gebhart/patrepeval huggingface dataset:
Effective in-device r_33 of 735 pm/V on electro-optic polymer infiltrated silicon photonic crystal slot waveguides (2011)

We design and fabricate a 320 nm slot for an electro-optic (E-O) polymer infiltrated silicon photonic crystal waveguide. Because of the large slot width, the poling efficiency of the infiltrated E-O polymer (AJCKL1/amorphous polycarbonate) is significantly improved. When coupled with the slow light effect from the silicon photonic crystal waveguide, an effective in-device r(33) of 735 pm/V, which to our knowledge is a record high, is demonstrated, which is ten times higher than the E-O coefficient achieved in thin film material. Because of this ultrahigh E-O efficiency, the V(π)L of the device is only 0.44 V mm, which is to our knowledge the best result of all E-O polymer modulators.
Something more to say about calcium homeostasis: the role of vitamin K2 in vascular calcification and osteoporosis. (2013)

Vitamin K2 deficiency has recently been recognized as a protagonist in the development of vascular calcification and osteoporosis. Data reported so far are promising and, dietary supplementation seems a useful tool to contrast these diseases. However, large studies or solid clinical correlations regarding vitamin K2 deficiency and its pathologic consequences are needed to confirm these preliminary experiences.
Drug-coated stents (2002)

Drug-coated stents appear to be the most promising approach among all interventional strategies to prevent restenosis. These stents both suppress geometric remodeling and inhibit neointimal hyperplasia with a therapeutic agent. Animal studies and recent randomised clinical trials with sirolimus-eluting stents have achieved excellent results in the prevention of restenosis. These stents also have a good safety record and demonstrate a durable clinical benefit for patients at long-term follow-up. This article summarises experimental and clinical experiences with local drug delivery via a stent coating in the prevention of restenosis after coronary angioplasty, outlining the clinician's view of current trends.
Determination of the Activation Parameters for the Bergman Cyclization of Aromatic Enediynes (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of the Activation Parameters for the Bergman Cyclization of Aromatic EnediynesJanet Wisniewski Grissom, Trevor L. Calkins, Heidi A. McMillen, and Yueheng JiangCite this: J. Org. Chem. 1994, 59, 19, 5833–5835Publication Date (Print):September 1, 1994Publication History Published online1 May 2002Published inissue 1 September 1994https://pubs.acs.org/doi/10.1021/jo00098a055https://doi.org/10.1021/jo00098a055research-articleACS PublicationsRequest reuse permissionsArticle Views499Altmetric-Citations52LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Proposal to stabilize and detect half-quantum vortices in strontium ruthenate thin films: Non-Abelian braiding statistics of vortices in apx+ipysuperconductor (2006)

We propose a simple way to stabilize half-quantum vortices in superconducting strontium ruthenate, assuming the order parameter is of chiral ${p}_{x}+i{p}_{y}$ symmetry, as is suggested by recent experiments. The method, first given by Salomaa and Volovik in the context of Helium-3, is very naturally suited for strontium ruthenate, which has a layered, quasi-two-dimensional, perovskite crystal structure. We propose possible experiments to detect their non-Abelian braiding statistics. These experiments are of potential importance for topological quantum computation.
Young Adult Bone Marrow–Derived Endothelial Precursor Cells Restore Aging-Impaired Cardiac Angiogenic Function (2002)

Delivery of young bone marrow-derived stem cells offers a novel approach for restoring the impaired senescent cardiac angiogenic function that may underlie the increased morbidity and mortality associated with ischemic heart disease in older individuals. Recently, we reported that alterations in endothelial cells of the aging heart lead to a dysregulation in the cardiac myocyte platelet-derived growth factor (PDGF)-B-induced paracrine pathway, which contributes to impaired cardiac angiogenic function. Based on these results, we hypothesized that cellular restoration of the PDGF pathway by bone marrow-derived endothelial precursor cells (EPCs) could reverse the aging-associated decline in angiogenic activity. In vitro studies revealed that young murine (3-month-old) bone marrow-derived EPCs recapitulated the cardiac myocyte-induced expression of PDGF-B, whereas EPCs from the bone marrow of aging mice (18-month-old) did not express PDGF-B when cultured in the presence of cardiac myocytes. Transplantation of young, but not old, genetically marked syngeneic bone marrow cells into intact, unirradiated aging mice that populated the endogenous senescent murine bone marrow incorporated into the neovasculature of subsequently transplanted syngeneic neonatal myocardium. Moreover, the young bone marrow-derived EPCs restored the senescent host angiogenic PDGF-B induction pathway and cardiac angiogenesis, with graft survival and myocardial activity in the aging murine host (cardiac allograft viability: 3-month-old controls, 8/8; 18-month-old controls, 1/8; 18-month-old donors receiving bone marrow from 3-month-old mice, 15/16; or 18-month-old mice, 0/6; P<0.05). These results may offer a foundation for the development of novel therapies for the prevention and treatment of cardiovascular disease associated with aging.
Characterization of a hyaluronan receptor on rat sinusoidal liver endothelial cells and its functional relationship to scavenger receptors (1999)

Hyaluronan is a widely distributed extracellular component of connective tissue with several mechanical and cell biological functions. The serum level of hyaluronan is elevated in rheumatic and liver diseases and in certain malignancies. The major route of hyaluronan clearance from the blood is via the liver, taken up predominantly by sinusoidal liver endothelial cells. We have purified a novel hyaluronan binding protein from liver that also has an affinity for the N-terminal propeptide of type I procollagen, a physiological scavenger receptor ligand. A polyclonal antibody raised against the protein was found to inhibit the binding and degradation of hyaluronan as well as two scavenger receptor ligands by cultured sinusoidal liver endothelial cells. Immunostaining of nonpermeabilized liver cells and liver sections showed that the antibody specifically stains the surface of sinusoidal liver endothelial cells. After pretreatment with monensin to block the recirculation of endocytic receptors, the immunostaining was specifically associated with early endosomes of these cells. Thus, this rat sinusoidal liver endothelial cell hyaluronan receptor shares functional properties with the scavenger receptor family, a group of proteins shown to play a key role in the uptake of atherogenic lipids and other waste products from the tissues.
Characterizaton of the promoter region of Tetrahymena genes (1990)

The regions between adjacent histone H3 and H4 genes, as well as portions of the genes, from 22 species of Tetrahymena have been amplified using the polymerase chain reaction and sequenced. Both histone genes are transcribed divergently with initiation occurring within the intergenic region, thus 2 sets of 22 homologous Tetrahymena promoters can be compared. A sequence comparison of these regions reveals a single putative promoter element, with a consensus sequence TATCCAATTCARA, present in front of each gene. This sequence contains a 'CCAAT' box, which also occurs at 8 locations preceding other ciliate genes. No other putative promoter sequences are found in front of these sets of histone genes. Sequences searched for include 'TATA' boxes, 'GC' boxes and other sequences suggested as putative promoter elements for ciliate genes. The coding strand immediately preceding ciliate genes is very high in A content and the consensus sequence at the site of protein synthesis is AAAATGG.
Topology of outer membrane porins in pathogenic Neisseria spp (1991)

In Escherichia coli, membrane-spanning amphipathic beta-sheet structures are characteristic of many outer membrane proteins. By applying the principles that have been recognized for them to the four classes of neisserial porins, we have constructed a model for the topology of the porins within the outer membrane. This model predicts eight surface-exposed loops, both in the meningococcal class 1 and 2 proteins and in the gonococcal PIA and PIB proteins. The transmembrane sequences are highly conserved among these porins and are able to form an amphipathic beta-sheet structure. The surface-exposed hydrophilic loops show extensive variation in both length and sequence. Experimental evidence in support of this model has been obtained by using antisera against synthetic peptides which correspond to surface-exposed loops in class 1 and 2 proteins. Thus, binding to the cell surface was observed with antibodies against loops 1, 4, and 5 of class 1 and loops 1 and 5 of class 2. In class 1, these loops are the longest ones and show the highest sequence diversity among strains of different subtypes. Mapping of epitopes recognized by monoclonal antibodies with bactericidal activity has also provided strong support for the model. The epitopes are located in loops 1 and 4 of class 1 protein, loop 5 of PIB, and loop 6 of PIA. A nonbactericidal antibody that binds only weakly to whole cells was shown to recognize loop 3 of PIB. These results suggest that the longest loops are immunodominant, provide the binding sites for bactericidal antibodies, and display the greatest variation among different strains.
Polarity of flagellar assembly in Chlamydomonas. (1992)

During mating of the alga Chlamydomonas, two biflagellate cells fuse to form a single quadriflagellate cell that contains two nuclei and a common cytoplasm. We have used this cell fusion during mating to transfer unassembled flagellar components from the cytoplasm of one Chlamydomonas cell into that of another in order to study in vivo the polarity of flagellar assembly. In the first series of experiments, sites of tubulin addition onto elongating flagellar axonemes were determined. Donor cells that had two full-length flagella and were expressing an epitope-tagged alpha-tubulin construct were mated (fused) with recipient cells that had two half-length flagella. Outgrowth of the shorter pair of flagella followed, using a common pool of precursors that now included epitope-tagged tubulin, resulting in quadriflagellates with four full-length flagella. Immunofluorescence and immunoelectron microscopy using an antiepitope antibody showed that both the outer doublet and central pair microtubules of the recipient cells' flagellar axonemes elongate solely by addition of new subunits at their distal ends. In a separate series of experiments, the polarity of assembly of a class of axonemal microtubule-associated structures, the radial spokes, was determined. Wild-type donor cells that had two full-length, motile flagella were mated with paralyzed recipient cells that had two full-length, radial spokeless flagella. Within 90 min after cell fusion, the previously paralyzed flagella became motile. Immunofluorescence microscopy using specific antiradial spoke protein antisera showed that radial spoke proteins appeared first at the tips of spokeless axonemes and gradually assembled toward the bases. Together, these results suggest that both tubulin and radial spoke proteins are transported to the tip of the flagellum before their assembly into flagellar structure.
Tertiary Lymphoid Structures in Cancer: Drivers of Antitumor Immunity, Immunosuppression, or Bystander Sentinels in Disease? (2017)

Secondary lymphoid organs are integral to initiation and execution of adaptive immune responses. These organs provide a setting for interactions between antigen-specific lymphocytes and antigen-presenting cells recruited from local infected or inflamed tissues. Secondary lymphoid organs develop as a part of a genetically preprogrammed process during embryogenesis. However, organogenesis of secondary lymphoid tissues can also be recapitulated in adulthood during <i>de novo</i> lymphoid neogenesis of tertiary lymphoid structures (TLSs). These ectopic lymphoid-like structures form in the inflamed tissues afflicted by various pathological conditions, including cancer, autoimmunity, infection, or allograft rejection. Studies are beginning to shed light on the function of such structures in different disease settings, raising important questions regarding their contribution to progression or resolution of disease. Data show an association between the tumor-associated TLSs and a favorable prognosis in various types of human cancer, attracting the speculation that TLSs support effective local antitumor immune responses. However, definitive evidence for the role for TLSs in fostering immune responses <i>in vivo</i> are lacking, with current data remaining largely correlative by nature. In fact, some more recent studies have even demonstrated an immunosuppressive, tumor-promoting role for cancer-associated TLSs. In this review, we will discuss what is known about the development of cancer-associated TLSs and the current understanding of their potential role in the antitumor immune response.
Linear predictive hidden Markov models and the speech signal (2005)

A method for modelling time series is presented and then applied to the analysis of the speech signal. A time series is represented as a sample sequence generated by a finite state hidden Markov model with output densities parameterized by linear prediction polynomials and error variances. These objects are defined and their properties developed. The theory culminates in a theorem that provides a computationally efficient iterative scheme to improve the model. The theorem has been used to create models from speech signals of considerable length. One such model is examined with emphasis on the relationship between states of the model and traditional classes of speech events. A use of the method is illustrated by an application to the talker verification problem.
Large-Scale Multi-Label Learning with Incomplete Label Assignments (2014)

Multi-label learning deals with the classification problems where each instance can be assigned with multiple labels simultaneously. Conventional multi-label learning approaches mainly focus on exploiting label correlations. It is usually assumed, explicitly or implicitly, that the label sets for training instances are fully labeled without any missing labels. However, in many real-world multi-label datasets, the label assignments for training instances can be incomplete. Some ground-truth labels can be missed by the labeler from the label set. This problem is especially typical when the number instances is very large, and the labeling cost is very high, which makes it almost impossible to get a fully labeled training set. In this paper, we study the problem of large-scale multi-label learning with incomplete label assignments. We propose an approach, called MPU, based upon positive and unlabeled stochastic gradient descent and stacked models. Unlike prior works, our method can effectively and efficiently consider missing labels and label correlations simultaneously, and is very scalable, that has linear time complexities over the size of the data. Extensive experiments on two real-world multi-label datasets show that our MPU model consistently outperform other commonly-used baselines.
BH3 Mimetics: Status of the Field and New Developments (2013)

Targeting apoptosis is an attractive approach in cancer therapy. The BH3-only proteins of the BCL-2 family (having only the BCL-2 homology domain BH3) can trigger apoptosis by binding to the prosurvival members of this family and neutralizing their functional activity (sequestration of the proapoptotic Bcl-2 family members). The "BH3 mimetic" concept has prompted the development of small molecules capable of mimicking BH3-only proteins and thus inducing apoptosis. The prototype BH3 mimetic ABT-737 selectively targets the three prosurvival proteins BCL-XL, BCL-2, and BCL-W (but not MCL-1 or A1) and its oral derivative ABT-263 has proved promising in clinical trials. Some putative BH3 mimetics are also tested clinically while others are still being characterized. This article recapitulates the various known BH3 mimetics and presents the recent developments in the field. The latter include (i) the identification of molecular determinants responsible for the specific interactions between BH3 motifs and the binding grooves of prosurvival proteins and (ii) the characterization of new compounds and particularly BH3 mimetics that antagonize either selectively MCL-1 or BCL-2 or a broad range of prosurvival proteins. These data are critical advances toward the discovery of novel anticancer agents.
Mud Gas Isotope Logging using Mass Spectrometry (2009)

Abstract Mud Gas Isotope Logging (MGIL) is a gas fingerprinting technique that uses isotopic analyses of mud stream. The primary purpose of MGIL is to assess the extent of a reservoir and identify communication with any other formations. A Gas chromatograph is the main component used in MGIL. Although analysis using a GC will give amounts of methane, ethane, propane (paraffins); napthenes and aromatics are not explicitly analyzed. Also it is very difficult to distinguish between wet gas, condensate and oil using present day GC instrumentation. Another critical element is the speed at which readings can be taken with typical GC cycles of 3–6 minutes which may lead to thin zones not being traced at high ROP. It is not possible with GC based methods to distinguish compounds that exist as a free phase in the pore system from those that may be dissolved in an aqueous pore fluid since GC does not measure a wide range of Carbon species. This paper proposes the use of Mass Spectrometry to analyze mud samples at wellsite. Samples can be analyzed to produce mass spectra of mass to charge ratio {MCR} across a range encompassing both abundant and trace inorganic and organic elements. MS holds a upper hand on GC because the latter does not provide chemical information, is comparatively slower compared to MS which gives real time results; and does not have baseline sensitivity to analyze fluid inclusions. MS also allows tracing of minute fractions of elements since MCR is unique for every element and compound. A further aspect of the paper is to create a chemical log which is a combination of species detected in the gas sample and species extracted from the mud system. Accordingly the chemical log can be used to influence drilling testing and well completion decisions. Some other applications of MGIL-MS include distinguishing between thermogenic &amp; biogenic gas, monitoring H2S concentrations, identifying original fluid contact and CO2 flood breakthrough detection.
Patterns of hemopoietic reconstitution in nonobese diabetic mice: dichotomy of allogeneic resistance versus competitive advantage of disease-resistant marrow (1997)

Complete replacement of the immune system via allogeneic bone marrow transplantation is sufficient to prevent diabetes in the nonobese diabetic (NOD) mouse model. In the present study we examined whether mixed allogeneic reconstitution would be sufficient to interrupt the autoimmune process with respect to occurrence of overt diabetes, as well as preexisting autoimmune insulitis. NOD mice were lethally irradiated and reconstituted with a mixture of NOD and B10.BR marrow. A relative resistance to allogeneic bone marrow engraftment was noted in NOD recipients of the mixed bone marrow inoculum, compared with disease-resistant controls. Moreover, unlike disease-resistant controls, all animals that initially repopulated as mixed donor/host chimeras became predominantly allogeneic by 4 mo, suggesting a competitive advantage for long term engraftment for disease-resistant marrow. All but one mouse in the group that engrafted with allogeneic marrow remained free of diabetes for the entire follow-up period (n = 22). Moreover, in all animals examined, virtually all islets were free of insulitis. In contrast, 74% of NOD mice that received similar conditioning and failed to engraft with donor marrow developed acute diabetes and intra-islet insulitis was present in all animals examined. These data suggest that NOD mice exhibit a relative resistance to engraftment compared with disease-resistant recipients. Conversely, animals that initially repopulated as a mixture of syngeneic and donor marrow become converted to virtually all donor by 4 mo. These data provide additional support that a defective stem cell is responsible for autoimmune diabetes in this experimental model.
Annotation of functional variation in personal genomes using RegulomeDB (2012)

As the sequencing of healthy and disease genomes becomes more commonplace, detailed annotation provides interpretation for individual variation responsible for normal and disease phenotypes. Current approaches focus on direct changes in protein coding genes, particularly nonsynonymous mutations that directly affect the gene product. However, most individual variation occurs outside of genes and, indeed, most markers generated from genome-wide association studies (GWAS) identify variants outside of coding segments. Identification of potential regulatory changes that perturb these sites will lead to a better localization of truly functional variants and interpretation of their effects. We have developed a novel approach and database, RegulomeDB, which guides interpretation of regulatory variants in the human genome. RegulomeDB includes high-throughput, experimental data sets from ENCODE and other sources, as well as computational predictions and manual annotations to identify putative regulatory potential and identify functional variants. These data sources are combined into a powerful tool that scores variants to help separate functional variants from a large pool and provides a small set of putative sites with testable hypotheses as to their function. We demonstrate the applicability of this tool to the annotation of noncoding variants from 69 full sequenced genomes as well as that of a personal genome, where thousands of functionally associated variants were identified. Moreover, we demonstrate a GWAS where the database is able to quickly identify the known associated functional variant and provide a hypothesis as to its function. Overall, we expect this approach and resource to be valuable for the annotation of human genome sequences.
Effect of heat and moisture exchanger (HME) positioning on inspiratory gas humidification (2006)

Although placement proximal to the ETT improved both AH and TEMP in both HMEs tested, one HME performed better in the distal position than the other HME in the proximal position. We conclude the both the type and placement of HME can make a significant difference in maintaining AH and TEMP during adult ventilation.