only Kir channel so far shown to be expressed in brain glial cells. We examined the distribution of Kir4.1 in rat brain with a specific antibody. The Kir4.1 immunostaining distributed broadly but not diffusely in the brain. It was strong in some regions such as the glomerular layer of the olfactory bulb, the Bergmann glia in the cerebellum, the ependyma, and pia mater, while little activity was detected in white matter of the corpus callosum or cerebellar peduncle. In the olfactory bulb, Kir4.1 immunoreactivity was detected in a scattered manner in about one-half of the glial fibrillary acidic protein-positive astrocytes. Immunoelectron microscopic examination revealed that Kir4.1 channels were enriched on the processes of astrocytes wrapping synapses and blood vessels. These data suggest that Kir4.1 is expressed in a limited population of brain astrocytes and may play a specific role in the glial K(+)-buffering action.
Complex promoter and coding region β 2 -adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness (2000)

The human beta(2)-adrenergic receptor gene has multiple single-nucleotide polymorphisms (SNPs), but the relevance of chromosomally phased SNPs (haplotypes) is not known. The phylogeny and the in vitro and in vivo consequences of variations in the 5' upstream and ORF were delineated in a multiethnic reference population and an asthmatic cohort. Thirteen SNPs were found organized into 12 haplotypes out of the theoretically possible 8,192 combinations. Deep divergence in the distribution of some haplotypes was noted in Caucasian, African-American, Asian, and Hispanic-Latino ethnic groups with >20-fold differences among the frequencies of the four major haplotypes. The relevance of the five most common beta(2)-adrenergic receptor haplotype pairs was determined in vivo by assessing the bronchodilator response to beta agonist in asthmatics. Mean responses by haplotype pair varied by >2-fold, and response was significantly related to the haplotype pair (P = 0.007) but not to individual SNPs. Expression vectors representing two of the haplotypes differing at eight of the SNP loci and associated with divergent in vivo responsiveness to agonist were used to transfect HEK293 cells. beta(2)-adrenergic receptor mRNA levels and receptor density in cells transfected with the haplotype associated with the greater physiologic response were approximately 50% greater than those transfected with the lower response haplotype. The results indicate that the unique interactions of multiple SNPs within a haplotype ultimately can affect biologic and therapeutic phenotype and that individual SNPs may have poor predictive power as pharmacogenetic loci.
Translocation of the B Cell Antigen Receptor into Lipid Rafts Reveals a Novel Step in Signaling (2001)

The cross-linking of the B cell Ag receptor (BCR) leads to the initiation of a signal transduction cascade in which the earliest events involve the phosphorylation of the immunoreceptor tyrosine-based activation motifs of Ig alpha and Ig beta by the Src family kinase Lyn and association of the BCR with the actin cytoskeleton. However, the mechanism by which BCR cross-linking initiates the cascade remains obscure. In this study, using various A20-transfected cell lines, biochemical and genetic evidence is provided that BCR cross-linking leads to the translocation of the BCR into cholesterol- and sphingolipid-rich lipid rafts in a process that is independent of the initiation of BCR signaling and does not require the actin cytoskeleton. Translocation of the BCR into lipid rafts did not require the Ig alpha/Ig beta signaling complex, was not dependent on engagement of the FcR, and was not blocked by the Src family kinase inhibitor PP2 or the actin-depolymerizing agents cytochalasin D or latrunculin. Thus, cross-linking or oligomerization of the BCR induces the BCR translocation into lipid rafts, defining an event in B cell activation that precedes receptor phosphorylation and association with the actin cytoskeleton.
Special Sunrise & Sunset Solar Energy Stored Papers and Their Clinical Applications for Intractable Pain, Circulatory Disturbances & Cancer: Comparison of Beneficial Effects between Special Solar Energy Stored Paper and Qigong Energy Stored Paper (2004)

Various phases of solar energy were evaluated for possible medical application, using the Bi-Digital O-Ring Test. A 2-4 minute interval of highly beneficial phase during sunrise and sunset which is comparable or is stronger than (+) Qigong Energy was detected. This energy was stored on 3 x 5 inch index cards. The sun energy stored on the exposed surface had a Bi-Digital O-Ring Test extremely strong positive (+) response, and the opposite side of the index card which was not exposed to the sun showed an equally strong negative (-) response. When the Bi-Digital O-Ring Test strong positive side (+) was applied to the patient's skin above various intractable painful areas with circulatory disturbances, including gangrenous pain, muscle pain, joint pain, & migraine headache, most of the pain disappeared or was significantly reduced within between 10 seconds and 5 minutes, with accelerated wound healing compared with Qigong energy stored paper of the same exposure, which caused pain to disappear within between 1.5 minutes and 15 minutes. When this Special Solar Energy Stored Paper was applied either directly to the skin above cancer positive areas or the midline of the upper chest above the thymus gland representation area, or the occipital area above the medulla oblongata, various cancer related parameters returned to close to normal values, with immediate clinical improvement. The beneficial effects of 10-60 seconds of application of the Special Solar Energy Stored Paper lasted for between 7 and 40 days, depending on the individual and their environmental electromagnetic field, how the special solar energy was stored, and how it was applied to the patient.
Tandem array of nanoelectronic readers embedded coplanar to a fluidic nanochannel for correlated single biopolymer analysis (2014)

We have developed a two-step electron-beam lithography process to fabricate a tandem array of three pairs of tip-like gold nanoelectronic detectors with electrode gap size as small as 9 nm, embedded in a coplanar fashion to 60 nm deep, 100 nm wide, and up to 150 μm long nanochannels coupled to a world-micro-nanofluidic interface for easy sample introduction. Experimental tests with a sealed device using DNA-protein complexes demonstrate the coplanarity of the nanoelectrodes to the nanochannel surface. Further, this device could improve transverse current detection by correlated time-of-flight measurements of translocating samples, and serve as an autocalibrated velocimeter and nanoscale tandem Coulter counters for single molecule analysis of heterogeneous samples.
<title>Application of anisotropic conductive films for realization of interconnects in micromechanical structures</title> (1998)

A new micromachining process, the application of an anisotropic conductive film (ACF) for micromechanical structures as well as interconnection both mechanically and electrically, is reported. The film acts as a spacer and adhesive as well as an electrical conductor in the vertical direction. The process provides very flexible design scheme and simple fabrication process. New micropump structure was proposed, and simple microstructures have been fabricated and tested successfully. The full details of experiment are reported, experiments where ACF type CP 7621 (Sony Chemical Co) was used to bond p type (100) silicon wafers.
A CONVENIENT SYNTHESIS OF ALKYL AND DIALKYL 1-BENZYLOXYAMINO ALKYL PHOSPHONATES AND PHOSPHINATES (1990)

Abstract The synthesis of diethyl 1-benzyloxyamino alkyl phosphonates was achieved via reduction of diethyl 1-benzyloxyirnino alkyl phosphonates by amino-bordne. However, the best result was obtained by esterification of 1-benzyloxyamino alkyl phosphonic and phosphinic acids with O-alkylisoureas.
Human Multidrug-Resistant Cell Lines: Increased mdr 1 Expression Can Precede Gene Amplification (1986)

The development of simultaneous resistance to multiple structurally unrelated drugs is a major impediment to cancer chemotherapy. Multidrug resistance in human KB carcinoma cells selected in colchicine, vinblastine, or Adriamycin is associated with amplification of specific DNA sequences (the multidrug resistance locus, mdr1). During colchicine selection resistance is initially accompanied by elevated expression of a 4.5-kilobase mdr1 messenger RNA (mRNA) without amplification of the corresponding genomic sequences. During selection for increased levels of resistance, expression of this mRNA is increased simultaneously with amplification of mdr1 DNA. Increased expression and amplification of mdr1 sequences were also found in multidrug-resistant sublines of human leukemia and ovarian carcinoma cells. These results suggest that increased expression of mdr1 mRNA is a common mechanism for multidrug resistance in human cells. Activation of the mdr1 gene by mutations or epigenetic changes may precede its amplification during the development of resistance.
Visible retinal lesions from ultrashort laser pulses in the primate eye. (1995)

Laser pulses for pulsewidths between 4 ns and 90 fs are capable of producing visible lesions in monkey eyes with energies less than 1 microJ. Fluorescein angiography is not as sensitive in determining threshold levels as visually observing the retina through a fundus camera.
An NMR study of the equilibria involved with benzotriazole, carbonyl compounds, and their adducts (1990)

A 1H and 13C NMR study of the equilibrium mixtures of benzotriazole and several carbonyl compounds with their adducts, in [2H6]benzene and other solvents, affords the equilibrium constants for the reversible formation of N-1 (K1) and N-2 (K2) isomeric adducts. Thermodynamic parameters have been computed. Adduct formation is generally less predominant in sterically crowded cases. In general the N-1 isomer predominates over the N-2 isomer, however, with the sterically hindered 4,7-dimethylbenzotriazole this order is reversed.
Transportable natural-language interfaces (1982)

Article Free Access Share on Transportable natural-language interfaces: problems and techniques Author: Barbara J. Grosz SRI International, Menlo Park, CA SRI International, Menlo Park, CAView Profile Authors Info & Claims ACL '82: Proceedings of the 20th annual meeting on Association for Computational LinguisticsJune 1982 Pages 46–50https://doi.org/10.3115/981251.981262Online:16 June 1982Publication History 3citation155DownloadsMetricsTotal Citations3Total Downloads155Last 12 Months4Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Detection of plasma tumor DNA in head and neck squamous cell carcinoma by microsatellite typing and p53 mutation analysis. (2000)

Recent arguments have suggested that tumor DNA in cancer patients could be found in plasma, but different points remain unclear. Using a series of 117 head and neck squamous cell carcinoma tumors, our goals for this study were: (a) to quantify the amount of plasma DNA; (b) to evaluate the presence of plasma tumor DNA; and (c) to analyze the clinical relevance of tests based on plasma DNA analyses. Low levels of plasma DNA were found in most samples, but all were successfully amplified. Two different methods were used to detect tumor-specific genetic alterations: (a) microsatellite instability at UT5085 with an established sensitivity of 1:500; and (b) p53 mutation screening. Of the 117 tumors typed at UT5085, 65 demonstrated bandshifts (55%). Plasma and tumor DNA a showed similar alteration in only one case among these samples, and the prevalence of tumor DNA in plasma was estimated to be <2% using microsatellite analysis. Tumor DNA was detected in plasma at a higher prevalence (2 of 11 cases) when using p53 mutant allele-specific amplification. These results showed that in plasma, tumor DNA is largely diluted by normal DNA. By comparison with previously published studies, the prevalence of microsatellite alterations in plasma in this series of head and neck squamous cell carcinomas is very low, despite the fact that a large series of tumors was analyzed. To explain this discrepancy, we analyzed the possibility of PCR artifacts as suspected by the presence of loss of heterozygosity in two plasma DNA samples without a similar tumor DNA alteration. When DNA concentrations were under the threshold of detection (<100 ng/ml), we demonstrated that PCR artifacts could occur at random, and, if misinterpreted, these false genetic alterations could artificially enhance the frequency of plasma DNA alterations. This may have been suspected in previously published series, but it has never been discussed before. Microsatellite analysis on plasma DNA is difficult to interpret and can frequently be misleading. Plasma DNA should be analyzed with very sensitive and specific methods such as mutant allele-specific amplification, which excludes artifacts but requires specific optimization that is probably not compatible with routine and clinical use.
PMD second-order effects on pulse propagation in single-mode optical fibers (1998)

The time-space varying birefringence in single-mode optical fibers causes the polarization mode dispersion (PMD) to be a serious problem in high bit-rate transmissions. The PMD first- and second-order statistics are well known in the literature, but second-order PMD-induced pulse distortions have still to be clarified for sequences of pulses of arbitrary shape. We give, for the first time, the exact PMD time impulse response, up to second order. We show, both numerically and experimentally, that the effect of the rotation of the principal states of polarization (PSP) is to generate power overshoots on the "1" and "0" bit sequences.
Clinical Trial of New Polyurethane Vascular Grafts for Hemodialysis: Compared with Expanded Polytetrafluoroethylene Grafts (1995)

We developed a new polyurethane vascular access graft coated with gelatin and reinforced with knitted polyester fibers (PE-PEUG). Advantages over expanded-polytetrafluoroethylene graft (E-PTFEG) were previously reported in experimental studies. Between May 1990 and August 1992, 39 PE-PEUGs including 34 loop and 5 straight and 18 E-PTFEGs including 18 loop were implanted to create arteriovenous (AV) fistulas in a total of 52 adult patients on maintenance hemodialysis (HD). They were followed up until October 1994. Hemostasis on the suture line was achieved within 3 min in all patients implanted with PE-PEUGs. Bleeding from the needle holes of PE-PEUG stopped within 10 min with gentle finger pressure. Minimal local edema developed in only a few patients implanted with PE-PEUG while most patients implanted with E-PTFEG developed moderate local edema. One seroma formation was found in an E-PTFE case. Aneurysmal dilatations were observed twice in a PE-PEUG patient 9 and 17 months after the implantation and once in a E-PTFEG patient 2 years after the implantation. The cumulative patency rate at 1 year in the PE-PEUG and E-PTFEG groups were 53.2 and 70.8%, respectively. Our clinical study showed that the PE-PEUG had several advantages over E-PTFEG: prompt hemostasis, no persistent edema and no formation of seroma, no change in elasticity, and sufficient mechanical strength. However, the cumulative patency rate was inferior to that with E-PTFEG implanted in our series. Further modifications are therefore necessary to improve the patency rate.
Reconstitution of antigen presentation in HLA class I-negative cancer cells with peptide-β2m fusion molecules (2001)

Engineered MHC-peptide targets capable of inducing recognition by CTL may prove useful in designing vaccines for infectious disease and cancer. We tested whether peptides directly linked to beta2-microglobulin (beta2m) could complex with human HLA class I heavy chain, and could be recognized by human CTL, both as soluble reagents and as cell surface constituents. An HLA-A2-restricted peptide epitope was physically linked to the N terminus of human beta2m. This fusion protein refolded efficiently in vitro with HLA-A2 heavy chain, and when multimerized, the resultant complexes ("fusamers") bound specifically to appropriate CTL clones. These fused peptide/MHC complexes were as efficient as standard tetrameric peptide/MHC complexes in recognizing antigen-specific CTL. When the fusion protein was delivered to target cells using a retroviral vector, these cells were recognized and killed by appropriate CTL clones. Efficient sensitization to CTL lysis was achieved in TAP-negative and beta2m-negative cell lines, as well as in unmutated B cell lines, proving that such constructs may be effective in inducing CTL even when the MHC class I pathway has been disrupted. Specific peptides covalently linked to beta2m and delivered via retroviral vectors may be useful reagents for in vivo priming of CTL against epitopes of clinical relevance.