gebhart/patrepeval huggingface dataset:
Antimicrobial polypeptides (2003)

The respiratory tract presents a large and potentially vulnerable surface to inhaled microbes. It is coated by a thin layer of secretions generated by airway epithelial cells, submucosal glands, resident and recruited phagocytes (neutrophils, eosinophils, monocytes, and macrophages) and alveolar epithelial cells, as well as substances that enter from blood plasma. More than 80 years ago, Alexander Fleming observed that respiratory secretions have microbicidal and microbistatic properties. He described the activity of lysozyme, one of the principal polypeptides of these secretions. Since then, a number of additional antimicrobial components have been identified, and there is increasing insight into their complex interactions. This review is an update of my previous summary of this area.
Identification and characterization of a gene product that regulates type 1 piliation in Escherichia coli (1984)

The recombinant plasmid pSH2 confers type 1 piliation (Pil+) on a nonpiliated (Pil-) strain of Escherichia coli K-12. At least four plasmid-encoded gene products are involved in pilus biosynthesis and expression. We present evidence which indicates that one gene encodes an inhibitor of piliation. Hyperpiliated (Hyp) mutants were isolated after Tn5 insertion mutagenesis of pSH2 and introduction of the plasmid DNA into a Pil- strain of E. coli as unique small, compact colonies. Also, Hyp mutants clumped during growth in static broth and were piliated under several cultural conditions that normally suppressed piliation. Electron microscopic examination of Hyp mutants associated an observed 40-fold increase in pilin antigen with an increase in the number and length of pili per cell. All Hyp mutants examined failed to produce a 23-kilodalton protein that was encoded by a gene adjacent to the structural (pilin) gene for type 1 pili, and all Tn5 insertion mutations that produced the Hyp phenotype mapped in this region (hyp). Piliation in Hyp mutants could be reduced to near parental levels by introducing a second plasmid containing a parental hyp gene. Thus the 23-kilodalton (hyp) protein appears to act in trans to regulate the level of piliation.
Ionic Liquid Electrolyte for Lithium Metal Batteries: Physical, Electrochemical, and Interfacial Studies of N-Methyl-N-butylmorpholinium Bis(fluorosulfonyl)imide (2010)

The ionic liquid (IL) N-methyl-N-butylmorpholinium bis(fluorosulfonyl)imide (C4mmor FSI) is examined from physical and electrochemical perspectives. Pulsed field gradient NMR spectroscopy shows that ion diffusivities are low compared with similar, non-ethereal ILs. Ionicity values indicate that above room temperature, less than 50% of ions contribute to conductivity. Lithium cycling in symmetrical cells using a C4mmor FSI-based electrolyte is best demonstrated at elevated temperatures. Specific capacities of 130 mAh g−1 are achieved in a Li−LiFePO4 battery at 85 °C. FT-IR spectroscopic investigations of lithium electrodes suggest the presence of alkoxide species in the solid electrolyte interphase (SEI), implying a ring-opening reaction of C4mmor with lithium metal. In contrast, the SEI derived from N-methyl-N-propylpiperidinium FSI lacks the alkoxide signature but shows signs of alkyl unsaturation, and the activation energy for Li+ transport through this SEI is slightly lower than that for the C4mmor-derived SEI. Our detailed findings give insight into the capabilities and limitations of rechargeable lithium metal batteries utilizing a C4mmor FSI electrolyte.
Induction of CD8 T-Cell-Specific Systemic and Mucosal Immunity against Herpes Simplex Virus with CpG-Peptide Complexes (2002)

Oligodeoxynucleotides (ODN) containing unmethylated CpG motifs exert powerful adjuvant activity in vivo and in vitro. Administered with antigen they induce a population of antigen-specific CD8+ T cells. In this study we immunized C57BL/6 mice with bioactive CpG ODN combined with an immunodominant epitope derived from herpes simplex virus (HSV) glycoprotein B (amino acids 498 to 505; SSIEFARL) and analyzed the magnitude and durability of the peptide-specific response. The effectiveness of the CD8+ T-cell response as measured by peptide-specific tetramers, peptide-induced intracellular gamma interferon expression, and resistance to systemic and mucosal challenge during the acute and memory phases was compared with the response induced by immunization with recombinant vaccinia virus encoding SSIEFARL as a minigene (VvgB(498-505)). Confirming the reports of others, our results demonstrate that the CpG ODN-peptide approach generates an antigen-specific CD8+ T-cell population, but the frequency of CD8+ T cells is lower than that induced by VvgB(498-505). Nevertheless, the protection level was comparable when mice were systemically and mucosally challenged during the acute phase. However, such responses by both groups waned with time and were functionally less effective. Still, our results indicate that the CpG ODN-peptide immunization system holds promise as a means of selectively inducing a CD8+ T-cell response against HSV.
The β-Lactone Route to β-Hydroxy or α,β-Unsaturated γ- and δ-Lactones. Syntheses of (±)-Massoialactone and (±)-Prelactone B (2002)

Aqueous HF promotes the translactonization of silyloxy β-lactones into β-hydroxy or α,β-unsaturated γ- and δ-lactones. The reaction is studied from a theoretical point of view and applied to the racemic synthesis of two natural bioactive δ-lactones.
Analytical Validation of Serum Proteomic Profiling for Diagnosis of Prostate Cancer: Sources of Sample Bias (2007)

Abstract Background: This report and a companion report describe a validation of the ability of serum proteomic profiling via SELDI-TOF mass spectrometry to detect prostatic cancer. Details of this 3-stage process have been described. This report describes the development of the algorithm and results of the blinded test for stage 1. Methods: We derived the decision algorithm used in this study from the analysis of serum samples from patients with prostate cancer (n = 181) and benign prostatic hyperplasia (BPH) (n = 143) and normal controls (n = 220). We also derived a validation test set from a separate, geographically diverse set of serum samples from 42 prostate cancer patients and 42 controls without prostate cancer. Aliquots were subjected to randomization and blinded analysis, and data from each laboratory site were subjected to the decision algorithm and decoded. Results: Using the data collected from the validation test set, the decision algorithm was unsuccessful in separating cancer from controls with any predictive utility. Analysis of the experimental data revealed potential sources of bias. Conclusion: The ability of the decision algorithm to successfully differentiate between prostate cancer, BPH, and control samples using data derived from serum protein profiling was compromised by bias.
The Elicitor-Inducible Alfalfa Isoflavone Reductase Promoter Confers Different Patterns of Developmental Expression in Homologous and Heterologous Transgenic Plants (1994)

Abraham Oommen, Richard A. Dixon, Nancy L. Paiva, The Elicitor-Inducible Alfalfa Isoflavone Reductase Promoter Confers Different Patterns of Developmental Expression in Homologous and Heterologous Transgenic Plants, The Plant Cell, Vol. 6, No. 12 (Dec., 1994), pp. 1789-1803
TNFa inhibitor C87 sensitizes EGFRvIII transfected glioblastoma cells to gefitinib by a concurrent blockade of TNFa signaling (2019)

Our findings provide a possible explanation for the primary resistance of glioblastoma to EGFR inhibitors and suggest that dual blockade of TNFα and EGFR may be a viable therapeutic strategy for the treatment of patients with chemotherapy-refractory advanced glioblastoma.
Preparation and dioxygen binding properties of a new cobalt(II) complex and the crystal structure of the corresponding copper(II) adduct (1991)

The synthesis and characterization of a new cobalt(II) complex [Co(Me2H2Me2malox)(py)2][Me2H2Me2malox = 4,4′-oxalyldinitrilodi(pent-2-en-2-olato)(2–), py = pyridine], based on a chelating ligand containing no saturated chelate rings, is described together with the corresponding cobalt(III) complex. The cobalt(II) complex binds dioxygen in a reversible manner in pyridine solution at temperatures near –20 °C. The corresponding copper(II) complex [Cu(Me2H2Me2Me2malox)] crystallizes in the monoclinic system P21/c with a= 8.866(1), b= 16.029(1), c= 9.106(1)Å, β= 97.57(2)° and Z= 4. Structural refinement resulted in R= 0.0423 and R′= 0.0436 for 2153 observed reflections. Studies of [Cu(Me2H2Me2malox)] using X-ray crystallography and IR spectroscopy guided the development of the synthetic procedure used in the isolation of the cobalt(II) adduct. A six-co-ordinate cobalt(III) complex is reported as a model for the cobalt–dioxygen adduct. Proton exchange with solvent has been observed using NMR spectroscopy and implications for the rational design of dioxygen carriers is discussed.
A DNA deletion associated with multiple impaired transcripts in the visual mutant TRP. (1987)

The transient receptor potential (trp) mutant in Drosophila is known to manifest retinal degeneration and involves defects in the intermediate steps of visual transduction. The chromosome walking technique has been conducted at the cytogenetic location of trp. Overlapping phage clones that cover a DNA stretch of 73 kb were obtained. Southern blotting studies detected a 2.3 kb DNA deletion within this region in the mutant. The deleted DNA fragment contains exons of three transcripts with lengths of 3.5, 1.5 and 0.8 kb. The transcription of the 3.5 and 1.5 kb RNAs is completely abolished in the mutant, whereas that of 0.8 kb RNA appears to be modified. The impairment in production of three RNAs, due to the DNA deletion, offers a possible molecular basis of the multiple defects displayed by the trp- phenotype.
Fabrication of Sub-5 nm Nanochannels in Insulating Substrates Using Focused Ion Beam Milling (2010)

The use of focused ion beam (FIB) milling to fabricate nanochannels with critical dimensions extending below 5 nm is described. FIB milled lines have narrowing widths as they are milled deeper into a substrate. This focusing characteristic is coupled with a two-layered architecture consisting of a relatively thick (>100 nm) metal film deposited onto a substrate. A channel is milled through the metal layer until it penetrates a prescribed depth into the substrate material. The metal is then removed, leaving a nanochannel with smooth surfaces and lateral dimensions as small as sub-5 nm. These open nanochannels can be sealed with a cover plate and the resulting devices are well-suited for single-molecule DNA transport studies. This methodology is used with quartz, single-crystal silicon, and polydimethylsiloxane substrates to demonstrate its general utility.
Saposin C Is Required for Normal Resistance of Acid β-Glucosidase to Proteolytic Degradation (2003)

Saposins (A, B, C, and D) are small sphingolipid activator proteins that are derived by proteolytic processing of a common precursor, prosaposin. In the lysosomal sphingolipid degradation pathway, acid beta-glucosidase (GCase) requires saposin C for optimal in vitro and in vivo hydrolysis of glucocerebroside. The deficiency of prosaposin/saposins (PS-/-) in humans and mice leads to a decrease of GCase activity in selected tissues. Concordant decreases (>50%) of GCase protein and in vitro activity were detected in extracts of cultured fibroblasts and hepatocytes from PS-/- mice and human prosaposin-deficient fibroblasts. GCase RNA in the PS-/- cells was at wild-type levels. Compared with that in wild-type cells (t(1/2) >24 h), the GCase protein in the PS-/- cells had a faster disappearance rate (t(1/2) approximately 1 h in mouse and approximately 8 h in human) as determined by metabolic labeling and immunoprecipitation with anti-GCase antibodies. Treatment of PS-/- cells with leupeptin, an inhibitor of cysteine proteases, led to significant increases (approximately 2-fold) in GCase protein and in vitro activity. Loading saposin C to human PS-/- fibroblasts resulted in an enhancement of GCase protein and in vitro activity. Saposin D loading had no effect. These data indicate that saposin C is required for GCase resistance to proteolytic degradation in the cell. Thus, diminished in vivo GCase activity would be greater than expected only from the lack of GCase activation by saposin C. These results indicate a new property for saposin C, an anti-proteolytic protective function toward GCase.
The Best Setting for Working With School-Age Children is in the Schools! (2003)

No AccessPerspectives on Language Learning and EducationArticle1 Jul 2003The Best Setting for Working With School-Age Children is in the Schools! June Haerle Campbell June Haerle Campbell Private PracticeCarmel, CA Google Scholar More articles by this author https://doi.org/10.1044/lle10.2.12 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationTrack Citations ShareFacebookTwitterLinked In References Chmela, K., & Reardon, N. (2001). The school-age child who stutters: Working effectively with attitudes ad emotions. Memphis, TN: Stuttering Foundation of America. Google Scholar Gregory, H. H., Campbell, J. H., Gregory, C. B., & Hill, D. H. (2003). Stuttering therapy. Rationale and procedures. Boston: Allyn and Bacon. Google Scholar Piaget, J., & Inhelder, B. (1958). The growth of logical thinking from childhood to adolescence. New York: Basic Books. Google Scholar Suggested Readings and Videotapes Faber, A., & Mazlish, E. (1980). How to talk so kids will listen and listen so kids will talk. New York: Avon Books. Google Scholar Conture, E. G. (2002) Stuttering: Its nature, diagnosis and treatment. Boston: Allyn and Bacon. Google Scholar Guitar, B. (1998). Stuttering: An integrated approach to its nature and treatment. Baltimore: Williams and Wilkins. Google Scholar J. S. Yaruss (Ed.). (2002). Facing the challenge of treating stuttering in the schools Part 1: Selecting goals and strategies for success.Seminars in Speech and Language, 23(3). Google Scholar J. S. Yaruss (Ed.). (2003). Facing the challenge of treating stuttering in the schools Part II: Selecting goals and strategies for success.Seminars in Speech and Language, 24(1). Google Scholar Stuttering Foundation of America. Videotapes. 1-800-992-9392 (2001). Stuttering and the preschool child: Help for families. (. (1998). Therapy in action: The school-age child who stutters. (. (2003). Do you stutter: Straight talk for teens. (. (2002) Stuttering: Straight talkfor teachers. (. (2003). Coun-seling: Listening to and talking with parents of children who stutter. Google Scholar Additional Resources FiguresReferencesRelatedDetails Volume 10Issue 2July 2003Pages: 12-16 Get Permissions Add to your Mendeley library History Published in issue: Jul 1, 2003 Metrics Topicsasha-topicsasha-article-typesasha-sigsCopyright & Permissions© 2003 American Speech-Language-Hearing AssociationPDF DownloadLoading ...
Phase Interferometry Direction Finding (2012)

This paper describes the development of a phase interferometry direction finding system for an airborne platform developed for MIT Lincoln Laboratory. A phase interferometer uses the phase difference to determine the Angle of Arrival (AoA) of a received signal. The team utilized three antennas to resolve phase ambiguities and determined the AoA for received electromagnetic signals in the X band to within 0.1 degrees in simulations including realistic noise models for a 170 degree field of view. A prototype was implemented using an FPGA-based board for data acquisition connected via USB to a PC for analysis, which connected to another PC via a TCP connection for display. The team developed a graphical user interface for the system to display results to a system operator.
Gene Targeting in Malaria Parasites (1997)

Gene targeting, which permits alteration of a chosen gene in a predetermined way by homologous recombination, is an emerging technology in malaria research. Soon after the development of techniques for stable transformation of red blood cell stages of Plasmodium falciparum and Plasmodium berghei, genes of interest were disrupted in the two species. The main limitations of gene targeting in malaria parasites result from the intracellular growth and slow replication of these parasites. On the other hand, the technology is facilitated by the very high rate of homologous recombination following transformation with targeting constructs (approximately 100%). Here, we describe (i) the vector design and the type of mutation that may be generated in a target locus, (ii) the selection and screening strategies that can be used to identify clones with the desired modification, and (iii) the protocol that was used for disrupting the circumsporozoite protein (CS) and thrombospondin-related anonymous protein (TRAP) genes of P. berghei.
Developmental Regulation of Lectin and Alliinase Synthesis in Garlic Bulbs and Leaves (1997)

Using a combination of northern blot analysis and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, a detailed study was made of the temporal and spatial regulation of garlic (Allium sativum L.) lectins and alliinase throughout the life cycle of the plant. The two bulb-specific lectins (ASAI and ASAII), which are the most predominant bulb proteins, accumulate exclusively in the developing garlic cloves and progressively disappear when the old clove is consumed by the plant. On the basis of these observations, ASAI and ASAII can be regarded as typical vegetative storage proteins. The leaf-specific lectin (ASAL), on the contrary, is specifically synthesized in young leaves and remains present until withering. Because ASAL is only a minor protein, it probably fulfills a specific function in the plant. Unlike the lectins, alliinase is present in large quantities in bulbs as well as in leaves. Moreover, intact alliinase mRNAs are present in both tissues as long as they contain living cells. The latter observation is in good agreement with the possible involvement of alliinase in the plant's defense against pathogens and/or predators.
In SituGABAergic Modulation of Synchronous Gonadotropin Releasing Hormone-1 Neuronal Activity (2002)

Evidence indicates that gonadotropin releasing hormone-1 [GnRH-1, also known as luteinizing hormone releasing hormone (LHRH)] neurons can exhibit synchronized neuroendocrine secretory activity before entrance into the CNS. In this study, we used calcium imaging to evaluate patterns of activity in individual, embryonic, GnRH-1 neurons as well as population dynamics of GnRH-1 neurons in mouse nasal explants maintained for 1 versus 3 weeks. Independent of age, GnRH-1 neurons displayed significant calcium peaks that synchronized at an interval of approximately 20 min across multiple GnRH-1 cells within an explant. Acute tetrodotoxin treatment decreased the amplitude of calcium peaks in individual GnRH-1 neurons and the duration but not the frequency of synchronized activity in the population of GnRH-1 neurons. Acute GABA(B) receptor antagonism increased the frequency of synchronized neuronal activity at both ages, whereas acute GABA(A) receptor antagonism decreased calcium oscillations in individual GNRH-1 cells as well as synchronization of the calcium pulses within the GnRH-1 population at the 1 week time point to background non-GNRH-1 cell levels. These results indicate that developing GnRH-1 neurons rely heavily on GABAergic signaling to initiate synchronized bouts of activity but thereafter, possess an innate capacity for synchronized activity patterns that are modulated by, but not completely dependent on GABAergic signaling.
Fine specificity and HLA restriction of myelin basic protein-specific cytotoxic T cell lines from multiple sclerosis patients and healthy individuals. (1990)

Myelin basic protein (MBP) is a candidate Ag for the autoimmune process believed to be involved in the pathogenesis of multiple sclerosis (MS). To investigate the fine specificity and HLA restriction of human MBP-specific CTL, long term T cell lines (TCL) were established from 22 MS patients and 16 healthy individuals by repeated antigenic restimulation. By using this approach, MBP-specific cytotoxic TCL were generated from 81% of the lines from MS patients and 69% of those from controls. TCL from both groups expressed the CD3+, CD4+, CD8- phenotype and secreted substantial amounts of IFN-gamma. By using large enzymatic and small synthetic peptides of MBP, TCL were primarily specific for the C-terminal part of the molecule and to a lesser extent for the N-terminal portion. Two regions of the molecule, MBP peptide 87-106 and MBP peptide 154-172, were recognized by the majority of the polyspecific lines and by four and three of 14 monospecific TCL, respectively. These highly immunogenic regions are of interest because they include sequences encephalitogenic in other species. The HLA restriction of each line was determined by using antibody blocking as well as various target cells including EBV-transformed B cells, homozygous typing cells, and fibroblasts transfected with cDNA for DR-alpha and DR-beta genes. All TCL were restricted by HLA-DR Ag. Several HLA-DR molecules restricted multiple cathepsin D-derived and synthetic MBP peptides, including the regions of peptides 87-106 and 154-172 which, respectively, were recognized in conjunction with four and three HLA-DR types. Three of these HLA-DR types are overrepresented in MS patients in different geographic regions. Together, these findings suggest that the MBP-specific cytotoxic T cell response, although not sufficient for disease, may be important for the pathogenesis of MS.
The Dose of a Putative Ubiquitin-Specific Protease Affects Position-Effect Variegation in Drosophila melanogaster (1996)

A dominant insertional P-element mutation enhances position-effect variegation in Drosophila melanogaster. The mutation is homozygous, viable, and fertile and maps at 64E on the third chromosome. The corresponding gene was cloned by transposon tagging. Insertion of the transposon upstream of the open reading frame correlates with a strong reduction of transcript level. A transgene was constructed with the cDNA and found to have the effect opposite from that of the mutation, namely, to suppress variegation. Sequencing of the cDNA reveals a large open reading frame encoding a putative ubiquitin-specific protease (Ubp). Ubiquitin marks various proteins, frequently for proteasome-dependent degradation. Ubps can cleave the ubiquitin part from these proteins. We discuss the link established here between a deubiquitinating enzyme and epigenetic silencing processes.
MRI systems as a mean of propulsion for a microdevice in blood vessels (2004)

The use of an MRI system as a mean of propulsion for a small robot for applications in blood vessels is being studied. The strong and variable magnetic field of the MRI system will exert three dimensional propulsion force to a ferromagnetic core that will be embedded onto the future small robot. The paper describes studies conducted concerning the ability of MRI gradients to propel a ferromagnetic body and the possibility to use MR images to track it. Experimental studies showed that a 3.175 mm diameter, 1010/1020 carbon steel sphere was able to withstand a maximum flow of 0.4115 l/min. in a 6.35 mm diameter tube when a magnetic field gradient of 18 mT/m was applied on it. Images made with spin echo and gradient echo sequences showed that imaging distortions (artifacts) caused by ferromagnetic cores are several times larger than the size of the core itself. It is critical to measure accurately the position of the future robot. The elimination or reduction of such ferromagnetic artifacts is currently a serious problem. Therefore, alternative solutions to the imaging problems like artifact cancellation, artifact pattern tracking softwares or magnetic tracking systems need to be developed.