gebhart/patrepeval huggingface dataset:
Bactericidal activity of synthetic peptides based on the structure of the 55-kilodalton bactericidal protein from human neutrophils (1994)

Short (10- to 11-mer) hydrophilic peptides based on the structure of the 55-kDa bactericidal protein (BP55, B/PI, and CAP57) from human neutrophil granules were identified from the hydropathy plot of the 456-amino-acid sequence predicted from the nucleotide sequences of cDNA clones for BP55 and B/PI. Peptides corresponding to amino acid residues 90 to 99 (peptide #90-99), 86 to 99, or 90 to 102 of BP55 were bactericidal toward 5 x 10(6) Pseudomonas aeruginosa cells at 0.6 x 10(-5) to 1.5 x 10(-5) M and killed an Escherichia coli rough strain at 3 x 10(-5) M. The #90-99 peptide with a cysteine added at the amino terminus (C#90-99) was approximately 10 times more active than #90-99, killing P. aeruginosa at 1.5 x 10(-6) M. Peptides representing amino acid residues 27 to 37, 118 to 127, and 160 to 170 and the first 10 amino acids of the signal sequence for BP55 were not bactericidal. When coupled to either keyhole limpet hemocyanin or ovalbumin protein carriers through the thiol group, the C#90-99 peptide was not diminished on a molar basis in its capacity for killing of P. aeruginosa. Two other relatively hydrophilic peptides with an added amino-terminal cysteine, peptides C#227-236 and C#418-427, were not bactericidal at 1.2 x 10(-4) M or at 100 times the effective bactericidal concentration of C#90-99. The C#90-99 peptide killed E. coli at 1.5 x 10(-5) M, or at 10 times the concentration required to kill an equal number of P. aeruginosa cells. Although Pseudomonas cepacia and Staphylococcus aureus were resistent to killing by the parent BP55 molecule, they were susceptible to the C#90-99 and #90-99 peptides in the same concentration range as was E. coli. When all peptides were compared for the ability to neutralize E. coli O55:B5 endotoxin in a Limulus amoebocyte lysate assay, the C#227-236, C#418-427, and #160-170 peptides completely inhibited gelation at a 10(-4) M concentration. All other synthetic peptides, including bactericidal peptide #90-99 and its congeners, lacked endotoxin-neutralizing activity at the highest concentration tested (4.5 x 10(-4) M). A hybrid of the C#227-236 and #90-99 peptides (CHybrid) was identical to the C#227-236 peptide component in effectiveness for carrying out endotoxin neutralization and was fivefold better than the #90-99 peptide in its capacity for killing P. aeruginosa.
A Breakthrough in the Safety of Lithium Secondary Batteries by Coating the Cathode Material with AlPO4 Nanoparticles (2003)

The hard cell! There have been numerous reports highlighting the questionable safety of lithium secondary batteries, an example of which is shown here, where exothermic reactions of LiCoO2 electrodes have considerable fire and explosion potential. The coating of such electrodes with a layer of AlPO4 nanoparticles is shown to reduce these risks significantly, even where a short circuit of the cell was observed.
BIOCLIM - a bioclimate analysis and prediction system (1991)

BIOCLIM can be used to map the distribution of any entity, including pest species. For pest species, this enables control efforts to be focussed on areas of most likely spread or where it is most probable that further populations will be found. BIOCLIM also has the capacity to predict alterations in the potential distribution of a species brought about by a climate change.
Multiple Paths for Activation of Naive CD8+ T Cells: CD4-Independent Help (2001)

CD8(+) CTLs play a pivotal role in immune responses against many viruses and tumors. Two models have been proposed. The "three-cell" model focuses on the role of CD4(+) T cells, proposing that help is only provided to CTLs by CD4(+) T cells that recognize Ag on the same APC. The sequential "two-cell" model proposes that CD4(+) T cells can first interact with APCs, which in turn activate naive CTLs. Although these models provide a general framework for the role of CD4(+) T cells in mediating help for CTLs, a number of issues are unresolved. We have investigated the induction of CTL responses using dendritic cells (DCs) to immunize mice against defined peptide Ags. We find that help is required for activation of naive CTLs when DCs are used as APCs, regardless of the origin or MHC class I restriction of the peptides we studied in this system. However, CD8(+) T cells can provide self-help if they are present at a sufficiently high precursor frequency. The important variable is the total number of T cells responding, because class II-knockout DCs pulsed with two noncompeting peptides are effective in priming.
Sleeve-Type Ultra Miniature Optical Fiber Pressure Sensor Fabricated by DRIE (2008)

A diaphragm-type optical fiber pressure sensor, which has a sleeve for fiber insertion, is proposed, and its fundamental characteristics are demonstrated. The sleeve structure is fabricated by deep reactive ion etching (DRIE). The diaphragm with the sleeve is suitable for highly reliable and easy bonding between the sleeve and an optical fiber. The light intensity change by a Fabry-Perot interferometer according to pressure is increases by an improved DRIE method. The mesa attached to the diaphragm increased reflectance. The method of mass production for the developed diaphragm will be useful for realizing a low-cost pressure sensor.
Resisting Electronic Payment Systems: Burning Down the House? (1999)

This commentary explains the phenomena of path dependence, hysteresis, and network economies using lively historical and contemporary examples. The author shows how the path dependence and network economies can interact to produce a variety of undesirable ends-inefficient payment systems, the adoption of inferior technology, or disasters like the 1834 fire that destroyed the British House of Lords.
Enantioselektive Synthese von α‐Methyl‐α‐amino‐carbonsäuren durch Alkylierung des Lactimethers von cyclo‐(L‐Ala‐L‐Ala) (1979)

Präparativ wertvolle asymmetrische Aminosäuresynthesen müssen einfach auszuführen sein, optische Ausbeuten &gt; 90% ergeben und ggf. die Wiedergewinnung des chiralen Hilfsagens ermöglichen. Die neue Synthese über cyclo ‐( L ‐Ala‐ L ‐Ala) erfüllt diese Anforderungen. magnified image
Differential in vitro activation of CD4+CD8- and CD8+CD4- herpes simplex virus-specific human cytotoxic T cells. (1989)

In order to clarify the differential activation of CD4+ and CD8+ HSV-specific CTL, we compared the characteristics of CTL generated by different methods of in vitro HSV stimulation by treatment of effectors with anti-CD4 and anti-CD8 mAb and C after the elimination of nonspecific cytotoxic effector cells. Cell-free HSV mainly activated CD4+ CTL precursors, whereas HSV-infected fibroblasts were more effective in activating CD8+ CTL precursors than CD4+ CTL precursors. In addition, limiting dilution analyses with enriched T cells from two HSV-seropositive donors revealed that the frequency of HSV-specific CD4+ CTL precursors responsive to stimulation with free HSV was approximately 1/4,000 to 6,000 CD4+ T cells, whereas that of precursors responsive to stimulation with HSV-infected fibroblasts was approximately 1/19,000 to 22,000 CD4+ T cells. Conversely, the frequency of CD8+ CTL precursors in peripheral blood responsive to stimulation with free HSV was approximately 1/28,000 to 30,000 CD8+ T cells, whereas that of precursors responsive to stimulation with HSV-infected fibroblasts was approximately 1/10,000 to 11,000 CD8+ T cells. The present data suggest that generalized viral infection due to cell-free viruses is fought mainly by CD4+ CTL, which have previously been reported to possess both cytotoxicity and helper function, and that localized viral infection on HLA class II-negative fibroblasts is prevented from spreading to adjacent cells mainly by CD8+ CTL. Such differential activation of CD4+ and CD8+ CTL seems probable when considering the protective mechanisms against viral infection.
Histone Deacetylase 6 and Heat Shock Protein 90 Control the Functions of Foxp3 + T-Regulatory Cells (2011)

Foxp3(+) T-regulatory cells (Tregs) are key to immune homeostasis such that their diminished numbers or function can cause autoimmunity and allograft rejection. Foxp3(+) Tregs express multiple histone/protein deacetylases (HDACs) that regulate chromatin remodeling, gene expression, and protein function. Pan-HDAC inhibitors developed for oncologic applications enhance Treg production and Treg suppression function but have limited nononcologic utility given their broad actions and various side effects. We show, using HDAC6-deficient mice and wild-type (WT) mice treated with HDAC6-specific inhibitors, that HDAC6 inhibition promotes Treg suppressive activity in models of inflammation and autoimmunity, including multiple forms of experimental colitis and fully major histocompatibility complex (MHC)-incompatible cardiac allograft rejection. Many of the beneficial effects of HDAC6 targeting are also achieved by inhibition of the HDAC6-regulated protein heat shock protein 90 (HSP90). Hence, selective targeting of a single HDAC isoform, HDAC6, or its downstream target, HSP90, can promote Treg-dependent suppression of autoimmunity and transplant rejection.
Conjugate addition of nitrogen nucleophiles to an alpha,beta-unsaturated pyrrolidinone (1997)

The conjugate addition of nitrogen nucleophiles to α,β-unsaturated lactam 1b under very mild conditions occurs in good yield with high diastereoselectivity. Deprotection provides a simple access to β-aminopyrrolidinones in excellent overall yield.
Inflammatory Markers and Risk of Developing Type 2 Diabetes in Women (2004)

We conducted a prospective, nested, case-control study of inflammatory markers as predictors of type 2 diabetes among 32,826 women who provided blood samples in 1989 through 1990 in the Nurses' Health Study. Among women free of diabetes, cardiovascular disease, or cancer at baseline, 737 had developed diabetes by 2000. Control women (n = 785) were selected matched on age, fasting status, race, and BMI for cases in the top BMI decile. Baseline levels of tumor necrosis factor (TNF)-alpha receptor 2, interleukin (IL)-6, and C-reactive protein (CRP) were significantly higher among case than control subjects (all P </= 0.001). After adjusting for BMI and other lifestyle factors, all three biomarkers significantly predicted diabetes risk; the odds ratios (ORs) comparing extreme quintiles were 1.64 (95% CI 1.10-2.45) for TNF-alphaR2, 1.91 (1.27-2.86) for IL-6, and 4.36 (2.80-6.80) for CRP (P for trend <0.001 for all biomarkers). In a multivariate model simultaneously including the three biomarkers, only CRP levels were significantly associated with risk of diabetes (OR comparing extreme quintiles of CRP = 3.99, P for trend <0.001). These data support the role of inflammation in the pathogenesis of type 2 diabetes. Elevated CRP levels are a strong independent predictor of type 2 diabetes and may mediate associations of TNF-alphaR2 and IL-6 with type 2 diabetes.
Microvesicles Released from Human Renal Cancer Stem Cells Stimulate Angiogenesis and Formation of Lung Premetastatic Niche (2011)

Recent studies suggest that tumor-derived microvesicles (MV) act as a vehicle for exchange of genetic information between tumor and stromal cells, engendering a favorable microenvironment for cancer development. Within the tumor mass, all cell types may contribute to MV shedding, but specific contributions to tumor progression have yet to be established. Here we report that a subset of tumor-initiating cells expressing the mesenchymal stem cell marker CD105 in human renal cell carcinoma releases MVs that trigger angiogenesis and promote the formation of a premetastatic niche. MVs derived only from CD105-positive cancer stem cells conferred an activated angiogenic phenotype to normal human endothelial cells, stimulating their growth and vessel formation after in vivo implantation in immunocompromised severe combined immunodeficient (SCID) mice. Furthermore, treating SCID mice with MVs shed from CD105-positive cells greatly enhanced lung metastases induced by i.v. injection of renal carcinoma cells. Molecular characterization of CD105-positive MVs defines a set of proangiogenic mRNAs and microRNAs implicated in tumor progression and metastases. Our results define a specific source of cancer stem cell-derived MVs that contribute to triggering the angiogenic switch and coordinating metastatic diffusion during tumor progression.
Mode conversion in planar-dielectric separating waveguides (1975)

The mode-conversion behavior of branching or separating planar-dielectric waveguides is studied theoretically as a function of branch asymmetry and taper slope. When the taper slope is large in a near-symmetric structure, considerable mode conversion will occur and the structure will act as a power divider. In an asymmetric structure with small taper slope, mode conversion is negligible and the structure will act as a mode splitter. A quantitative formula is presented which can be used to determine the behavior of a given separating structure.
Zwitterionic Polysaccharides Stimulate T Cells by MHC Class II-Dependent Interactions (2002)

Polysaccharides of pathogenic extracellular bacteria commonly have negatively charged groups or no charged groups at all. These molecules have been considered classic T cell-independent Ags that do not elicit cell-mediated immune responses in mice. However, bacterial polysaccharides with a zwitterionic charge motif (ZPSs), such as the capsular polysaccharides of many strains of Bacteroides fragilis, Staphylococcus aureus, and Streptococcus pneumoniae type 1 elicit potent CD4(+) T cell responses in vivo and in vitro. The cell-mediated response to ZPS depends on the presence of both positively charged and negatively charged groups on each repeating unit of the polysaccharide. In this study, we define some of the requirements for the presentation of ZPS to CD4(+) T cells. We provide evidence that direct interactions of T cells with APCs are essential for T cell activation by ZPS. Monocytes, dendritic cells, and B cells are all able to serve as APCs for ZPS-mediated T cell activation. APCs lacking MHC class II molecules do not support this activity. Furthermore, mAb to HLA-DR specifically blocks ZPS-mediated T cell activation, while mAbs to other MHC class II and class I molecules do not. Immunoprecipitation of lysates of MHC class II-expressing cells following incubation with ZPS shows binding of ZPS and HLA-DR. Electron microscopy reveals colocalization of ZPS with HLA-DR on the cell surface and in compartments of the endocytic pathway. These results indicate that MHC class II molecules expressing HLA-DR on professional APCs are required for ZPS-induced T cell activation. The implication is that binding of ZPS to HLA-DR may be required for T cell activation.
An early effect of retinoic acid: cloning of an mRNA (Era-1) exhibiting rapid and protein synthesis-independent induction during teratocarcinoma stem cell differentiation. (1988)

Vitamin A and its derivatives (retinoids) exhibit profound effects on the proliferation and differentiation of many cell types. However, the molecular mechanism by which retinoids exert these effects is unknown. Cultured murine F9 teratocarcinoma stem cells, which differentiate into nontumorigenic endoderm cells in response to retinoic acid (RA), have been used to identify genes regulated by RA. A cDNA library synthesized from F9 cells treated with RA for 8 hr has been screened with a cDNA probe enriched for sequences rapidly induced by RA, and a gene that exhibits the characteristics of a primary target for RA has been identified. This gene, early retinoic acid-1 (Era-1), encodes a 2.2- to 2.4-kilobase polyadenylylated RNA; the level of Era-1 mRNA rapidly and transiently increases up to 35-fold, depending on the concentration of exogenous RA. The increase in Era-1 mRNA is dependent on the continuous presence of exogenous RA. The RA-associated increase in Era-1 mRNA is seen even in the presence of protein synthesis inhibitors, but the increase is prevented by inhibitors of RNA synthesis such as actinomycin D. This increase in the steady-state level of Era-1 mRNA in F9 cells is a very early effect of retinoic acid on gene expression in this differentiation system.
Selection criteria for radical prostatectomy based on morphometric studies in prostate carcinoma. (1988)

Morphometric reconstruction of 122 consecutive radical prostatectomy specimens were analyzed for cancer volume and grade, seminal vesicle (SV) invasion, lymph node (LN) metastasis, and complete capsular penetration. The mean cancer volume for 91 specimens without SV invasion or LN metastasis was 3.7 cm3; for 14 with only SV invasion, 9.0 cm3; for 17 with LN metastasis, 15.2 cm3; and for 12 with both SV invasion and LN metastasis, 17.8 cm3. The mean cancer volume for 60 specimens without capsular penetration was 2.5 cm3, and for 62 it was 9.0 cm3. Grade of cancer correlated well with tumor volume. We believe that radical prostatectomy for cure should be performed on patients with tumors less than 3.8 cm3 in volume. Methods for accurate assessment of tumor volume before surgery should be given research priorities.
Low-noise Brillouin laser on a chip at 1064  nm (2014)

We demonstrate narrow-linewidth-stimulated Brillouin lasers at 1064 nm from ultra-high-Q silica wedge disk resonators on silicon. Fundamental Schawlow-Townes frequency noise of the laser is on the order of 0.1 Hz2/Hz. The technical noise spectrum of the on-chip Brillouin laser is close to the thermodynamic noise limit of the resonator (thermorefractive noise) and is comparable to that of ultra-narrow-linewidth Nd:YAG lasers. The relative intensity noise of the Brillouin laser also is reduced by using an intensity-stabilized pump laser. Finally, low-noise microwave synthesis up to 32 GHz is demonstrated by heterodyne of first and third Brillouin Stokes lines from a single resonator.
Immunocytochemistry of NMDA Receptors (2003)

This chapter covers the major immunocytochemical methods used in our laboratory for NMDA receptor localization. There are three methods: pre-embedding immunoperoxidase for light microscopy (LM), the same for electron microscopy (EM), and postembedding immunogold (1–5). General versions of these techniques, as well as related techniques (immunofluorescence, immunocytochemistry of cultures) have been discussed and compared for immunolabeling of all types of glutamate receptors in Petralia and Wenthold (6). Also, for more information on interpretation of immunolabeling data for glutamate receptors, see Petralia and Wenthold (7) and Petralia (8). Various modifications of these methods have been described briefly (9–17).
Design of a superior cytokine antagonist for topical ophthalmic use (2013)

IL-1 is a key inflammatory and immune mediator in many diseases, including dry-eye disease, and its inhibition is clinically efficacious in rheumatoid arthritis and cryopyrin-associated periodic syndromes. To treat ocular surface disease with a topical biotherapeutic, the uniqueness of the site necessitates consideration of the agent’s size, target location, binding kinetics, and thermal stability. Here we chimerized two IL-1 receptor ligands, IL-1β and IL-1Ra, to create an optimized receptor antagonist, EBI-005, for topical ocular administration. EBI-005 binds its target, IL-1R1, 85-fold more tightly than IL-1Ra, and this increase translates to an ∼100-fold increase in potency in vivo. EBI-005 preserves the affinity bias of IL-1Ra for IL-1R1 over the decoy receptor (IL-1R2), and, surprisingly, is also more thermally stable than either parental molecule. This rationally designed antagonist represents a unique approach to therapeutic design that can potentially be exploited for other β-trefoil family proteins in the IL-1 and FGF families.
Memory fading Volterra series model for high power infrastructure amplifiers (2010)

This paper presents a novel technique of adapting the generalized Volterra series behavioral model to describe, with improved accuracy, power amplifiers targeting cellular infrastructure applications. The generalized Volterra series is reformulated with respect to the discrete time domain to allow impendent specification of memory depth for each kernel. A memory fading concept is then adopted to align memory depth to increasing kernel order. The number of Volterra coefficients needed to represent a strong PA non-linearity are significantly reduced (to a manageable level), while retaining certain high order kernels essential for realizing exceptional model fidelity. Results show model residuals better than -60 dBc for single- and two-carrier WCDMA signals when applied to a 350 W LDMOS Doherty power amplifier circuit.
Clonal, in vivo behavior of the totipotent hematopoietic stem cell. (1991)

Classical and more recent studies have provided a description of the in vivo behavior of the totipotent hematopoietic stem cell and its clonal progeny. These reconstitution experiments, employing clonotypic markers have shown that single or few engrafted lymphoid-myeloid stem cells are both necessary and sufficient for long-term, stable hematopoiesis in a reconstituted mouse. This underscores the remarkable developmental capacity of individual stem cell clones. Furthermore, the long-term and retransplantation studies have provided an indication of stem cell self-renewal ability. Taken together, the long-term analyses have also shed light on the dynamic behavior of engrafted stem cell clones and of the entire reconstituted hematopoietic system. A model is presented where the developmental and proliferative behavior of totipotent stem cells is a function of time. In this model commitment versus self-renewal decisions may be governed by stochastic mechanisms. However, the actual contribution by stem cells to particular mature cell populations may be more a function of lineage specific demands as they change over post-engraftment time.
Implantation of two self‐expanding aortic bioprosthetic valves during the same procedure—Insights into valve‐in‐valve implantation (“Russian doll concept”) (2008)

Transcatheter aortic valve implantation has gained acceptance as a treatment for elderly patients considered high risk for surgical aortic valve replacement. There are still, however, many unresolved clinical and technical issues. The occurrence of transcatheter aortic valve-in-valve implantation has been reported anecdotally. Aside from a single case report, there is little literature on this topic. This study was conducted to evaluate the procedural, imaging, and clinical outcomes of patients who underwent transcatheter valve-in-valve implantation with two self-expanding aortic valve bioprostheses during the same procedure. We discuss also the potential valve of on-line quantitative angiography for assessing the depth of valve implantation and the need to implant a second valve.