gebhart/patrepeval huggingface dataset:
Mathematical modelling of marine and oceanic currents (2001)

- Mathematical models of the general circulation in oceans and seas are reviewed. Basic model equations which in oceanology are traditionally called primitive equations are considered. They follow from the classic hydrodynamical equations of a rotating fluid with the use of Boussinesq, hydrostatic, incompressibility, turbulent viscosity, and diffusivity approximations.
Review: Manipulating the extracellular matrix and its role in brain and spinal cord plasticity and repair (2013)

Brain and spinal cord injury can result in permanent cognitive, motor, sensory and autonomic deficits. The central nervous system (CNS) has a poor intrinsic capacity for regeneration, although some functional recovery does occur. This is mainly in the form of sprouting, dendritic remodelling and changes in neuronal coding, firing and synaptic properties; elements collectively known as plasticity. An important approach to repair the injured CNS is therefore to harness, promote and refine plasticity. In the adult, this is partly limited by the extracellular matrix (ECM). While the ECM typically provides a supportive framework to CNS neurones, its role is not only structural; the ECM is homeostatic, actively regulatory and of great signalling importance, both directly via receptor or coreceptor-mediated action and via spatially and temporally relevant localization of other signalling molecules. In an injury or disease state, the ECM represents a key environment to support a healing and/or regenerative response. However, there are aspects of its composition which prove suboptimal for recovery: some molecules present in the ECM restrict plasticity and limit repair. An important therapeutic concept is therefore to render the ECM environment more permissive by manipulating key components, such as inhibitory chondroitin sulphate proteoglycans. In this review we discuss the major components of the ECM and the role they play during development and following brain or spinal cord injury and we consider a number of experimental strategies which involve manipulations of the ECM, with the aim of promoting functional recovery to the injured brain and spinal cord.
Purification and Characterization of a New Class of Insect α‐Amylase Inhibitors from Barley (1997)

ABSTRACT Barley seeds contain proteins that apparently protect them against attack by microorganisms and insects. Studies of these barley defensive proteins may lead to the development of barleys with improved natural resistance to pests. We have purified two low molecular weight proteins, designated BIα1 and BIα2, from barley grain, using ion‐exchange chromatography and reversed‐phase and gel‐permeation high‐performance liquid chromatography (HPLC). Both BIα1 and BIα2 inhibited insect (yellow meal worm, Tenebrio molitor ) α‐amylase activities. For the T. molitor α‐amylase, the IC50 values of BIα1 and BIα2 were 80 μg/mL (12.5 μ M ) and 34 μg/mL (6.8 μ M ), respectively. Neither protein inhibited either human salivary α‐amylase, barley α‐amylase, or trypsin activities. N‐terminal amino acid sequences of the inhibitors were highly homologous with those of the plant proteins called defensins . The first 20 N‐terminal amino acids of BIα2 were identical to those of γ‐hordothionin, but neither BIα1 nor BIα2 protein showed any homology with the chloroform‐methanol (CM) soluble protein amino acid consensus sequence. The two inhibitors therefore apparently comprise another group of low molecular weight barley proteins that inhibit the α‐amylase activities of some insects that attack cereal grains.
Open reading frame cloning: identification, cloning, and expression of open reading frame DNA. (1982)

A plasmid was constructed that facilitates the cloning and expression of open reading frame DNA. A DNA fragment containing a bacterial promoter and the amino terminus of the cI gene of bacteriophage lambda was fused to an amino-terminally deleted version of the lacZ gene. An appropriate cloning site was inserted between these two fragments such that a frameshift mutation was introduced upstream of the lacZ-encoding DNA. This cloning vehicle produces a relatively low level of beta-galactosidase activity when introduced into Escherichia coli. The insertion of foreign DNA at the cloning site can reverse the frameshift mutation and generate plasmids that produce a relatively high level of beta-galactosidase activity. A large fraction of these plasmids produce a fusion protein that has a portion of the lambda cI protein at the amino terminus, the foreign protein segment in the middle, and the lacZ polypeptide at the carboxyl terminus. The production of a high level of beta-galactosidase and a large fusion polypeptide guarantees the cloning of a DNA fragment with at least one open reading frame that traverses the entirety of the fragment. Hence, the method can identify, clone, and express (as part of a larger fusion polypeptide) open reading frame DNA from among a large collection of DNA fragments.
<title>Making sensors out of disarray: optical sensor microarrays</title> (1998)

We present a new approach to array fabrication for multianalyte sensing. Sensor arrays are prepared in a random fashion such that each sensor in the array occupies a different location from fiber to fiber. Using optical encoding schemes, the identity of each sensor can be ascertained and registered on the detector. The approach alleviates the need for preregistration of each sensing element during the array fabrication process.
Cannabidiol rather than Cannabis sativa extracts inhibit cell growth and induce apoptosis in cervical cancer cells (2016)

In conclusion, these data suggest that cannabidiol rather than Cannabis sativa crude extracts prevent cell growth and induce cell death in cervical cancer cell lines.
Inhibition of T lymphocyte mitogenesis by 1,25-dihydroxyvitamin D3 (calcitriol). (1984)

Recent studies have suggested that vitamin D may have other important biologic activities in addition to its well-characterized role in the maintenance of calcium homeostasis. Discovery of cytosolic receptors for vitamin D in human peripheral blood monocytes and lectin-stimulated lymphocytes prompted us to study the effects of 1,25-dihydroxyvitamin D3 (calcitriol), the most biologically active metabolite of vitamin D, upon phytohemagglutinin (PHA)-induced lymphocyte blast transformation. We have found that calcitriol is a potent inhibitor of PHA-induced lymphocyte proliferation, achieving 70% inhibition of tritiated thymidine incorporation after 72 h in culture. Furthermore, calcitriol suppressed interleukin-2 (IL-2) production by PHA-stimulated peripheral blood mononuclear cells in a concentration-dependent fashion. Lastly, the suppressive effect of calcitriol on cellular proliferation was partially reversed by the addition of saturating amounts of purified IL-2. We conclude that calcitriol is a potent inhibitor of PHA-induced lymphocyte blast transformation and that this effect is mediated, in part, through suppression of IL-2 production. Thus, calcitriol appears to possess immunoregulatory properties that have been unappreciated heretofore.
Apolipoprotein E and the CNS Response to Injury (1998)

Apolipoprotein E (apoE) is a multifunctional protein with an expanding role in the neurobiology of disease. Although originally described in the context of cholesterol metabolism, interest in the neurobiology of apoE has intensified following the association between apoE genotype and risk of developing Alzheimer's disease. Recent clinical observations also suggest that apoE genotype may influence recovery after a variety of neurological insults. Thus, in addition to the study of disease-specific mechanisms by which apoE may modulate susceptibility of developing Alzheimer's disease, there has been an increasing focus on its role in modulating the CNS response to acute injury. Although the neurobiology of apoE in the injured brain remains incompletely defined, there is evidence to suggest neurotrophic, immunomodulatory, and antioxidant effects.
Detecting malicious HTTP redirections using trees of user browsing activity (2014)

The web has become a platform that attackers exploit to infect vulnerable hosts, or deceive victims into buying rogue software. To accomplish this, attackers either inject malicious scripts into popular web sites or manipulate content delivered by servers to exploit vulnerabilities in users' browsers. To hide malware distribution servers, attackers employ HTTP redirections, which automatically redirect users' requests through a series of intermediate web sites, before landing on the final distribution site. In this paper, we develop a methodology to identify malicious chains of HTTP redirections. We build per-user chains from passively collected traffic and extract novel statistical features from them, which capture inherent characteristics from malicious redirection cases. Then, we apply a supervised decision tree classifier to identify malicious chains. Using a large ISP dataset, with more than 15K clients, we demonstrate that our methodology is very effective in accurately identifying malicious chains, with recall and precision values over 90% and up to 98%.
Retinobenzoic acids. 1. Structure-activity relationships of aromatic amides with retinoidal activity (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRetinobenzoic acids. 1. Structure-activity relationships of aromatic amides with retinoidal activityHiroyuki Kagechika, Emiko Kawachi, Yuichi Hashimoto, Koichi Shudo, and Toshiyuki HimiCite this: J. Med. Chem. 1988, 31, 11, 2182–2192Publication Date (Print):November 1, 1988Publication History Published online1 May 2002Published inissue 1 November 1988https://pubs.acs.org/doi/10.1021/jm00119a021https://doi.org/10.1021/jm00119a021research-articleACS PublicationsRequest reuse permissionsArticle Views2093Altmetric-Citations199LEARN 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-Alertsclose Get e-Alerts
Use of IMP3 in Identification of Carcinoma in Fine Needle Aspiration Biopsies of Pancreas (2008)

IMP3 is a promising new marker with high specificity and sensitivity for pancreatic adenocarcinoma.
Spontaneous tumor rejection by cbl-b –deficient CD8+ T cells (2007)

The concept of tumor surveillance implies that specific and nonspecific components of the immune system eliminate tumors in the early phase of malignancy. Understanding the biochemical mechanisms of tumor immunosurveillance is of paramount significance because it might allow one to specifically modulate spontaneous antitumor activity. We report that inactivation of the E3 ligase Casitas B cell lymphoma-b (Cbl-b) confers spontaneous in vivo rejection of tumor cells that express human papilloma virus antigens. Moreover, cbl-b(-/-) mice develop significantly fewer ultraviolet B (UVB)-induced skin malignancies and reject UVB-induced skin tumors. CD8(+) T cells were identified as key players in the spontaneous tumor rejection response. Loss of Cbl-b not only enhances antitumor reactivity of CD8(+) T cells but also occurs in the absence of CD4(+) T cells. Mechanistically, cbl-b(-/-) CD8(+) T cells are resistant to T regulatory cell-mediated suppression and exhibit enhanced activation and rapid tumor infiltration. Importantly, therapeutic transfer of naive cbl-b(-/-) CD8(+) T cells is sufficient to mediate rejection of established tumors. Even up to 1 yr after the first encounter with the tumor cells, cbl-b(-/-) mice carry an "anticancer memory." These data identify Cbl-b as a key signaling molecule that controls spontaneous antitumor activity of cytotoxic T cells in different cancer models. Inhibition of Cbl-b is a novel approach to stimulate long-lasting immunity against cancer.
Computational methods for large-scale 3D acoustic finite-difference modeling: A tutorial (2007)

Abstract We present a set of methods for modeling wavefields in three dimensions with the acoustic-wave equation. The primary applications of these modeling methods are the study of acquisition design, multiple suppression, and subsalt imaging for surface-streamer and ocean-bottom recording geometries. We show how to model the acoustic wave equation in three dimensions using limited computer memory, typically using a single workstation, leading to run times on the order of a few CPU hours to a CPU day. The structure of the out-of-core method presented is also used to improve the efficiency of in-core modeling, where memory-to-cache-to-memory data flow is essentially the same as the data flow for an out-of-core method. Starting from the elastic-wave equation, we develop a vector-acoustic algorithm capable of efficiently modeling multicomponent data in an acoustic medium. We show that data from this vector-acoustic algorithm can be used to test upgoing/downgoing separation of P-waves recorded by ocean-bottom seismic acquisition.
Cloning, nucleotide sequence, and enzymatic characterization of an alpha-amylase from the ruminal bacterium Butyrivibrio fibrisolvens H17c (1991)

A Butyrivibrio fibrisolvens amylase gene was cloned and expressed by using its own promoter on the recombinant plasmid pBAMY100 in Escherichia coli. The amylase gene consisted of an open reading frame of 2,931 bp encoding a protein of 976 amino acids with a calculated Mr of 106,964. In E. coli(pBAMY100), more than 86% of the active amylase was located in the periplasm, and TnphoA fusion experiments showed that the enzyme had a functional signal peptide. The B. fibrisolvens amylase is a calcium metalloenzyme, and three conserved putative calcium-binding residues were identified. The amylase showed high sequence homology with other alpha-amylases in the three highly conserved regions which constitute the active centers. These and other conserved regions were located in the N-terminal half, and no similarity with any other amylase was detected in the remainder of the protein. Deletion of approximately 40% of the C-terminal portion of the amylase did not result in loss of amylolytic activity. The B. fibrisolvens amylase was identified as an endo-alpha-amylase by hydrolysis of the Phadebas amylase substrate, hydrolysis of gamma-cyclodextrin to maltotriose, maltose, and glucose and the characteristic shape of the blue value and reducing sugar curves. Maltotriose was the major initial hydrolysis product from starch, although extended incubation resulted in its hydrolysis to maltose and glucose.
Linear vs Exponential Formation of Molecular-Based Assemblies (2010)

Here we present the critical role of the molecular structure and reaction parameters on the nature of thin-film growth, using a versatile two-step assembly method with organic and metal-organic chromophores cross-linked with palladium. It was found that the polypyridyl complexes exhibit exponential growth, whereas, under identical conditions, the organic systems exhibit linear behavior. The internal film morphology plays a pivotal role in the storage and usage of the palladium, where a more porous structure results in exponential growth. Interestingly, through proper tuning of the reaction conditions, the growth of the molecular assemblies can be controlled, resulting in a changeover from exponential to linear growth. These findings unequivocally demonstrate the importance of both the internal film structure and deposition conditions on the assembly of molecular-based films.
Synthesis and Antifungal Activity of Novel Thiazole-Containing Triazole Antifungals. II. Optically Active ER-30346 and Its Derivatives. (1998)

A series of novel thiazole-containing triazole antifungals was synthesized and evaluated for antifungal activity against a variety of clinically isolated pathogenic fungi in vitro and against systemic candidosis in vivo. These compounds showed potent antifungal activities in vitro and in vivo. In particular, (2R,3R)-3-[4-(4-cyanophenyl)thiazol-2-yl]-2-(2,4- difluorophenyl)-1-(1H-1,2,4-triazol-1-yl)-2-butanol (12g; ER-30346) showed potent and well-balanced in vitro activities and potent in vivo efficacy, and had a good safety profile.
Detecting Eyelash and Reflection for Accurate Iris Segmentation (2003)

Accurate iris segmentation is presented in this paper, which is composed of two parts, reflection detection and eyelash detection. Eyelashes are classified into two categories, separable and multiple. An edge detector is applied to detect separable eyelashes, and intensity variances are used to recognize multiple eyelashes. Reflection is also divided into two types, strong and weak. A threshold and statistical model is proposed to recognize the strong and weak reflection, respectively. We have developed an iris recognition approach for testing the effectiveness of the proposed segmentation method. The results show that the proposed method can reduce recognition error for the iris recognition approach.
45. Solvent-modified polymer networks. Part IV. Styrene–divinyl-benzene copolymers made in the presence of non-solvating diluents (1965)

J. R. Millar, D. G. Smith and T. R. E. Kressman, J. Chem. Soc., 1965, 304 DOI: 10.1039/JR9650000304
Identification of the Binding Site for the Extrahelical Target Base in N 6-Adenine DNA Methyltransferases by Photo-cross-linking with Duplex Oligodeoxyribonucleotides Containing 5-Iodouracil at the Target Position (1999)

DNA methyltransferases flip their target bases out of the DNA double helix for catalysis. Base flipping of C5-cytosine DNA methyltransferases was directly observed in the protein-DNA cocrystal structures of M.HhaI and M.HaeIII. Indirect structural evidence for base flipping of N6-adenine and N4-cytosine DNA methyltransferases was obtained by modeling DNA into the three-dimensional structures of M.TaqI and M.PvuII in complex with the cofactor. In addition, biochemical evidence of base flipping was reported for different N6-adenine DNA methyltransferases. As no protein-DNA cocrystal structure for the related N6-adenine and N4-cytosine DNA methyltransferases is available, we used light-induced photochemical cross-linking to identify the binding site of the extrahelical target bases. The N6-adenine DNA methyltransferases M.TaqI and M.CviBIII, which both methylate adenine within the double-stranded 5'-TCGA-3' DNA sequence, were photo-cross-linked to duplex oligodeoxyribonucleotides containing 5-iodouracil at the target position in 50-60% and almost quantitative yield, respectively. Proteolytic fragmentation of the M. CviBIII-DNA complex followed by Edman degradation and electrospray ionization mass spectrometry indicates photo-cross-linking to tyrosine 122. In addition, the mutant methyltransferases M. TaqI/Y108A and M.TaqI/F196A were photo-cross-linked with 6-fold and 2-fold reduced efficiency, respectively, which suggests that tyrosine 108 is the primary site of modification in M.TaqI. Our results indicate a close proximity between the extrahelical target base and tyrosine 122 in M.CviBIII or tyrosine 108 in M.TaqI. As both residues belong to the conserved motif IV ((N/D/S)(P/I)P(Y/F/W)) found in all N6-adenine and N4-cytosine DNA as well as in N6-adenine RNA methyltransferases, a similar spatial relationship between the target bases and the aromatic amino acid residue within motif IV is expected for all these methyltransferases.
Passive transfer of respiratory syncytial virus (RSV) antiserum suppresses the immune response to the RSV fusion (F) and large (G) glycoproteins expressed by recombinant vaccinia viruses (1988)

In young infants who possess maternally derived respiratory syncytial virus (RSV) antibodies, the antibody response to RSV glycoproteins is relatively poor, despite extensive replication of RSV. In the present study, it was found that cotton rat RSV hyperimmune antiserum suppressed the antibody response to the RSV glycoproteins but not the response to vaccinia virus antigens when the antiserum was passively transferred to cotton rats prior to infection with vaccinia recombinant viruses expressing the RSV envelope glycoproteins. The cotton rats which had their immune responses suppressed by passively transferred antibodies were more susceptible to infection with RSV than were animals inoculated with control serum lacking RSV antibodies. Furthermore, many of the immunosuppressed animals infected with the vaccinia recombinant viruses developed RSV glycoprotein antibodies which had abnormally low neutralizing activities. Thus, preexisting serum RSV antibodies had dramatic quantitative and qualitative effects on the immune response to RSV glycoproteins, which may explain, in part, the poor RSV antibody response of young human infants to infection with RSV. Our observations also suggest that immunosuppression by preexisting, passively acquired RSV antibodies may constitute a major obstacle to RSV immunoprophylaxis during early infancy, when immunization is most needed.
Ectodomain of Coxsackievirus and Adenovirus Receptor Genetically Fused to Epidermal Growth Factor Mediates Adenovirus Targeting to Epidermal Growth Factor Receptor-Positive Cells (2000)

Human adenovirus (Ad) is extensively used for a variety of gene therapy applications. However, the utility of Ad vectors is limited due to the low efficiency of Ad-mediated gene transfer to target cells expressing marginal levels of the Ad fiber receptor. Therefore, the present generation of Ad vectors could potentially be improved by modification of Ad tropism to target the virus to specific organs and tissues. The fact that coxsackievirus and adenovirus receptor (CAR) does not play any role in virus internalization, but functions merely as the virus attachment site, suggests that the extracellular part of CAR might be utilized to block the receptor recognition site on the Ad fiber knob domain. We proposed to design bispecific fusion proteins formed by a recombinant soluble form of truncated CAR (sCAR) and a targeting ligand. In this study, we derived sCAR genetically fused with human epidermal growth factor (EGF) and investigated its ability to target Ad infection to the EGF receptor (EGFR) overexpressed on cancer cell lines. We have demonstrated that sCAR-EGF protein is capable of binding to Ad virions and directing them to EGFR, thereby achieving targeted delivery of reporter gene. These results show that sCAR-EGF protein possesses the ability to effectively retarget Ad via a non-CAR pathway, with enhancement of gene transfer efficiency.