gebhart/patrepeval huggingface dataset:
Single-molecule Photoswitching and Localization1 (2011)

Within only a few years super-resolution fluorescence imaging based on single-molecule localization and image reconstruction has attracted considerable interest because it offers a comparatively simple way to achieve a substantially improved optical resolution down to ~20 nm in the image plane. Since super-resolution imaging methods such as photoactivated localization microscopy, fluorescence photoactivation localization microscopy, stochastic optical reconstruction microscopy, and direct stochastic optical reconstruction microscopy rely critically on exact fitting of the centre of mass and the shape of the point-spread-function of isolated emitters unaffected by neighbouring fluorophores, controlled photoswitching or photoactivation of fluorophores is the key parameter for resolution improvement. This review will explain the principles and requirements of single-molecule based localization microscopy, and compare different super-resolution imaging concepts and highlight their strengths and limitations with respect to applications in fixed and living cells with high spatio-temporal resolution.
AN INTELLIGENT MULTI-TRACK AUDIO EDITOR (2007)

Audio editing software allows multi-track recordings to be manipulated by moving notes, correcting pitch, and making other fine adjustments, but this is a tedious process.An "intelligent audio editor" uses a machinereadable score as a specification for the desired performance and automatically makes adjustments to note pitch, timing, and dynamic level.
Knowledge Discovery in a Facility Condition Assessment Database Using Text Clustering (2006)

Knowledge discovery in databases (KDD) has been applied in many different areas of study including DNA sequence analysis, pattern discovery, document classification, image recognition, and speech recognition. This paper presents the application of KDD in the analysis of a facility condition assessment (FCA) database. The FCA database contains information on facilities located at three campuses within a statewide university system. The case study utilizes cluster analysis for text mining. Cluster analysis is the grouping of objects that are similar within the same cluster and dissimilar to the other clusters. In this analysis, deficiency descriptions from a university’s FCA database are the objects being grouped together into clusters. Deficiency descriptions were gathered from 15 housing facilities and 15 academic facilities located at 3 campuses. The results show how some clusters of facility deficiencies are unique with respect to the type of facility and the influence of location on deficiencies of academic facilities. The paper begins with a presentation of background on clustering approaches in KDD. Next, a case study based on a higher education FCA database is presented. Last, the paper concludes by exploring other potential areas of application of the described clustering approach.
Developmental and genetic aspects of congenital heart disease (1999)

Congenital heart defects (CHDs) are the result of abnormal cardiac mesoderm or cardiac neural crest development. The molecular cause of most congenital heart disease remains unknown, although numerous cardiac regulatory factors have recently been described. dHAND and eHAND are basic helix-loop-helix transcription factors expressed differentially in the right and left ventricles, respectively, and in the cardiac neural crest. Mice lacking dHAND have a hypoplastic right ventricle and abnormal development of vessels arising from the heart and cell death of craniofacial precursors. By searching for dHAND-dependent genes, a gene likely responsible for the cardiac and craniofacial defects associated with chromosome 22q11 deletion has been identified. A systematic dissection of molecular pathways involved in cardiogenesis should allow for further identification of genes responsible for CHD.
Dynamic Memory Networks for Visual and Textual Question Answering (2016)

Neural network architectures with memory and attention mechanisms exhibit certain reasoning capabilities required for question answering. One such architecture, the dynamic memory network (DMN), obtained high accuracy on a variety of language tasks. However, it was not shown whether the architecture achieves strong results for question answering when supporting facts are not marked during training or whether it could be applied to other modalities such as images. Based on an analysis of the DMN, we propose several improvements to its memory and input modules. Together with these changes we introduce a novel input module for images in order to be able to answer visual questions. Our new DMN+ model improves the state of the art on both the Visual Question Answering dataset and the \babi-10k text question-answering dataset without supporting fact supervision.
Deriving database queries from logical forms by abductive definition expansion (1992)

The paper describes a principled approach to the problem of deriving database queries from logical forms produced by a general NL interface. Our method attempts to construct a database query and a set of plausible assumptions, such that the logical form is equivalent to the query given the assumptions. The domain information needed is provided as declarative meaning postulates, including "definitional equivalences". The technical basis for the approach is that a "definition" of the form Head ∧ Conditions ↔ Body can be read procedurally as "Expand Head to Body if it occurs in an environment where Conditions can be inferred". The "environment" is provided by the other conjuncts occurring together with Head in the original logical form, together with other meaning postulates and the contents of the database. The method has been implemented in CLARE, a language and reasoning system whose linguistic component is the SRI Core Language Engine.
Prosthetic Valve Endocarditis (1973)

In 38 cases of prosthetic valve endocarditis, 19 were early cases (onset ≦ 60 days after insertion of prosthesis) and 19, late cases (onset ≧ 60 days). Nine late cases had onsets 12 to 53 months after surgery. The sources or predisposing factors in late cases included dental disease or manipulation; genitourinary tract procedures; and skin, urinary, or wound infections. In contrast, most early cases were secondary to complications of operation. Streptococci were the most common organisms causing late endocarditis, whereas staphylococci were most common among early cases. Four of the six patients who survived early onset were treated with antibiotics alone; the others, with antibiotics plus reoperation. In contrast, seven of the 11 late cases that survived were treated with antibiotics alone; the other four, with antibiotics plus reoperation. The lower mortality (42% vs 68%) in the late group probably reflects the less virulent infecting organisms and the better clinical condition of the hosts. Regardless of whether prosthetic valve endocarditis occurs early or late , intensive and prolonged administration of appropriate antibiotics together with aggressive surgical reintervention in selected situations appears necessary for cure. Any patient who has a prosthetic valve and undergoes any procedure likely to produce bacteremia should receive antibiotic prophylaxis in an attempt to prevent late endocarditis.
Reconfigurable beam forming using phase-aligned Rotman lens (2012)

The authors describe how a standard Rotman lens design can be readily adapted in order to allow reconfigurable beam forming. This is achieved by applying concurrent excitations to the modified Rotman lens. A rationale for the design and underlying behaviour of the modified, phase-aligned, Rotman lens as well as the deficiencies of a conventional Rotman lens in this mode of operation are provided. Simulated and measured results are provided in order to illustrate the feasibility of the approach suggested.
Role of CCK/Gastrin Receptors in Gastrointestinal/Metabolic Diseases and Results of Human Studies Using Gastrin/CCK Receptor Agonists/Antagonists in these Diseases (2007)

In this paper, the established and possible roles of CCK1 and CCK2 receptors in gastrointestinal (GI) and metabolic diseases are reviewed and available results from human agonist/antagonist studies are discussed. While there is evidence for the involvement of CCK1R in numerous diseases including pancreatic disorders, motility disorders, tumor growth, regulation of satiety and a number of CCK-deficient states, the role of CCK1R in these conditions is not clearly defined. There are encouraging data from several clinical studies of CCK1R antagonists in some of these conditions, but their role as therapeutic agents remains unclear. The role of CCK2R in physiological (atrophic gastritis, pernicious anemia) and pathological (Zollinger-Ellison syndrome) hypergastrinemic states, its effects on the gastric mucosa (ECL cell hyperplasia, carcinoids, parietal cell mass) and its role in acid-peptic disorders are clearly defined. Furthermore, recent studies point to a possible role for CCK2R in a number of GI malignancies. Current data from human studies of CCK2R antagonists are presented and their potential role in the treatment of these conditions reviewed. Furthermore, the role of CCK2 receptors as targets for medical imaging is discussed.
Remote optical measurement of temperature using luminescent materials (1981)

A novel method of temperature measurement using optical fibres and luminescent materials is demonstrated. The delay time of an excited state in an inorganic material is shown to vary with temperature, and this is readily measured via the phase-shift technique.
Design of Phosphoramidite Monomer for Optimal Incorporation of Functional Intercalator to Main Chain of Oligonucleotide (2005)

Chirally pure phosphoramidite monomers bearing 9-amino-6-chloro-2-methoxyacridine were synthesized from D- or L-threoninol and omega-aminocarboxylic acid, and incorporated into oligonucleotides. These acridine-DNA conjugates formed stable duplexes with complementary RNA because of intercalation of the acridine to DNA/RNA heteroduplexes. The stability of duplexes was not very dependent on either the chirality of the central carbon bearing the acridine or the length of the side chain. However, the ability for site-selective activation of the phosphodiester linkage in front of the acridine, which induced Lu(III)-promoted RNA scission, was strongly dependent on these two factors. The largest activation was achieved when the monomer unit was prepared from L-threoninol and 4-aminobutyric acid and the acridine was bound to the amino group. By attaching the more acidic 9-amino-2-methoxy-6-nitroacridine to this optimized scaffold, a quite effective acridine-DNA conjugate for site-selective RNA scission was obtained.
Resistance modeling of test structures for accurate fault detection in backend process steps using a digital tester (2002)

A methodology is presented to enable the usage of a digital tester for an accurate detection of open circuits as well as short circuits in test structures to control backend process steps. Therefore, a novel graph model will be introduced to calculate the resistance values of test structures containing defects. The paper gives a comprehensive description of the procedure to adjust the tester parameters to those test structures.
Height of the energy barrier existing between cathodes and hydroxyquinoline–aluminum complex of organic electroluminescence devices (1996)

The properties of organic electroluminescence devices are largely affected by the kind of metals used as the cathode, because the barrier height formed at the interface depends on the electronic and chemical properties of the metals. On the basis of the temperature dependence of currents flowing through the interface between tris(8-hydroxyquinolino)aluminum and a magnesium cathode, the carrier injection mechanism at the interface was ascribed to the thermionic emission with the barrier height of about 0.58±0.03 eV at zero electric field. The barrier height became larger when metals with larger work functions were used as the cathode. The current density was also found to be dependent on the chemical structure of the interfaces.
Aerosolization of Lactide/Glycolide Copolymer (PLGA) Nanospheres for Pulmonary Delivery of Peptide-drugs (1995)

Lactide/glycolide copolymer (PLGA) nanospheres with nafarelin acetate (NA) used as a model peptide-drug have been developed by the emulsion-phase separation method in an oil phase as reported previously. In the present study, the aerosolization of nanospheres in dry and wet dispersion methods was investigated in vitro to evaluate their applications to pulmonary delivery of peptide-drug. The size distribution of aerosolized nanosphere dispersions and pulmonary deposition behaviors of inhaled particles were investigated using a lazer diffraction light-scattering particle sizer and an artificial model lung (Cascade Impactor: CI), respectively. It was found that the freeze-drying of nanospheres with a hydrophilic surface active agent effectively improved the inhalation behavior. Further, the mixing of nanospheres with lactose led to the reduction of their adhesion to an inhalation device (Spinhaler). It was supposed that the mists of nanosphere-suspension generated from a jet nebulizer might be inhaled into the lower bronchus and alveolus, because their respirable fraction (RF) value, i.e., the deposition percentage on stage 2 to 6 of CI, defined as a pulmonary inhalation index, reached a maximum of over 50%.
Host-bacteria interaction in inflammatory bowel disease (2008)

It has been disputed whether the primary defect in IBD is immunological or bacterial, and which bacteria are key. GROWING POINTS/AREAS FOR RESEARCH: 'M cells', the specialized epithelial cells that overlie Peyer's patches, are a major interface between gut bacteria and the immune system. Improved understanding is needed of the bacteria involved in IBD pathogenesis, their genotypes and phenotypes, their portal of entry and their mechanism for escaping attack from the immune system. Bacterial ligands involved in bacteria-epithelial adhesion are emerging, and molecular techniques are rapidly increasing our knowledge of the human intestinal microbiota.
A chemical perspective on the anthracycline antitumor antibiotics. (1985)

The anthracycline antitumor antibiotics occupy a central position in the chemotherapeutic control of cancer. They remain, however, antibiotics of the last resort and thus exhibit toxicity both to the neoplasm and to the host organism. As part of the continuing effort to dissociate the molecular processes responsible for these two separate toxicities, attention has been drawn to the intrinsic redox capacity of their tetrahydronapthacenedione aglycone moiety, and to the possible expression of this redox activity against those biomolecules for which anthracyclines have a particular affinity (polynucleotides and membranes). This review is a synopsis of the present trends and thoughts concerning this relationship, written from the point of view of the intrinsic chemical competence of the anthracyclines and their metabolites. While our ignorance is profound--the precise molecular locus of the antitumor expression of the anthracyclines remains unknown--there is now evidence that the relationship of the anthracyclines to the DNA (possibly requiring enzymatic cooperation) and to the membranes, with neither event requiring redox chemistry, may comprise the core of the antitumor effects. The adventitious expression of the redox activity under either aerobic conditions (in which circumstances molecular oxygen is reduced) or anaerobic conditions (in which circumstances potentially reactive aglycone tautomers are obtained) is therefore thought to contribute more strongly to the host toxicity. Yet little remains proven, and the understanding of the intrinsic chemical competence can do little more than lightly define the boundaries within which are found these and numerous other working hypotheses.
Affinity purification of alpha-galactosidase A from human spleen, placenta, and plasma with elimination of pyrogen contamination. Properties of the purified splenic enzyme compared to other forms. (1981)

The substrate analog alpha-D-galactosylamine was synthesized, linked to 6-aminohexanoic acid, and coupled to carboxyhexyl-Sepharose. This affinity support permitted the purification of human alpha-galactosidase A (alpha-D-galactoside galactohydrolase, EC 3.2.1.22) from spleen, placenta, and plasma. When used in conjunction with conventional procedures, affinity chromatography enabled the rapid and specific purification of alpha-galactosidase A from each source. Significantly, pyrogenic endotoxins were eliminated from enzyme preparations by the use of the affinity column. Splenic alpha-galactosidase A was purified in high yield (38%) with a specific activity of 1.9 X 10(6) units/mg. The purified enzyme was a homodimer with a native molecular weight of 101,000 and a subunit weight of 49,800. The UV absorption coefficient was E280 1% = 18 and the lambda max was 282 nm. The plasma form was purified with a markedly improved yield to a specific activity (229,000 units/mg) which was 3 times greater than that achieved previously. The enzymes from plasma, spleen, and placenta were immunologically identical. The physical and kinetic properties of the purified enzymes were consistent with and confirmed previous findings.
A Convenient and Efficient Workup of Ozonolysis Reactions Using Triethylamine (1993)

Abstract Comparison were made between triethylamine and methyl sulfide for their use as a quenching agent in the ozonolysis of a variety of alkenes. The reactions involving triethylamine often gave better yields and proceeded faster than those of involving methyl sulfide. The role of triethylamine played as base instead of reducing agent in the reaction.
Genetic Susceptibility to Death from Coronary Heart Disease in a Study of Twins (1994)

Our findings suggest that at younger ages, death from coronary heart disease is influenced by genetic factors in both women and men. The results also imply that the genetic effect decreases at older ages.
Promoter Cloning in the Radioresistant Bacterium Deinococcus radiodurans (2001)

Deinococcus radiodurans is a highly radiation-resistant bacterium that is classed in a major subbranch of the bacterial domain. Since very little is known about gene expression in this bacterium, an initial study of promoters was undertaken. In order to isolate promoters and study promoter function, a series of integrative vectors for stable chromosomal insertion in D. radiodurans were developed. These vectors are based on Escherichia coli replicons that are unable to replicate autonomously in D. radiodurans and carry homologous sequences for replacement recombination in the D. radiodurans chromosome. The resulting integration vectors were used to study expression of reporter genes fused to a number of putative promoters that were amplified from the D. radiodurans R1 genome. Further analysis of these and other putative promoters was performed by Northern hybridization and primer extension experiments. In contrast to previous reports, the -10 and -35 regions of these promoters resembled the sigma(70) consensus sequence of E. coli.
Cloning and characterization of two immunophilin-like genes, ilpA and fkpA, on a single 3.9-kilobase fragment of Aeromonas hydrophila genomic DNA (1997)

Antiserum to Aeromonas hydrophila A6 cell envelopes was shown in a previous study (C. Y. F. Wong, G. Mayrhofer, M. W. Heuzenroeder, H. M. Atkinson, D. M. Quinn, and R. L. P. Flower, FEMS Immunol. Med. Microbiol. 15:233-241, 1996) to protect mice against lethal infection by this organism. In this study, colony blot analysis of an A. hydrophila genomic library using antiserum to A. hydrophila A6 cell envelopes revealed a cosmid clone expressing a 30-kDa protein which has not been described previously in aeromonads. The nucleotide sequence of a 3.9-kb fragment derived from this cosmid which expressed the 30-kDa protein revealed two potential open reading frames (ORFs) with homology to known immunophilin proteins. ORF1 encoded a 212-amino-acid protein (molecular mass, 22.4 kDa) with 56% identity to the immunophilin SlyD protein of Escherichia coli. ORF1 was subsequently designated ilpA (immunophilin-like protein). ORF3 encoded a potential gene product of 268 amino acids with a typical signal sequence and a predicted molecular size of 28.7 kDa. The inferred amino acid sequence showed 46% identity with the sequence of the FkpA protein of E. coli and 40% identity with the sequence of the macrophage infectivity potentiator (Mip) protein of Legionella pneumophila. ORF3 was designated fkpA (FK506 binding protein) by analogy with the E. coli FkpA protein. Expression of the FkpA protein was confirmed by Western blot (immunoblot) analysis, which detected a 30-kDa protein, with antiserum to the Mip protein of Legionella longbeachae and a specific antiserum to anA. hydrophila 30-kDa membrane protein. PCR and Southern analysis showed that a DNA sequence encoding FkpA was found in all 178 aeromonads of diverse origins tested. A nonpolar insertion mutation in the fkpA gene did not attenuate virulence in a suckling mouse model nor did it affect the expression of hemolysins or DNase. This suggests that either the fkpA gene is not essential in the virulence of A. hydrophila under these conditions or there are other genes in A. hydrophila coding for proteins with similar functions.
Susceptibilities of Oral Bacteria and Yeast to Mammalian Cathelicidins (2001)

The effects of cathelicidins against oral bacteria and clinically important oral yeasts are not known. We tested the susceptibilities of Actinobacillus actinomycetemcomitans, Fusobacterium nucleatum, Porphyromonas gingivalis, Streptococcus sanguis, Candida krusei, Candida tropicalis and Candida albicans to the following cathelicidins: FALL39, SMAP29, and CAP18. SMAP29 and CAP18 were antimicrobial, whereas FALL39 did not exhibit antimicrobial activity. Future studies are needed to determine the potential use of these antimicrobial peptides in prevention and treatment of oral infections.
Inhibition of T cell and natural killer cell function by adenosine and its contribution to immune evasion by tumor cells (Review) (2008)

The resistance of many human cancers to immune-based therapies, including adoptive immunotherapy and the administration of therapeutic cancer vaccines, has been attributed to tumor-associated immune suppression, due in part to immunosuppressive molecules located within the tumor microenvironment. Adenosine is a purine nucleoside found within the interstitial fluid of solid tumors at concentrations that are able to inhibit cell-mediated immune responses to tumor cells. It is well established that extracellular adenosine inhibits T lymphocyte activation and effector function, including T cell adhesion to tumor cells and cytotoxic activity, by signaling primarily through A2a and A3 adenosine receptors on the surface of T cells. Importantly, A2a adenosine receptor-deficient mice exhibit enhanced anti-tumor immune responses by CD8+ T cells, as well as a dramatic reduction in the growth of experimental tumors in comparison to wild-type controls. A2a adenosine receptor signaling has also been implicated in adenosine-mediated inhibition of cytokine production and cytotoxic activity by activated natural killer (NK) cells, although the process of NK cell granule exocytosis is apparently suppressed via a distinct and as yet uncharacterized adenosine receptor. In this report, we review the evidence that adenosine is a potent inhibitor of cellular immune responses and may therefore be a major barrier to the successful immunotherapy of human carcinomas. The signaling pathways through which adenosine exerts its inhibitory effects on cell-mediated immune responses are also discussed. The accumulated evidence suggests that the effectiveness of immune-based therapies for solid tumors may be enhanced by selective antagonism of the adenosine receptor subtypes through which adenosine inhibits the anti-tumor activity of T lymphocytes and NK cells.