gebhart/patrepeval huggingface dataset:
The Superantigen GeneypmIs Located in an Unstable Chromosomal Locus ofYersinia pseudotuberculosis (2002)

Yersinia pseudotuberculosis produces YPM (Y. pseudotuberculosis-derived mitogen), a superantigenic toxin that exacerbates the virulence of the bacterium in vivo. To date, three alleles of the superantigen gene (ypmA, ypmB, and ypmC) have been described. These genes are not found in all Y. pseudotuberculosis strains and have a low GC content, suggesting their location on mobile genetic elements. To elucidate this question, the genetic environment of the superantigen-encoding genes was characterized and 11 open reading frames (ORFs) were defined. Sequence analysis revealed that the ypm genes were not associated with plasmids, phages, transposons, or pathogenicity islands and that the superantigen genes were always located in the chromosome between ORF3 and ORF4. Nonsuperantigenic strains exhibited the same genetic organization of the locus but lacked the ypm gene between ORF3 and ORF4. A new insertion sequence, designated IS1398, which displays features of the Tn3 family, was characterized downstream of the ypmA and ypmC genes. A 13.3-kb region containing the ypm genes was not found in the genome of Y. pestis (CO92 and KIM 5 strains). We experimentally induced deletion of the ypm gene from a superantigen-expressing Y. pseudotuberculosis: using the association of aph(3')-IIIa and sacB genes, we demonstrated that when these reporter genes were present in the ypm locus, deletion of these genes was about 250 times more frequent than when they were located in another region of the Y. pseudotuberculosis chromosome. These results indicate that unlike other superantigenic toxin genes, the Yersinia ypm genes are not associated with mobile genetic elements but are inserted in an unstable locus of the genome.
Image-adaptive watermarking using visual models (1998)

The huge success of the Internet allows for the transmission, wide distribution, and access of electronic data in an effortless manner. Content providers are faced with the challenge of how to protect their electronic data. This problem has generated a flurry of research activity in the area of digital watermarking of electronic content for copyright protection. The challenge here is to introduce a digital watermark that does not alter the perceived quality of the electronic content, while being extremely robust to attack. For instance, in the case of image data, editing the picture or illegal tampering should not destroy or transform the watermark into another valid signature. Equally important, the watermark should not alter the perceived visual quality of the image. From a signal processing perspective, the two basic requirements for an effective watermarking scheme, robustness and transparency, conflict with each other. We propose two watermarking techniques for digital images that are based on utilizing visual models which have been developed in the context of image compression. Specifically, we propose watermarking schemes where visual models are used to determine image dependent upper bounds on watermark insertion. This allows us to provide the maximum strength transparent watermark which, in turn, is extremely robust to common image processing and editing such as JPEG compression, rescaling, and cropping. We propose perceptually based watermarking schemes in two frameworks: the block-based discrete cosine transform and multiresolution wavelet framework and discuss the merits of each one. Our schemes are shown to provide very good results both in terms of image transparency and robustness.
Parenteral Iron Therapy (1957)

ALTHOUGH oral administration of iron salts is the therapy of choice in iron-deficiency anemia, certain circumstances make it advisable to administer iron by injection. Until recently, saccharated iron oxide was the only effective preparation for this purpose. This required intravenous injection and was potentially dangerous.1 In the search for a nontoxic effective preparation, British investigators combined iron with a dextran of low molecular weight. This compound can be injected intravenously or intramuscularly, although the latter route is recommended. It has been reported to be both effective and nontoxic.2 , 3 The present investigation was undertaken to evaluate further these properties of the . . .
A strategy for constructing photosynthetic models: porphyrin-containing modules assembled around transition metals (1996)

A. Harriman and J. Sauvage, Chem. Soc. Rev., 1996, 25, 41 DOI: 10.1039/CS9962500041
Nuclear Hormone Receptor Coregulators In Action: Diversity For Shared Tasks (2000)

The nuclear hormone receptors are transcriptional regulators that activate gene expression upon binding of their respective ligands. A new class of protein, termed coregulators, has emerged during the last few years. These proteins have the faculty to repress (corepressors) or to enhance (coactivators) the activity of genes regulated by nuclear hormone receptors in a ligand-dependent fashion. In this review we describe most of these coregulators and discuss their mode of action. In particular, we comment on the link between coregulators and histone acetylation, which is a crucial event in the transcriptional response within chromatin. We describe novel alternative pathways, which elicit the recruitment of coregulators independently of the presence of any ligand and speculate on how the convergence of ligand-dependent and -independent mechanisms might enhance the transcriptional response of target genes.
Gene structure of mouse BIT/SHPS-1 (1999)

BIT/SHPS-1/SIRPα/P84 is a unique molecule with a high degree of homology with immune antigen recognition molecules (immunoglobulin, T-cell receptor and MHC), and is highly expressed in the brain. The extracellular region contains three immunoglobulin-like domains (V-type, C1-type and C1-type), and the intracellular region contains two signalling motifs that interact with SHP-2 protein tyrosine phosphatase. BIT-coated plates support cell-substrate adhesion and neurite extension of neurons, and BIT participates in neuronal signal transduction. Diversity of the V-type domain sequences of human BIT has been reported. In the present study we analysed the structure of the mouse BIT gene (Bit). The protein coding region consists of eight exons corresponding to a signal peptide, a V-type domain, a C1-type domain, a C1-type domain, a transmembrane region and three parts of one cytoplasmic region. The two signalling motifs are encoded in one exon. Four splicing forms of mouse BIT were revealed. We also found the sequence diversity in three mouse strains, namely BALB/c, 129/Sv and C57BL/6. The substitution patterns of amino acids and nucleotides indicate positive pressure to alter the amino acids in the V-type domain in evolution. Immunoblot analyses showed that mouse BIT and human BITα are predominantly expressed in the brain. On the bases of these findings we discuss the possibility that BIT contributes to the genetic individuality and diversity of the brain.
Impact of Cyclosporine-A Concentration on the Incidence of Severe Acute Graft-versus-Host Disease after Allogeneic Stem Cell Transplantation (2009)

This single-center retrospective study analyzed 85 consecutive patients who underwent allogeneic stem cell transplantation (allo-SCT) with the aim to assess whether there is a correlation between exposure to cyclosporine-A (CsA; as measured by CsA concentrations during the first month after allo-SCT) and the risk for developing severe grade III-IV acute graft-versus-host disease (aGVHD). The median concentrations of CsA in the blood at 1, 2, 3, and 4 weeks after allo-SCT were 348 (range: 172-733), 284 (range: 137-535), 274 (range: 107-649), and 247 (range: 37-695) ng/mL, respectively. Overall, grade II-IV aGVHD occurred in 36 patients (42%) at a median of 29 (range: 6-100) days after allo-SCT. The incidence of grade III-IV aGVHD (n = 20) was 23% (95% confidence interval [CI], 14%-32%). In univariate analysis, patients receiving allo-SCT from an HLA-matched unrelated donor had a higher risk of grade III-IV aGVHD, and patients having the lowest CsA concentration in the first and second weeks after allo-SCT had a significantly higher risk of grade III-IV aGVHD. In a multivariate logistic regression analysis, a higher CsA concentration measured during the first week following graft infusion was the strongest parameter significantly associated with a reduced risk of severe grade II-IV aGVHD (P = .012; relative risk [RR] = 0.24; 95% CI, 0.08-0.73). Of note, when adjusted by donor type, CsA concentration in week 1 remained significantly associated with risk of severe grade II-IV aGVHD (P = .014). We conclude that precise monitoring of CsA concentrations and adjustment of CsA dose early after allo-SCT may be effective to prevent onset of severe aGVHD.
Cytokine-mediated immunotherapy following autologous bone marrow transplantation in lymphoma and evidence of interleukin-2-induced immunomodulation in allogeneic transplants. (1997)

Following autoBMT, GVL effects may be induced with a combination of rIL-2 and IFN-alpha, resulting in a reduced rate of relapse. The combination of both allogeneic donor lymphocytes and rIL-2 seemed synergistic. Because DLI plus rIL-2 was effective, even following failure of myeloablative conditioning, future strategies for treatment of leukemia should be based on T-cell-dependent immunotherapy rather than high-dose chemoradiotherapy.
18- and 22-π-Electron macrocycles containing furan, pyrrole, and thiophen rings (1969)

The preparation of a number of novel aromatic macrocycles related to porphins, but containing furan and thiophen rings in addition to pyrrole rings, is described, together with deuterium exchange studies on some of the macrocycles.
Deficiency of the DNA repair enzyme ATM in rheumatoid arthritis (2009)

In rheumatoid arthritis (RA), dysfunctional T cells sustain chronic inflammatory immune responses in the synovium. Even unprimed T cells are under excessive replication pressure, suggesting an intrinsic defect in T cell regeneration. In naive CD4 CD45RA(+) T cells from RA patients, DNA damage load and apoptosis rates were markedly higher than in controls; repair of radiation-induced DNA breaks was blunted and delayed. DNA damage was highest in newly diagnosed untreated patients. RA T cells failed to produce sufficient transcripts and protein of the DNA repair kinase ataxia telangiectasia (AT) mutated (ATM). NBS1, RAD50, MRE11, and p53 were also repressed. ATM knockdown mimicked the biological effects characteristic for RA T cells. Conversely, ATM overexpression reconstituted DNA repair capabilities, response patterns to genotoxic stress, and production of MRE11 complex components and rescued RA T cells from apoptotic death. In conclusion, ATM deficiency in RA disrupts DNA repair and renders T cells sensitive to apoptosis. Apoptotic attrition of naive T cells imposes lymphopenia-induced proliferation, leading to premature immunosenescence and an autoimmune-biased T cell repertoire. Restoration of DNA repair mechanisms emerges as an important therapeutic target in RA.
Probability model for molecular recognition in biological receptor repertoires: significance to the olfactory system. (1993)

A generalized phenomenological model is presented for stereospecific recognition between biological receptors and their ligands. We ask what is the distribution of binding constants psi(K) between an arbitrary ligand and members of a large receptor repertoire, such as immunoglobulins or olfactory receptors. For binding surfaces with B potential subsite and S different types of subsite configurations, the number of successful elementary interactions obeys a binomial distribution. The discrete probability function psi(K) is then derived with assumptions on alpha, the free energy contribution per elementary interaction. The functional form of psi(K) may be universal, although the parameter values could vary for different ligand types. An estimate of the parameter values of psi(K) for iodovanillin, an analog of odorants and immunological haptens, is obtained by equilibrium dialysis experiments with nonimmune antibodies. Based on a simple relationship, predicted by the model, between the size of a receptor repertoire and its average maximal affinity toward an arbitrary ligand, the size of the olfactory receptor repertoire (Nolf) is calculated as 300-1000, in very good agreement with recent molecular biological studies. A very similar estimate, Nolf = 500, is independently derived by relating a theoretical distribution of maxima for psi(K) with published human olfactory threshold variations. The present model also has implications to the question of olfactory coding and to the analysis of specific anosmias, genetic deficits in perceiving particular odorants. More generally, the proposed model provides a better understanding of ligand specificity in biological receptors and could help in understanding their evolution.
Sequential Processing of Lexical, Grammatical, and Phonological Information Within Broca’s Area (2009)

Words, grammar, and phonology are linguistically distinct, yet their neural substrates are difficult to distinguish in macroscopic brain regions. We investigated whether they can be separated in time and space at the circuit level using intracranial electrophysiology (ICE), namely by recording local field potentials from populations of neurons using electrodes implanted in language-related brain regions while people read words verbatim or grammatically inflected them (present/past or singular/plural). Neighboring probes within Broca's area revealed distinct neuronal activity for lexical (approximately 200 milliseconds), grammatical (approximately 320 milliseconds), and phonological (approximately 450 milliseconds) processing, identically for nouns and verbs, in a region activated in the same patients and task in functional magnetic resonance imaging. This suggests that a linguistic processing sequence predicted on computational grounds is implemented in the brain in fine-grained spatiotemporally patterned activity.
Colocalization of Multiple Laminin Isoforms Predominantly beneath Hemidesmosomes in the Upper Lamina Densa of the Epidermal Basement Membrane (2005)

Multiple laminin isoforms including laminins 5 (alpha3 beta3 gamma2), 6 (alpha3 beta1 gamma1), 10 (alpha5 beta1 gamma1), and possibly laminins 7 (alpha3 beta2 gamma1) and 11 (alpha5 beta2 gamma1) are present in the epidermal basement membrane. However, only the precise epidermal ultrastructural localization of laminin 5 (alpha3 beta3 gamma2) has been elucidated. We therefore determined the precise expression and ultrastructural localization of the alpha5, beta1, beta2, and gamma1 chains in the epidermis. The expression of laminin chains in skin samples was analyzed from patients with epidermolysis bullosa (EB, n=15) that harbor defects in specific hemidesmosome (HD)-associated components. The expression of the alpha5, beta1, and gamma1 chains (present in laminins 10/11) and beta2 chain (laminins 7/11) was unaffected in all intact (unseparated) skin of EB patients including Herlitz junctional EB with laminin-5 defects (n=6). In the basement membrane of human epidermis, the alpha5, beta1, beta2, and gamma1 chains were expressed but also localized to the dermal vessels. Immunogold electron microscopy of normal human epidermis localized the alpha5, beta1, beta2, and gamma1 chains to the upper lamina densa, with between 84% and 92% of labeling restricted to beneath the HDs, similar to laminin 5 (n> or =200 gold particles per sample, sample number n=4) but distinct from collagen IV labeling (with only 63% labeling beneath HDs, p<0.001). Taken together, the majority of the alpha5beta1/beta2gamma1 laminin chains are located beneath HDs. This suggests that laminin-10-associated chains have specific functions or molecular interactions beneath HDs in the epidermal basement membrane.
ChemInform Abstract: The Synthesis, Reactions, and Properties of Nucleoside Mono‐, Di‐, Tri‐ , and Tetraphosphates and Nucleotides with Changes in the Phosphoryl Residue (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Comparison of Differentially Corrected GPS Sources for Support of Site-Specific Management in Agriculture (2003)

Citation: Coyne, P., Casey, S., &amp; Milliken, G. (2003). Comparison of Differentially Corrected GPS Sources for Support of Site-Specific Management in Agriculture. Kansas State University. Agricultural Experiment Station and Cooperative Extension Service. Ag. Res. Center, Hays, Kansas.
Possible interactions with terfenadine or astemizole. (1994)

Concurrent use of terfenadine or astemizole with erythromycin or ketoconazole can prolong the QT interval and produce potentially fatal ventricular arrhythmias. We examine the frequency and patterns of concurrent prescribing and suggest methods to reduce the incidence of serious drug interactions. By retrospectively reviewing Oregon Medicaid prescription claims data over 22 months, we determined the frequency of concurrent prescribing of terfenadine or astemizole with macrolide antibiotics or ketoconazole. From 1991 to 1992, terfenadine use increased by 29%, with a seasonal peak in June of each year. Terfenadine was one of the most prescribed medications from March through July 1992. During the 22 months reviewed, there were 122 episodes of concurrent use of terfenadine or astemizole with macrolide antibiotics or ketoconazole. Most of these episodes (94%) involved terfenadine. The frequency of concurrent use increased more than threefold from 1991 to 1992. Although patients received prescriptions from different physicians in 48% of these episodes, they used different pharmacies only 3% of the time. We demonstrate that terfenadine use is extensive and increasing, thus increasing the possibility of serious interactions, and many physicians may remain unaware of this potential. Effective prospective screening by pharmacists could dramatically reduce the incidence of concurrent prescribing. Physicians must be aware of the potential for these drug interactions, avoid prescribing these medications concurrently, and consider these interactions in the evaluation of syncope and cardiac arrhythmias.
TRPM1 Forms Ion Channels Associated with Melanin Content in Melanocytes (2009)

TRPM1 (melastatin), which encodes the founding member of the TRPM family of transient receptor potential (TRP) ion channels, was first identified by its reduced expression in a highly metastatic mouse melanoma cell line. Clinically, TRPM1 is used as a predictor of melanoma progression in humans because of its reduced abundance in more aggressive forms of melanoma. Although TRPM1 is found primarily in melanin-producing cells and has the molecular architecture of an ion channel, its function is unknown. Here we describe an endogenous current in primary human neonatal epidermal melanocytes and mouse melanoma cells that was abrogated by expression of microRNA directed against TRPM1. Messenger RNA analysis showed that at least five human ion channel-forming isoforms of TRPM1 could be present in melanocytes, melanoma, brain, and retina. Two of these isoforms are encoded by highly conserved splice variants that are generated by previously uncharacterized exons. Expression of these two splice variants in human melanoma cells generated an ionic current similar to endogenous TRPM1 current. In melanoma cells, TRPM1 is prevalent in highly dynamic intracellular vesicular structures. Plasma membrane TRPM1 currents are small, raising the possibility that their primary function is intracellular, or restricted to specific regions of the plasma membrane. In neonatal human epidermal melanocytes, TRPM1 expression correlates with melanin content. We propose that TRPM1 is an ion channel whose function is critical to normal melanocyte pigmentation and is thus a potential target for pigmentation disorders.
Reaction Chemistry and Ligand Exchange at Cadmium−Selenide Nanocrystal Surfaces (2008)

The surface chemistry of cadmium selenide nanocrystals, prepared from tri-n-octylphosphine selenide and cadmium octadecylphosphonate in tri-n-octylphosphine oxide, was studied with 1H and {1H}31P NMR spectroscopy as well as ESI-MS and XPS. The identity of the surface ligands was inferred from reaction of nanocrystals with Me3Si-X (X = -S-SiMe3, -Se-SiMe3, -Cl and -S-(CH2CH2O)4OCH3)) and unambiguous assignment of the organic byproducts, O,O'-bis(trimethylsilyl)octadecylphosphonic acid ester and O,O'-bis(trimethylsilyl)ocatdecylphosphonic acid anhydride ester. Nanocrystals isolated from these reactions have undergone exchange of the octadecylphosphonate ligands for -X as was shown by 1H NMR (X = -S-(CH2CH2O)4OCH3) and XPS (X = -Cl). Addition of free thiols to as prepared nanocrystals results in binding of the thiol to the particle surface and quenching of the nanocrystal fluorescence. Isolation of the thiol-ligated nanocrystals shows this chemisorption proceeds without displacement of the octadecylphosphonate ligands, suggesting the presence of unoccupied Lewis-acidic sites on the particle surface. In the presence of added triethylamine, however, the octadecylphosphonate ligands are readily displaced from the particle surface as was shown with 1H and {1H}31P NMR. These results, in conjunction with previous literature reports, indicate that as-prepared nanocrystal surfaces are terminated by X-type binding of octadecylphosphonate moieties to a layer of excess cadmium ions.
Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA. (1996)

DNA methyltransferases modify specific cytosines and adenines within 2-6 bp recognition sequences. We used scanning force microscopy and gel shift analysis to show that M.HhaI, a cytosine C-5 DNA methyltransferase, causes only a 2 degree bend upon binding its recognition site. Our results are consistent with prior crystallographic analysis showing that the enzyme stabilizes an extrahelical base while leaving the DNA duplex otherwise unperturbed. In contrast, similar analysis of M.EcoRI, an adenine N6 DNA methyltransferase, shows an average bend angle of approximately 52 degrees. This distortion of DNA conformation by M.EcoRI is shown to be important for sequence-specific binding.
Protection against lethal Sendai virus infection by in vivo priming of virus-specific cytotoxic T lymphocytes with a free synthetic peptide. (1991)

The only peptide of Sendai virus that is recognized by cytotoxic T lymphocytes (CTL) in B6 mice was found with (i) the use of recombinant vaccinia virus constructs containing separate genes of Sendai virus and (ii) a set of overlapping peptides completely spanning the identified nucleoprotein (NP) gene product. This immunodominant NP peptide is recognized by Sendai virus-specific CTL that are known to have therapeutic effects in vivo. By subcutaneous immunization, this peptide induced Sendai virus and NP peptide-specific CTL memory responses in vivo. Most importantly, mice that had been immunized with this peptide were protected against a lethal virus dose, indicating that viral peptides can be used as antiviral T-cell vaccines. The induction of T-cell memory by free peptide immunization potentially has wide applicability in biology and medicine, including protection against infectious disease.