gebhart/patrepeval huggingface dataset:
General Theory and Design of Optimum Quarter-Wave TEM Filters (1965)

The exact synthesis and design of a broad class of quarter-wave TEM mode filters is presented in a three-step procedure. The theory is applicable to all microwave filter forms consisting entirely of a cascade of quarter-wave lines, quarter-wave stubs, and coupled quarter-wave lines. The exact design of many conventional filter forms that heretofore could only be designed using approximate methods is possible using the techniques and functions described. General approximating functions that give the "best" transmission response in a Butterworth or Chebyshev sense are derived. The use of a maximum number of available singularities to augment the filter skirt response leads to a minimum element filter termed "optimum multiple." An optimum multipole design insures the "best" possible response for the minimum element and all corresponding redundant element networks. The designer has the freedom of introducing sufficient redundancy to obtain a design that is practical to construct, but which still realizes the optimum response. Judicious choice of network form often results in improved performance and reduced size in comparison with many conventional filter forms. Design procedures are presented that allow the practical realization of distributed filter networks in the form of quarter-wave lines. A design example and experimental results are given to confirm the theory.
The Pathobiology of Periodontal Diseases May Affect Systemic Diseases: Inversion of a Paradigm (1998)

A new paradigm for the pathobiology of periodontitis is presented, and the manner in which periodontitis may relate to susceptibility for certain systemic diseases such as cardiovascular disease and preterm labor is described. Periodontitis is caused by a small group of Gram-negative bacteria present on the tooth root surfaces as bioffilms. Lipopolysaccharide (LPS) and other substances gain access to the gingival tissues, initiate and perpetuate immunoinflammation, resulting in production of high levels of proinflammatory cytokines. These induce production of matrix metalloproteinases which destroy the connective tissues of the gingiva and periodontal ligament, and prostaglandins which mediate alveolar bone destruction. Periodontitis may enhance susceptibility to systemic diseases in several ways. LPS and viable Gram-negative bacteria from the biofilms and proinflammatory cytokines from the inflamed periodontal tissues may enter the circulation in pathogenic quantities. In addition, periodontitis and certain systemic diseases, such as cardiovascular disease, share risk factors including tobacco smoking, male gender, race/ethnicity, stress, and aging.
Light-Induced Superconductivity in a Stripe-Ordered Cuprate (2011)

One of the most intriguing features of some high-temperature cuprate superconductors is the interplay between one-dimensional "striped" spin order and charge order, and superconductivity. We used mid-infrared femtosecond pulses to transform one such stripe-ordered compound, nonsuperconducting La(1.675)Eu(0.2)Sr(0.125)CuO(4), into a transient three-dimensional superconductor. The emergence of coherent interlayer transport was evidenced by the prompt appearance of a Josephson plasma resonance in the c-axis optical properties. An upper limit for the time scale needed to form the superconducting phase is estimated to be 1 to 2 picoseconds, which is significantly faster than expected. This places stringent new constraints on our understanding of stripe order and its relation to superconductivity.
Enhanced light absorption in GaAs solar cells with internal Bragg reflectors (2002)

The use of epitaxial multilayer dielectric mirrors (Bragg reflectors) as back-surface reflectors in thin-film GaAs solar cells on GaAs and silicon substrates is investigated. Al/sub 0.3/Ga/sub 0.9/As/Al/sub 0.85/Ga/sub 0.15/As Bragg reflectors were grown by low-pressure MOCVD on GaAs substrates and shown to exhibit near-ideal optical reflectance and excellent structural perfection. Thin GaAs solar cells grown on Bragg reflectors showed increases in short-circuit current (0.5 to 1.0 mA/cm/sup 2/) and efficiency (0.7 percentage points) relative to cells without back reflectors. Efficiencies of 24.7% at one sun AM 1.5 were measured for GaAs cells only 2 mu m thick on Bragg reflectors. In addition to the optical enhancements, Bragg reflectors also appear to improve the defect structure of GaAs-on-Si solar cells. This approach should lead to improved efficiency for GaAs-on-Si solar cells and improved radiation resistance on GaAs cells.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Relationship between Nerve Fiber Layer and Perimetry Measurements (2007)

SAP measures of visual field defects and OCT measures of RNFL defects are correlated measures of glaucomatous neuropathy. The normal intersubject variability and the dynamic ranges of the measurements suggest that RNFL thickness may be a more sensitive measurement for early stages and perimetry a better measure for moderate to advanced stages of glaucoma.
Robert R. Holmes (2020)

Robert R. Holmes, 91, died on Feb. 25 in Poway, California. “Bob served in the Chemistry Department at the University of Massachusetts Amherst for more than 40 years, having joined the faculty in 1966. He also acted as editor of the journal Phosphorus, Sulfur, and Silicon and the Related Elements for more than 20 years before retiring in 2008. He published more than 250 articles covering main group chemistry, especially structural, mechanistic, and synthetic phosphorus and silicon chemistry. He enjoyed painting, sailing, traveling the world, the beauty of New Hampshire, and tinkering on projects. He treasured his time with his family most of all.”—Martin D. Rudd, friend and colleague Professor of chemistry, University of Massachusetts Amherst BS, chemistry, Illinois Institute of Technology, 1950; PhD, organic chemistry, Purdue University, 1953 Daughters, Mary Anne Jones and Kathryn Webber; son, Robert To recognize your late loved one or colleague, submit obituary information at
Diversity in the Protein N-Glycosylation Pathways Within the Campylobacter Genus (2012)

The foodborne bacterial pathogen, Campylobacter jejuni, possesses an N-linked protein glycosylation (pgl) pathway involved in adding conserved heptasaccharides to asparagine-containing motifs of >60 proteins, and releasing the same glycan into its periplasm as free oligosaccharides. In this study, comparative genomics of all 30 fully sequenced Campylobacter taxa revealed conserved pgl gene clusters in all but one species. Structural, phylogenetic and immunological studies showed that the N-glycosylation systems can be divided into two major groups. Group I includes all thermotolerant taxa, capable of growth at the higher body temperatures of birds, and produce the C. jejuni-like glycans. Within group I, the niche-adapted C. lari subgroup contain the smallest genomes among the epsilonproteobacteria, and are unable to glucosylate their pgl pathway glycans potentially reminiscent of the glucosyltransferase regression observed in the O-glycosylation system of Neisseria species. The nonthermotolerant Campylobacters, which inhabit a variety of hosts and niches, comprise group II and produce an unexpected diversity of N-glycan structures varying in length and composition. This includes the human gut commensal, C. hominis, which produces at least four different N-glycan structures, akin to the surface carbohydrate diversity observed in the well-studied commensal, Bacteroides. Both group I and II glycans are immunogenic and cell surface exposed, making these structures attractive targets for vaccine design and diagnostics.
The effect of Gi‐protein inactivation on basal, and β1‐ and β2AR‐stimulated contraction of myocytes from transgenic mice overexpressing the β2‐adrenoceptor (2000)

The atria and ventricles of transgenic mice (TGbeta(2)) with cardiac overexpression of the human beta(2)-adrenoceptor (beta(2)AR) were initially reported to show maximum contractility in the absence of beta-AR stimulation. However, we have previously observed a different phenotype in these mice, with myocytes showing normal contractility but reduced betaAR responses. We have investigated the roles of cyclic AMP and Gi in basal and betaAR function in these myocytes. ICI 118,551 at inverse agonist concentrations decreased contraction by 32%. However, the cyclic AMP antagonist Rp-cAMPS had no effect on contraction in TGbeta(2) myocytes, indicating that there was no tonic influence of raised cyclic AMP. These findings cannot be explained by the proposed model for inverse agonism, where the activated receptor (R*) raises cyclic AMP levels and so increases contraction in the absence of agonist. After pertussis toxin (PTX) pretreatment to produce inactivation of Gi, the basal contraction in 1 mM Ca(2+) was increased in TGbeta(2) mice (7.82+/-0.47%, n=23) compared to LM mice (3.60+/-0.59%, n=11) (P<0.001). The contraction amplitude of myocytes to the maximal concentration of isoprenaline was also increased significantly by PTX in TGbeta(2) mice (9.40+/-1.22%, n=8) and was no longer reduced compared to LM mice (8.93+/-1.50%, n=11). Both beta(1)- and beta(2)AR subtypes were affected both by the original desensitization and by the resensitization with PTX. PTX treatment has therefore restored the original phenotype, with high basal contractility and little further effect of isoprenaline. We suggest that both beta-AR desensitization and lack of increased basal contraction in ventricular myocytes from our colony of TGbeta(2) mice were due to increased activity of PTX-sensitive G-proteins.
Cloning and physical mapping of the HLA class I region spanning the HLA-E-to-HLA-F interval by using yeast artificial chromosomes. (1992)

The HLA class I genes are located within a 2-million-base pair (2-Mbp) region constituting the telomeric half of the human major histocompatibility complex. The large majority of the class I sequences, including the HLA-A, -E, -F, and -G genes, is found within the telomeric 1 Mbp. We report here the isolation and characterization of yeast artificial chromosome (YAC) clones that span a contiguous region of greater than 1.2 Mbp and include 14 of the 18 characterized class I sequences. Restriction enzyme mapping and the use of locus-specific probes have allowed all of the class I genes and sequences to be ordered and positioned within the region. In addition, the transcriptional orientation of the four class I genes has been determined. Using probes derived from the ends of YAC inserts and from class I pseudogenes, we describe a highly polymorphic region between the HLA-A and HLA-G genes. This region appears to be deleted in certain HLA haplotypes, shortening the distance between HLA-A and HLA-G by greater than 50 kilobase pairs (kbp). As part of the characterization of the YAC clones, unique sequence probes derived from the ends of each YAC insert were identified. When combined with probes derived from HLA genes and pseudogenes, 25 locus-specific probes spanning the 1.2-Mbp region have been identified for an average of 1 probe every 48 kbp.
Identification of new genes associated with breast cancer progression by gene expression analysis of predefined sets of neoplastic tissues (2008)

Gene expression profiles were studied by microarray analysis in 2 sets of archival breast cancer tissues from patients with distinct clinical outcome. Seventy-seven differentially expressed genes were identified when comparing 30 cases with relapse and 30 cases without relapse within 72 months from surgery. These genes had a specific ontological distribution and some of them have been linked to breast cancer in previous studies: AIB1, the two keratin genes KRT5 and KRT15, RAF1, WIF1 and MSH6. Seven out of 77 differentially expressed genes were selected and analyzed by qRT-PCR in 127 cases of breast cancer. The expression levels of 6 upregulated genes (CKMT1B, DDX21, PRKDC, PTPN1, SLPI, YWHAE) showed a significant association to both disease-free and overall survival. Multivariate analysis using the significant factors (i.e., estrogen receptor and lymph node status) as covariates confirmed the association with survival. There was no correlation between the expression level of these genes and other clinical parameters. In contrast, SERPINA3, the only downregulated gene examined, was not associated with survival, but correlated with steroid receptor status. An indirect validation of our genes was provided by calculating their association with survival in 3 publicly available microarray datasets. CKMT1B expression was an independent prognostic marker in all 3 datasets, whereas other genes confirmed their association with disease-free survival in at least 1 dataset. This work provides a novel set of genes that could be used as independent prognostic markers and potential drug targets for breast cancer.
Parenteral and mucosal prime-boost immunization strategies in mice with hepatitis B surface antigen and CpG DNA (2002)

Synthetic oligodeoxynucleotides (ODN) containing immunostimulatory CpG motifs (CpG ODN) are potent adjuvants to protein antigens administered by parenteral or mucosal routes to BALB/c mice. To date, there have been no studies using combined parenteral/mucosal approaches with CpG DNA as adjuvant. In this study we evaluated different parenteral prime-mucosal boost and mucosal prime-parenteral boost strategies using hepatitis B surface antigen (HBsAg) alone or with different adjuvants: aluminum hydroxide (alum), cholera toxin (CT), CpG ODN. In addition, since CpG ODN has previously been shown to act synergistically with other adjuvants after parenteral or mucosal delivery, we also evaluated adjuvant combinations: alum+CpG ODN and CT+CpG ODN. The effects of adjuvant and administration strategy on systemic and mucosal humoral responses were measured, as well as cell-mediated immune responses (cytotoxic T lymphocyte activity). These results were compared to parenteral only or mucosal only strategies. Our findings demonstrate that parenteral immunization can prime for mucosal responses even when different lymph nodes were being targeted. HBsAg-specific immune responses (IgG in plasma, cytotoxic T lymphocytes) induced by parenteral prime could all be significantly enhanced by mucosal boosting and despite the fact that intramuscular immunization alone could not induce mucosal IgA, it could prime for a subsequent mucosal boost. In addition, the presence of adjuvant at time of boosting could influence the nature of subsequent immune responses (Th1 vs. Th2). Mice primed intranasally could have their systemic immune responses boosted with a parenteral administration and it was also possible to enhance mucosal responses induced by intranasal prime with an intramuscular boost.
Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3 (2019)

The RNase Regnase-1 is a master RNA regulator in macrophages and T cells that degrades cellular and viral RNA upon NF-κB signaling. The roles of its family members, however, remain largely unknown. Here, we analyzed <i>Regnase-3</i>-deficient mice, which develop hypertrophic lymph nodes. We used various mice with immune cell-specific deletions of <i>Regnase-3</i> to demonstrate that Regnase-3 acts specifically within myeloid cells. <i>Regnase-3</i> deficiency systemically increased IFN signaling, which increased the proportion of immature B and innate immune cells, and suppressed follicle and germinal center formation. Expression analysis revealed that Regnase-3 and Regnase-1 share protein degradation pathways. Unlike Regnase-1, Regnase-3 expression is high specifically in macrophages and is transcriptionally controlled by IFN signaling. Although direct targets in macrophages remain unknown, Regnase-3 can bind, degrade, and regulate mRNAs, such as <i>Zc3h12a</i> (<i>Regnase-1</i>), in vitro. These data indicate that Regnase-3, like Regnase-1, is an RNase essential for immune homeostasis but has diverged as key regulator in the IFN pathway in macrophages.
PD-L1 checkpoint blockade prevents immune dysfunction and leukemia development in a mouse model of chronic lymphocytic leukemia (2015)

Blockade of the programmed cell death 1 (PD-1)/programmed death-ligand 1 (PD-L1) immune checkpoint augments antitumor immunity and induces durable responses in patients with solid cancers, but data on clinical efficacy in leukemias are sparse. Chronic lymphocytic leukemia (CLL) is associated with a tumor-supportive microenvironment and a dysfunctional immune system, as shown by "exhausted" T cells, defective immunologic synapse formation, and immunosuppressive myeloid cells. These defects involve aberrant expression of PD-L1 and are closely mirrored in the Eµ-TCL1 mouse model for CLL. In this study, we treated mice after adoptive transfer of Eµ-TCL1 CLL with PD-L1-blocking antibodies, which prevented CLL development and was accompanied by a reactivation of immune effector functions. This included restoration of mature macrophages and major histocompatibility complex class II-expressing dendritic cells and prevention of aberrant and exhaustion-like T-cell phenotypes. In addition, PD-L1 blockade restored CD8 T-cell cytotoxicity and immune synapse formation and normalized T-cell cytokines and proliferation ex vivo and in vivo. Our data demonstrate that early PD-L1 blockade effectively corrects leukemia-induced immune dysfunction and thus prevents CLL development in mice. Targeting PD-L1/PD-1 interactions should therefore be further explored in clinical studies with CLL patients, ideally in combination with novel compounds to help eliminate CLL.
Inhibition of in Vitro Transcription by a Triplex-Forming Oligonucleotide Targeted to Human c-myc P2 Promoter (1995)

Triplex-forming oligonucleotides (TFOs) have been shown to bind in a sequence-specific manner to polypurine/polypyrimidine sequences in several human gene promoters, including the c-myc P1 promoter. TFOs have been shown to inhibit transcription in vitro and the expression of target genes in cell culture. The human c-myc protooncogene contains a 23 base pair purine-pyrimidine-rich motif (-62 to -40) within its predominant promoter, P2, that is a potential target for purine-purine-pyrimidine triplex formation. Using electrophoretic mobility shift analysis (EMSA) and competition experiments, we have demonstrated that a MAZ (myc-associated zinc finger protein) consensus sequence is capable of competing with the purine-pyrimidine motif for the binding of a HeLa nuclear protein. We have shown the formation of an intermolecular triplex using a 23-base purine-rich oligonucleotide antiparallel to the purine-rich target sequence. DNase I footprinting was performed to confirm the exact location of triplex formation. Triplex formation by this oligonucleotide prevents binding of a HeLa nuclear protein (presumably MAZ) to the target site. We have also shown that the P2-targeted TFO is a potent and specific inhibitor of c-myc transcription in vitro. These data demonstrate that this novel TFO inhibits transcription of the c-myc P2 promoter. We propose that the P2-targeted TFO has its effect by blocking the binding of the regulatory factor MAZ.
New Technologies for Ultra-High Throughput Genotyping in Plants (2009)

Molecular genetic markers represent one of the most powerful tools for the analysis of plant genomes and the association of heritable traits with underlying genetic variation. Molecular marker technology has developed rapidly over the last decade, with the development of high-throughput genotyping methods. Two forms of sequence-based marker, simple sequence repeats (SSRs), also known as microsatellites and single nucleotide polymorphisms (SNPs) now predominate applications in modern plant genetic analysis, along the anonymous marker systems such as amplified fragment length polymorphisms (AFLPs) and diversity array technology (DArT). The reducing cost of DNA sequencing and increasing availability of large sequence data sets permits the mining of this data for large numbers of SSRs and SNPs. These may then be used in applications such as genetic linkage analysis and trait mapping, diversity analysis, association studies and marker-assisted selection. Here, we describe automated methods for the discovery of molecular markers and new technologies for high-throughput, low-cost molecular marker genotyping. Genotyping examples include multiplexing of SSRs using Multiplex-Ready marker technology (MRT); DArT genotyping; SNP genotyping using the Invader assay, the single base extension (SBE), oligonucleotide ligation assay (OLA) SNPlex system, and Illumina GoldenGate and Infinium methods.
A Rapid and Sensitive Test for Diagnosing Heparin-Associated Thrombocytopenia (1991)

Heparin-associated thrombocytopenia (HAT) is a severe complication of heparin therapy. Its diagnosis is difficult. Conventional assays employ platelet aggregometry (PAA) and/or 14C-serotonin release (SRA) which are either insensitive (PAA) or require radioactive tracers (SRA). We here describe a newly developed sensitive and rapid assay based on visual evaluation of heparin-induced platelet activation (HIPA) in microtiter wells. Using sera of 34 patients with clinically suspected HAT we found the HIPA assay to be as sensitive as the SRA and superior to PAA. The HIPA assay allows investigation of crossreactivity with different types of heparins, low molecular weight (LMW) heparins and heparinoids. Three patients who required further parenteral anticoagulation and in whom the HIPA assay was negative before treatment with the LMW heparinoid Org 10172, were treated with this new heparinoid without adverse reactions. We conclude that the HIPA assay may be a useful tool for differential diagnosis and therapy in patients with HAT.
Sparse inverse covariance estimation with the graphical lasso (2007)

We consider the problem of estimating sparse graphs by a lasso penalty applied to the inverse covariance matrix. Using a coordinate descent procedure for the lasso, we develop a simple algorithm--the graphical lasso--that is remarkably fast: It solves a 1000-node problem ( approximately 500,000 parameters) in at most a minute and is 30-4000 times faster than competing methods. It also provides a conceptual link between the exact problem and the approximation suggested by Meinshausen and Bühlmann (2006). We illustrate the method on some cell-signaling data from proteomics.
Multimode add-drop multiplexing by adiabatic linearly tapered coupling (2005)

Multimode multiplexing can potentially replace WDM for implementing multichannel short reach interconnects. Multiple optical modes can thus be exploited as the channels for transferring optical data, where each mode represents an independent data channel. The basic building block of the system is a Mode Add/Drop which can be implemented based on adiabatic power transfer. We propose a new scheme for realization of such adiabatic mode add drop with a predefined coupling profile, and demonstrate it by employing a linearly decreasing coupling coefficient along the propagation length. Realization using Silicon-On- Insulator (SOI) platform is discussed - which offers the possibility of direct integration of the optoelectronic circuitry with the Si processor.