gebhart/patrepeval huggingface dataset:
Two-Dimensional Femtosecond Spectroscopy (2003)

The simplest two-dimensional (2D) spectra show how excitation with one (variable) frequency affects the spectrum at all other frequencies, thus revealing the molecular connections between transitions. Femtosecond 2D Fourier transform (2D FT) spectra are more flexible and share some of the remarkable properties of their conceptual parent, 2D FT nuclear magnetic resonance. When 2D FT spectra are experimentally separated into real absorptive and imaginary refractive parts, the time resolution and frequency resolution can both reach the uncertainty limit set for each resonance by the sample itself. Coherent four-level contributions to the signal provide new molecular phase information, such as relative signs of transition dipoles. The nonlinear response can be picked apart by selecting a single coherence pathway (e.g., specifying the relative signs of energy level difference frequencies during different time intervals as in the photon echo). Because molecules are frozen on the femtosecond timescale, femtosecond 2D FT experiments can separate a distribution of instantaneous molecular environments and intramolecular geometries as inhomogeneous broadening. This review provides an introduction to two-dimensional Fourier transform experiments exploiting second- and third-order vibrational and electronic nonlinearities.
Geometric Deep Learning on Graphs and Manifolds Using Mixture Model CNNs (2017)

Deep learning has achieved a remarkable performance breakthrough in several fields, most notably in speech recognition, natural language processing, and computer vision. In particular, convolutional neural network (CNN) architectures currently produce state-of-the-art performance on a variety of image analysis tasks such as object detection and recognition. Most of deep learning research has so far focused on dealing with 1D, 2D, or 3D Euclidean-structured data such as acoustic signals, images, or videos. Recently, there has been an increasing interest in geometric deep learning, attempting to generalize deep learning methods to non-Euclidean structured data such as graphs and manifolds, with a variety of applications from the domains of network analysis, computational social science, or computer graphics. In this paper, we propose a unified framework allowing to generalize CNN architectures to non-Euclidean domains (graphs and manifolds) and learn local, stationary, and compositional task-specific features. We show that various non-Euclidean CNN methods previously proposed in the literature can be considered as particular instances of our framework. We test the proposed method on standard tasks from the realms of image-, graph-and 3D shape analysis and show that it consistently outperforms previous approaches.
Prostate-Specific Antigen (1992)

The glycoprotein, prostate-specific antigen (PSA), was first identified in seminal plasma in 1971, and early on was referred to as gamma-seminoprotein.<sup>1</sup>Eight years later when its specificity with prostatic tissue was demonstrated, it became known as prostate-specific antigen.<sup>2</sup>Today, PSA is the the most useful tumor marker available for the diagnosis and management of prostate cancer. Indeed, the discovery of PSA represents one of the most significant advancements in the field of prostate cancer in recent times. See also pp 2191, 2215, and 2227. Currently, there is much interest in the medical community in improving our ability to detect prostate cancer before the lesion has escaped the confines of the prostate gland. This enthusiasm is based in part on the work by Jewett and associates,<sup>3</sup>who demonstrated that patients undergoing radical prostatectomy whose tumors are confined to the prostate have a survival comparable to that of age-matched
Altered protein kinase C (PKC) isoforms in non-small cell lung cancer cells: PKCdelta promotes cellular survival and chemotherapeutic resistance. (2003)

Drugs that target protein kinase C (PKC) are now being evaluated in patients with non-small cell lung cancer (NSCLC), but the role of PKC in NSCLC cells remains unclear. We report here that NSCLC cell lines show enhanced phosphorylation and altered expression of specific PKC isoforms compared with normal lung epithelial cells. PKC inhibition variably increased apoptosis, with rottlerin, a PKCdelta inhibitor, being most effective and potentiating chemotherapy-induced apoptosis, especially with trastuzumab. Consistent with PKCdelta being anti-apoptotic in NSCLC cells, transient transfection of a kinase-dead mutant of PKCdelta increased apoptosis and potentiated chemotherapy-induced apoptosis. Our studies provide a rationale for targeting PKC isoforms in NSCLC cells, especially PKCdelta.
Advances in the understanding of Barth syndrome (2013)

Barth syndrome (BTHS) is an X-linked autosomal recessive disorder characterized by neutropenia, cardiomyopathy and growth retardation. BTHS was first described as mitochondrial disease affecting neutrophils as well as cardiac and skeletal muscles. Patients with neutropenia may have extremely low levels of circulating neutrophils and suffer from recurring sometimes life-threatening bacterial infections. Sepsis is not infrequent, may occur unexpectedly in a patient with no history for pronounced bacterial infections and may lead to death. The reduced level of circulating neutrophils suggests either a reduced production of myeloid cells in the bone marrow and premature apoptosis or aberrant clearance of neutrophils in peripheral blood. The underlying molecular defects are truncation, deletion or substitution mutations in the TAZ gene that appear to result in loss-of-function of the gene product tafazzin. Molecular mechanisms triggering neutropenia and cardiomyopathy in BTHS remain largely unclear. The current review focusses on recent advances in the understanding of molecular and cellular bases of neutropenia in Barth syndrome and covers the functional implications of the TAZ mutations, experimental models for neutropenia, the specific cellular abnormalities triggered by loss of TAZ function and potential novel therapeutic strategies for restoring the normal phenotype.
Mechanism of Sequence-Specific DNA Recognition Elucidated (1988)

RETURN TO ISSUEPREVNewsNEXTMechanism of Sequence-Specific DNA Recognition ElucidatedSynthetic oligonucleotides, peptides, and antibiotic analogs can recognize specific DNA sequences up to 15 base pairs in lengthRUDY M. BAUMView Author Information C&EN San FranciscoCite this: Chem. Eng. News 1988, 66, 1, 20–25Publication Date (Print):January 4, 1988Publication History Published online8 November 2010Published inissue 4 January 1988https://pubs.acs.org/doi/10.1021/cen-v066n001.p020https://doi.org/10.1021/cen-v066n001.p020newsACS PublicationsCopyright © 1988 American Chemical SocietyArticle Views7Altmetric-Citations1LEARN 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 options SUBJECTS:Genetics Get e-Alerts
A promoter of Epstein-Barr virus that can function during latent infection can be transactivated by EBNA-1, a viral protein required for viral DNA replication during latent infection (1989)

A viral promoter that functions on recombinant plasmids in cells immortalized by Epstein-Barr virus was identified and characterized. It is identical to that mapped on the viral genome by Bodescot et al. (M. Bodescot, M. Perricaudet, and P.J. Farrell, J. Virol. 61:3424-3430, 1987) which functions during the latent phase of the viral life cycle in some but not all cells to encode several latent viral gene products. Experiments with these plasmids indicated that this promoter requires the enhancer within oriP of Epstein-Barr virus in cis to function efficiently. They also indicated that it requires the EBNA-1 gene in trans to function efficiently. The EBNA-1 gene therefore positively affects both viral DNA replication (J.L. Yates, N. Warren, and B. Sugden, Nature [London] 313:812-815, 1985) and viral transcription.
The source of the inter‐alpha trypsin inhibitor in pathologic hyaluronateprotein (1971)

Abstract Hyaluronateprotein isolated from pathologic synovial fluid has been shown to have different physical properties from hyaluronateprotein isolated from normal synovial fluid. The altered properties of hyaluronateprotein from pathologic synovial fluid are due to the presence of a serum protein identified immunologically as the inter‐alpha trypsin inhibitor (IATI). The IATI is undetectable in normal synovial fluid, but is present in pathologic synovial fluids. The IATI in pathologic synovial fluid is bound to hyaluronate. The concentration of IATI is always much higher in serum than synovial fluid indicating that the IATI in synovial fluid has passed from the serum into the diseased joint where it has become firmly bound to hyaluronate.
Biochemical analysis of human Dna2 (2006)

Yeast Dna2 helicase/nuclease is essential for DNA replication and assists FEN1 nuclease in processing a subset of Okazaki fragments that have long single-stranded 5' flaps. It is also involved in the maintenance of telomeres. DNA2 is a gene conserved in eukaryotes, and a putative human ortholog of yeast DNA2 (ScDNA2) has been identified. Little is known about the role of human DNA2 (hDNA2), although complementation experiments have shown that it can function in yeast to replace ScDNA2. We have now characterized the biochemical properties of hDna2. Recombinant hDna2 has single-stranded DNA-dependent ATPase and DNA helicase activity. It also has 5'-3' nuclease activity with preference for single-stranded 5' flaps adjacent to a duplex DNA region. The nuclease activity is stimulated by RPA and suppressed by steric hindrance at the 5' end. Moreover, hDna2 shows strong 3'-5' nuclease activity. This activity cleaves single-stranded DNA in a fork structure and, like the 5'-3' activity, is suppressed by steric hindrance at the 3'-end, suggesting that the 3'-5' nuclease requires a 3' single-stranded end for activation. These biochemical specificities are very similar to those of the ScDna2 protein, but suggest that the 3'-5' nuclease activity may be more important than previously thought.
γ-AApeptides: design, synthesis and evaluation (2011)

A new class of peptide mimics termed “γ-AApeptides” has been described. The design and synthesis of γ-AApeptides, and potential bioactivities towards p53/MDM2 interaction were demonstrated. γ-AApeptides were also found to be highly resistant to proteolysis. The development of sequence-specific γ-AApeptides may lead to a family of peptidomimetics with a new framework for drug discovery or peptide/protein mimicry.
Effects of Chaotic Temperature Fluctuations on the Heat Transfer Coefficient in Liquid-Liquid-Solid Fluidized Beds (2001)

The effect of chaotic temperature fluctuations on the immersed heater-to-bed heat transfer coefficient (h) are investigated in a liquid-liquid-solid fluidized bed (0.152 m ID × 2.5 m in height). The time series of temperature fluctuations are measured and analyzed by means of the multidimensional phase space portraits and Kolmogorov entropy (K), in order to characterize the chaotic behavior of heat transfer coefficient fluctuations in the bed. The overall heat transfer coefficient is inversely proportional to the Kolmogorov entropy of temperature fluctuations, as well as the fluctuation range of heat transfer coefficient (Δhi). The Kolmogorov entropy and fluctuation range of the heat transfer coefficient (Δhi) increase with increasing dispersed phase velocity, but decrease with increasing particle size. However, they attain their minima with variation of the continuous phase velocity as well as the bed porosity, at which point the flow regime of particles in the beds changes. The overall heat transfer coefficient is directly correlated with the Kolmogorov entropy, as well as the fluctuation range of heat transfer coefficient.
[Genetic analysis of bronchial asthma in Japanese population--Fc epsilon RI beta gene and beta 2 adrenergic receptor gene]. (1996)

Atopy and bronchial hyperresponsiveness are important elements for the development of bronchial asthma. On the basis of the progression of molecular biology, the genetic regulations of asthma are being examined extensively and, recently, the gene encoding a beta subunit of the high affinity receptor for IgE (Fc epsilon RI beta) and the gene encoding beta 2 adrenergic receptor (beta 2ADR) are considered to be responsible for asthma. The mutation in the Fc epsilon RI beta gene on chromosome 11q13 is reported to be associated with atopy in British families with maternal inheritance of atopy. However there is no such an association between atopy and 11q13 in Japanese families. The polymorphisms in the beta 2 adrenergic receptor gene are reported to be related to the degree of agonist promoted downregulation of the receptor, and these polymorphisms are found to affect the severity of asthma. There is also evidence which supports a relationship between the polymorphism of the receptor and airway hyperresponsiveness in Japanese families.
Reconstituted Botulinum Toxin Type A Does Not Lose Potency in Humans If It Is Refrozen or Refrigerated for 2 Weeks Before Use (1997)

Botulinum toxin type A (BTX-A) (Botox, Allergan, Irvine, CA) labeling recommends its use within 4 hours of reconstitution. Since BTX-A is available only in 100-unit vials, a substantial quantity is often discarded. Using eight volunteers, we measured the percent decline in extensor digitorum brevis (EDB) M-wave amplitude (percent paralysis) following injection of freshly reconstituted BTX (right EDB) and compared this with the decline following injection of BTX that was refrozen (-20 degrees C) or refrigerated (+4 degrees C) for 2 weeks (left EDB) after reconstitution. When analyzed as paired data, there was essentially no difference in the muscle paralysis resulting from fresh BTX compared with refrozen or refrigerated BTX, and no statistical difference between groups was noted. Reconstituted BTX-A that is subsequently refrigerated or refrozen for 2 weeks does not lose potency in humans.
Inhibitors of p38 kinase (1997)

AbstractInhibition of p38 kinase is evolving as an approach to the discovery of new anti-inflammatory agents. Inhibitors of this enzyme modulate cytokine production, especially pro-inflammatory TNF-α and IL-1. These cytokines and others mediate a wide spectrum of diseases, notably rheumatoid arthritis. Cytokine modulators are expected to be disease modifying agents. The lead molecules disclosed in the patent literature fall into a class termed 1-pyridinyl-2-phenylazoles; this class of compounds encompasses promising drug candidates that are non-peptide, orally active, of low molecular weight and selective for p38. Structural characteristics of inhibitors and p38 kinase background are discussed.Keywordsanti-inflammatorycytokinesinterleukin-1p38 kinase inhibitorsTNF-α
An evaluation of CAN8 as a Computer Assisted Language Learning tool in the context of current research (2001)

The CAN8 virtual language laboratory combines features of traditional language laboratory systems with typical CALL software and features of CBT to create a language learning environment which embraces many different theories of learning and more specifically of language learning.
Polymorphisms in the methylenetetrahydrofolate reductase gene were associated with both the efficacy and the toxicity of methotrexate used for the treatment of rheumatoid arthritis, as evidenced by single locus and haplotype analyses (2002)

5,10-Methylenetetrahydrofolate reductase (MTHFR), a key enzyme involved in folate metabolism, has two common polymorphisms that affect enzyme activity. The objective of this study was to examine whether there was a correlation between the genotype or haplotype of the MTHFR gene and the efficacy or toxicity of methotrexate (MTX) in the treatment of rheumatoid arthritis. MTX-treated rheumatoid arthritis patients (n = 106) were selected from outpatient clinics and used for a retrospective study to examine the correlation between genotypes or haplotypes concerning polymorphisms of the MTHFR gene, and the efficacy or toxicity of MTX. Estimation of the haplotype frequencies was performed by maximum likelihood estimation based on expectation maximization algorithm. Single locus analysis examining each locus separately showed that patients with 1298C were receiving significantly lower doses of MTX compared to patients without [P < 0.05, relative risk (RR) = 2.18, 95% confidence interval (CI) 1.17-4.06], while a higher rate of overall MTX toxicity was observed in patients with 677T than those without (P < 0.05, RR = 1.25, 95% CI 1.05-1.49). An estimation of haplotype frequencies showed that there was no 677T-1298C haplotype in the population. Posterior distribution of the diplotype configuration for each individual was concentrated on a single configuration. Patients with the 677C-1298C haplotype were receiving lower doses of MTX than those without (P < 0.05, RR = 2.14, 95% CI 1.13-4.07), while subjects with 677T-1298A had a higher frequency of side-effects from MTX (P < 0.05, RR = 1.42, 95% CI 1.11-1.82). Both single locus and haplotype analyses suggest that polymorphisms within the MTHFR gene are associated with both the efficacy and toxicity of MTX in rheumatoid arthritis patients. Pharmacokinetic studies are necessary to prove the association.
Bivalency Is Required for Anticapsular Monoclonal Antibodies To Optimally Suppress Activation of the Alternative Complement Pathway by theCryptococcus neoformansCapsule (1998)

Encapsulated cells of Cryptococcus neoformans are potent activators of the alternative complement pathway. Previous studies found that monoclonal antibodies (MAbs) specific for the major capsular polysaccharide, termed glucuronoxylomannan (GXM), can markedly suppress the ability of the capsule to accumulate C3 from normal human serum via the alternative pathway. The present study examined the abilities of F(ab)2 and Fab fragments of three MAbs (MAbs 439, 3C2, and 471) to mediate the suppressive effect. The results showed that F(ab)2 fragments of all three MAbs suppressed activation and binding of C3 via the alternative pathway in a manner similar to that of intact antibodies. In contrast, Fab fragments of MAb 439 and MAb 3C2 showed no suppressive activity, and Fab fragments of MAb 471 were markedly reduced in suppressive activity. Indeed, there was an earlier accumulation of C3 on encapsulated cryptococci in the presence of the Fab fragments. Study of subclass switch families of MAb 439 and MAb 471 found that MAbs of an immunoglobulin G (IgG) subclass with increased flexibility in the hinge region (IgG2b) had less suppressive activity than MAbs of IgG subclasses with less flexibility (IgG1 or IgG2a). Taken together, these results indicate that cross-linking of the capsular matrix is an essential component in suppression of the alternative complement pathway by anti-GXM MAbs.
Bacterial Flora of Endophytes in the Maturing Seed of Cultivated Rice (Oryza sativa) (2005)

Endophytic bacteria in the seeds of rice plants (Oryza sativa, cultivar Nipponbare) were studied during the rice maturation process by comparing them with the bacteria at the surface of rice seeds. The endophytic and surface bacteria were isolated from cultivated rice seeds by using a nutrient broth (NB) and a diluted nutrient broth (DNB) agar medium. The endophytes at the early stages of maturation were relatively diverse, consisting of strains closely related to the genera Bacillus, Sphingomonas and Pantoea. In contrast, the endophytic and surface bacteria at the middle and late stages of the maturation process (39 strains altogether) were all closely related only to the genus Bacillus with the exception of one isolate, and almost all of these strains were motile and spore-forming. It was deduced that these bacteria might have migrated into the rice seeds before they hardened that is, during the early stage (the endophytes at the early stage were also all motile and about half of them were spore-forming), subsisting as endospores during the middle and late stages of the maturation process. Furthermore, most of the isolates (19 of 23) from the surface bacteria and the endophytic bacteria grew better when sucrose (1.2 M) was added to the NB liquid medium. These bacteria may be able to adapt to a high osmotic pressure.
Involvement of TLR4/MD-2 complex in species-specific lipopolysaccharide-mimetic signal transduction by Taxol (2001)

Taxol, an antitumor agent derived from a plant, mimics the action of lipopolysaccharide (LPS) in mice, but not in humans. The LPS-mimetic activity of Taxol is not observed in LPS-hyporesponsive C3H/HeJ mice which possess a point mutation in Toll-like receptor 4 (TLR4); therefore, TLR4 appears to be involved in both Taxol and LPS signaling. In addition, TLR4 was recently shown to physically associate with MD-2, a molecule that confers LPS-responsiveness on TLR4. Here we examined whether or not TLR4/MD-2 complex mediates a Taxol-induced signal by using transformants of the mouse pro-B cell line, Ba/F3, expressing mouse TLR4 alone, both mouse TLR4 and mouse MD-2, and both mouse MD-2 and mouse TLR4 lacking the cytoplasmic portion. Our results demonstrated that co-expression of mouse TLR4 and mouse MD-2 was required for Taxol responsiveness, and that the TLR4/MD-2 complex is the shared molecule in Taxol and LPS signal transduction in mice. We also found that mouse MD-2, but not human MD-2, is involved in Taxol signaling, suggesting that MD-2 is responsible for the species-specific responsiveness to Taxol.
8-[18F]Fluoropenciclovir: an improved reporter probe for imaging HSV1-tk reporter gene expression in vivo using PET. (2001)

These results indicate that FPCV is a better reporter probe than is FGCV for imaging lower levels of HSV1 -tk gene expression in vivo. The results also reveal the ability to monitor the expression of two distinct reporter genes in the same animal using reporter probes specific for each gene.
Millicode in an IBM zSeries processor (2004)

Because of the complex architecture of the zSeries® processors, an internal code, called millicode, is used to implement many of the functions provided by these systems. While the hardware can execute many of the logically less complex and high-performance instructions, millicode is required to implement the more complex instructions, as well as to provide additional support functions related primarily to the central processor. This paper is a review of millicode on previous zSeries CMOS systems and also describes enhancements made to the z990 system for processing of the millicode. It specifically discusses the flexibility millicode provides to the z990 system.