gebhart/patrepeval huggingface dataset:
Photoinitiated polymerization of styrene from self‐assembled monolayers on gold. II. Grafting rates and extraction (2002)

Abstract Ultrathin films of polystyrene (PS) were grown from self‐assembled monolayers by the “grafting‐from” technique. The initiating system consisted of a dithiol azobisisobutyronitrile‐type free‐radical initiator that was activated by irradiation at 300 nm. The thickness of the PS films ranged from 7 to 190 nm and could be controlled by varying the reaction time or the monomer concentration. The films were characterized by ellipsometry and Fourier transform‐reflection absorption infrared spectroscopy after Soxhlet extraction of residual physisorbed polymer. These films were unstable above 60 °C, and a water‐jacketed Soxhlet extractor was designed to maintain solvent temperatures below 45 °C during extraction. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 3284–3291, 2002
Molecular biomimetics: nanotechnology and bionanotechnology using genetically engineered peptides (2009)

Nature provides inspiration for designing materials and systems that derive their functions from highly organized structures. Biological hard tissues are hybrid materials having inorganics within a complex organic matrix, the molecular scaffold controlling the inorganic structures. Biocomposites incorporate both biomacromolecules such as proteins, lipids and polysaccharides, and inorganic materials, such as hydroxyapatite, silica, magnetite and calcite. The ordered organization of hierarchical structures in organisms begins via the molecular recognition of inorganics by proteins that control interactions and is followed by the highly efficient self-assembly across scales. Following the molecular biological principle, proteins could also be used in controlling materials formation in practical engineering via self-assembled, hybrid, functional materials structures. In molecular biomimetics, material-specific peptides could be the key in the molecular engineering of biology-inspired materials. With the recent developments of nanoscale engineering in physical sciences and the advances in molecular biology, we now combine genetic tools with synthetic nanoscale constructs to create a novel methodology. We first genetically select and/or design peptides with specific binding to functional solids, tailor their binding and assembly characteristics, develop bifunctional peptide/protein genetic constructs with both material binding and biological activity, and use these as molecular synthesizers, erectors and assemblers. Here, we give an overview of solid-binding peptides as novel molecular agents coupling bio- and nanotechnology.
Killing of Chlorine-Resistant Bacteria by Chlorine-Bromine Solutions (1964)

The disinfective power of chlorine, bromine, and mixtures of chlorine and bromine at different ratios was compared. The influence of pH was also studied. The experiments were carried out in "purified" water and in natural waters of swimming pools, river, and sea. In the presence of high amounts of nitrogenous growth-promoting material (at neutral pH), bromine was more effective than chlorine; in waters containing low amounts of nitrogenous growth-promoting material, chlorine was found superior. Mixtures of chlorine and bromine at various ratios were found to increase in effectiveness inversely to the percentage of hypobromite generated, down to 10 or 5%. Such effectiveness was found at pH levels of 5.4 to 8.6 in both purified and natural water containing high and low amounts of nitrogenous growth-promoting material. Therefore, the above mixtures seem of practical value for the disinfection of various natural waters. Escherichia coli isolated in the presence of chlorine, either from swimming pools or after deliberate exposure to the halogen, were shown to be chlorine-resistant mutants. Their resistance was maintained for at least nine passages in the absence of the disinfectant, which accounts for the number of passages tested. Chlorine-resistant mutants were not affected by bromine alone but did show a marked sensitivity to low concentrations of bromine active in the presence of chlorine. This was achieved by admixing small amounts of bromide to hypochlorite. A hypothetical model is presented to explain the synergistic sequential block by the two disinfectants. Some chlorine-resistant mutants were found to have changed into relatively slow-growing organisms with a changed phase-sensitivity pattern.
A Practical Synthesis ofN1-Methyl-2′-deoxy-ψ-uridine (ψ-Thymidine) and Its Incorporation into G-Rich Triple Helix Forming Oligonucleotides (1995)

Abstract A convenient synthesis of N1-methyl-2′-deoxy-ψ-uridine (ψ-thymidine, ψT, 7a) has been accomplished in good yield. The structural conformation of 7a was derived by 2D NMR and 1D NOE experiments. The nucleoside 7a has been incorporated into G-rich triplex forming oligonucleotides (TFOs) by solid-support, phosphoramidite method. The triplex forming capabilities of the modified TFOs (S4, S5 and S6) containing ψT has been evaluated in antiparallel motif with a target duplex (duplex-31) 5′d(CTGAGACCGGGAAGGAGGAAGGGCCAGTGAC)3′-5′d(GACTCTGGCCCTTCCTCCTTCCCGGTCACTG)3′(D1) at pH 7.6. The triplex formation of modified homopyrimidine-oligomers (S1, S2 and S3) has also been studied in parallel motif with a duplex-10 (A10:T10) at pH 7.0.
Regulation of murine myelin proteolipid protein gene expression (1997)

To identify putative sequences that direct cell type-specific expression and/or enhance proteolipid protein (PLP) gene expression, glial or nonglial cells were transfected with various PLP-luciferase constructs that collectively span the entire mouse PLP-specific DNA present in a transgene known to direct cell type specificity in transgenic mice. These constructs were transfected into murine oligodendrocyte cell lines that transcribe the PLP gene and, hence, should contain the requisite trans-acting factors necessary for PLP gene expression. Mouse NIH/3T3 fibroblasts were used as a nonglial model. We have finely mapped the PLP promoter region for transcriptional regulatory elements and demonstrate both positive and negative elements, none of which appear to extinguish expression in nonglial cells. The 5'-flanking PLP DNA tested did not enhance the basal herpes simplex-1 virus thymidine kinase (TK) promoter, nor did PLP sequences present in the distal half of intron 1. The 5' portion of intron 1 did enhance TK promoter activity, suggesting that this region of the gene may contain enhancer elements that modulate PLP gene expression; however, the enhancement did not appear to be cell type-specific. Intriguingly, a 541 bp region of the intron that significantly enhanced TK promoter activity contains multiple JC virus repeated elements and other elements known to be important in restricting the virus to oligodendrocytes. These results suggest that intron 1 sequences may modulate expression of the PLP gene.
AZD5153: A Novel Bivalent BET Bromodomain Inhibitor Highly Active against Hematologic Malignancies (2016)

The bromodomain and extraterminal (BET) protein BRD4 regulates gene expression via recruitment of transcriptional regulatory complexes to acetylated chromatin. Pharmacological targeting of BRD4 bromodomains by small molecule inhibitors has proven to be an effective means to disrupt aberrant transcriptional programs critical for tumor growth and/or survival. Herein, we report AZD5153, a potent, selective, and orally available BET/BRD4 bromodomain inhibitor possessing a bivalent binding mode. Unlike previously described monovalent inhibitors, AZD5153 ligates two bromodomains in BRD4 simultaneously. The enhanced avidity afforded through bivalent binding translates into increased cellular and antitumor activity in preclinical hematologic tumor models. In vivo administration of AZD5153 led to tumor stasis or regression in multiple xenograft models of acute myeloid leukemia, multiple myeloma, and diffuse large B-cell lymphoma. The relationship between AZD5153 exposure and efficacy suggests that prolonged BRD4 target coverage is a primary efficacy driver. AZD5153 treatment markedly affects transcriptional programs of MYC, E2F, and mTOR. Of note, mTOR pathway modulation is associated with cell line sensitivity to AZD5153. Transcriptional modulation of MYC and HEXIM1 was confirmed in AZD5153-treated human whole blood, thus supporting their use as clinical pharmacodynamic biomarkers. This study establishes AZD5153 as a highly potent, orally available BET/BRD4 inhibitor and provides a rationale for clinical development in hematologic malignancies. Mol Cancer Ther; 15(11); 2563-74. ©2016 AACR.
The role of lenalidomide in the treatment of patients with chromosome 5q deletion and other myelodysplastic syndromes (2007)

Lenalidomide is an active immunomodulatory agent for the treatment of myelodysplastic syndrome with encouraging erythropoetic and cytogenetic remitting activity that is karyotype dependent.
Phase-Variable Changes in the Position ofO-Methyl Phosphoramidate Modifications on the Polysaccharide Capsule of Campylobacter jejuni Modulate Serum Resistance (2017)

<i>Campylobacter jejuni</i> polysaccharide capsules (CPS) are characterized by the presence of nonstoichiometric <i>O</i>-methyl phosphoramidate (MeOPN) modifications. The lack of stoichiometry is due to phase variation at homopolymeric tracts within the MeOPN transferase genes. <i>C. jejuni</i> strain 81-176 contains two MeOPN transferase genes and has been shown previously to contain MeOPN modifications at the 2 and 6 positions of the galactose (Gal) moiety in the CPS. We demonstrate here that one of the two MeOPN transferases, encoded by CJJ81176_1435, is bifunctional and is responsible for the addition of MeOPN to both the 2 and the 6 positions of Gal. A new MeOPN at the 4 position of Gal was observed in a mutant lacking the CJJ81176_1435 transferase and this was encoded by the CJJ81176_1420 transferase. During routine growth of 81-176, the CJJ81176_1420 transferase was predominantly in an off configuration, while the CJJ81176_1435 transferase was primarily on. However, exposure to normal human serum selected for cells expressing the CJJ81176_1420 transferase. MeOPN modifications appear to block binding of naturally occurring antibodies to the 81-176 CPS. The absence of MeOPN-4-Gal resulted in enhanced sensitivity to serum killing, whereas the loss of MeOPN-2-Gal and MeOPN-6-Gal resulted in enhanced resistance to serum killing, perhaps by allowing more MeOPN to be put onto the 4 position of Gal.<b>IMPORTANCE</b><i>Campylobacter jejuni</i> undergoes phase variation in genes encoding surface antigens, leading to the concept that a strain of this organism consists of multiple genotypes that are selected for fitness in various environments. Methyl phosphoramidate modifications on the capsule of <i>C. jejuni</i> block access of preexisting antibodies in normal human sera to the polysaccharide chain, thus preventing activation of the classical arm of the complement cascade. We show that the capsule of strain 81-176 contains more sites of MeOPN modifications than previously recognized and that one site, on the 4 position of galactose, is more critical to complement resistance than the others. Exposure to normal human serum selects for variants in the population expressing this MeOPN modification.
Frequent activation of the lck gene by promoter insertion and aberrant splicing in murine leukemia virus-induced rat lymphomas. (1993)

We have analysed DNA and RNA from 36 T-cell lymphomas induced in Fischer rats by Moloney murine leukemia virus for alterations affecting the structure or expression of the lck gene. At least five primary tumors (14%) have a proviral insertion upstream of lck. In at least four of the tumors, proviral insertion increases lck mRNA levels an average of eight-fold. Overexpression of lck results from transcription initiating in the viral promoter and extending into lck sequences. Three different structures of hybrid transcript were detected. In all three, the hybrid RNAs are spliced to a normal lck splice acceptor in the first exon of lck, resulting in removal of three out of frame ATG codons which would be expected to increase the translation efficiency of the hybrid message. In one tumor, the viral splice donor is used, in one tumor, proviral insertion generates a splice donor sequence one base pair downstream of the long terminal repeat boundary, and in two tumors, a cryptic splice donor in the upstream lck sequences is used. The significance of these unusual splicing patterns and of the higher frequency of proviral insertions adjacent to lck in rats relative to mice is discussed.
Postmenopausal hormone therapy and Alzheimer's disease risk: interaction with age (2004)

We examined the relation between oestrogen containing hormone therapy (HT) used for more than 6 months and Alzheimer's disease (AD) risk in 971 postmenopausal women (426 AD patients, 545 relatives without dementia). There was a significant interaction between age and HT use on AD risk (p = 0.03). In stratified analyses, a significant protective association was seen only in the youngest age tertile (50-63 years; odds ratio = 0.35, 95% confidence interval = 0.19 to 0.66). Results must be considered cautiously in light of recent clinical trial evidence that oestrogen plus progestin increases dementia incidence in older postmenopausal women. However, our observational findings are consistent with the view that HT may protect younger women from AD or reduce the risk of early onset forms of AD, or that HT used during the early postmenopause may reduce AD risk.
Effects of Ashwagandha (Roots of <i>Withania somnifera</i>) on Neurodegenerative Diseases (2014)

Neurodegenerative diseases commonly induce irreversible destruction of central nervous system (CNS) neuronal networks, resulting in permanent functional impairments. Effective medications against neurodegenerative diseases are currently lacking. Ashwagandha (roots of Withania somnifera Dunal) is used in traditional Indian medicine (Ayurveda) for general debility, consumption, nervous exhaustion, insomnia, and loss of memory. In this review, we summarize various effects and mechanisms of Ashwagandha extracts and related compounds on in vitro and in vivo models of neurodegenerative diseases such as Alzheimer's disease and spinal cord injury.
Attention to Scale: Scale-aware Semantic Image Segmentation (2015)

Incorporating multi-scale features in fully convolutional neural networks (FCNs) has been a key element to achieving state-of-the-art performance on semantic image segmentation. One common way to extract multi-scale features is to feed multiple resized input images to a shared deep network and then merge the resulting features for pixelwise classification. In this work, we propose an attention mechanism that learns to softly weight the multi-scale features at each pixel location. We adapt a state-of-the-art semantic image segmentation model, which we jointly train with multi-scale input images and the attention model. The proposed attention model not only outperforms average- and max-pooling, but allows us to diagnostically visualize the importance of features at different positions and scales. Moreover, we show that adding extra supervision to the output at each scale is essential to achieving excellent performance when merging multi-scale features. We demonstrate the effectiveness of our model with extensive experiments on three challenging datasets, including PASCAL-Person-Part, PASCAL VOC 2012 and a subset of MS-COCO 2014.
The RELIEF retrieval system (2002)

Introduces the RELIEF retrieval system, a system for image retrieval based on the conceptual graph formalism. Conceptual graphs can be used as a simple and expressive language for indexing and retrieving non-textual documents. In this formalism, the implementation of the matching function between a query and a document is obtained by using the so-called projection operator between two conceptual graphs. However, the first implementations of this operator have shown its lack of efficiency, as it is based on an exponential algorithm. The RELIEF system supports a new polynomial matching function for conceptual graphs which turns out to be equivalent to the projection operator but it has the important feature that it incorporates reasoning about relations. This allows for better qualitative results as well as improved time performance compared to the original system implementing the classical projection. RELIEF is developed on top of the object-oriented DBMS O/sub 2/, and any WWW navigator with Java facilities can be used to access its interface.
Neurovascular coupling in the normal brain and in hypertension, stroke, and Alzheimer disease (2005)

The brain is critically dependent on a continuous supply of blood to function. Therefore, the cerebral vasculature is endowed with neurovascular control mechanisms that assure that the blood supply of the brain is commensurate to the energy needs of its cellular constituents. The regulation of cerebral blood flow (CBF) during brain activity involves the coordinated interaction of neurons, glia, and vascular cells. Thus, whereas neurons and glia generate the signals initiating the vasodilation, endothelial cells, pericytes, and smooth muscle cells act in concert to transduce these signals into carefully orchestrated vascular changes that lead to CBF increases focused to the activated area and temporally linked to the period of activation. Neurovascular coupling is disrupted in pathological conditions, such as hypertension, Alzheimer disease, and ischemic stroke. Consequently, CBF is no longer matched to the metabolic requirements of the tissue. This cerebrovascular dysregulation is mediated in large part by the deleterious action of reactive oxygen species on cerebral blood vessels. A major source of cerebral vascular radicals in models of hypertension and Alzheimer disease is the enzyme NADPH oxidase. These findings, collectively, highlight the importance of neurovascular coupling to the health of the normal brain and suggest a therapeutic target for improving brain function in pathologies associated with cerebrovascular dysfunction.
Epstein-Barr virus-associated non-Hodgkin's lymphoma in patients infected with the human immunodeficiency virus [see comments] (1993)

Lymphoproliferations associated with Epstein-Barr virus (EBV) commonly arise in settings of immune dysfunction, including human immunodeficiency virus (HIV) infection. In this study, EBV was associated with 39 of 59 (66%) HIV-related systemic lymphomas. Unlike the lymphoproliferations that arise in the setting of transplantation, the HIV-related lymphomas were monoclonal, as evaluated by Ig heavy chain rearrangements and EBV termini analysis, and associated (40%) with c-MYC rearrangements. Furthermore, analysis of multiple lymphoma tissues from one autopsy showed evidence that a single lymphoma clone was responsible for dissemination. The latent EBV nuclear antigen (EBNA-1) transcripts detected in the HIV-related lymphomas were characteristic of the pattern found in Burkitt lymphoma (g1 EBNA1) and not in transplant-related lymphoproliferations. However, unlike Burkitt lymphoma, EBV latent membrane-associated protein (LMP) transcripts were also detected, thereby constituting an EBV expression pattern (g1 EBNA1+, LMP+) not previously observed in B-cell lymphomas. These findings demonstrate a high frequency of EBV-associated lymphomas in the setting of HIV infection that are distinct from the lymphoproliferations that arise during iatrogenic transplant-associated immuno-suppression or in the general population. However, it is also apparent that HIV-related lymphomas are biologically heterogeneous, which may reflect the multiple mechanisms or steps necessary for eventual malignant transformation.
[The duration of embryogenesis in mosquitoes of the genus Aedes]. (1996)

The duration of embryogenesis was determined in 12 mono- and polycyclic types of Aedes mosquitos in the mid-Russia and eastern Siberia at laboratory temperatures of 24-25 degrees C. It was ascertained that larval formation in the egg occurred in Aedes communis within 5-8 days, in Ae. cantans within 5-7 days, in Ae.dorsalis within 3-6 days, and in Ae.vexans within 4-6 days.
Salvage of Infarcted Myocardium by Angiogenic Action of Basic Fibroblast Growth Factor (1992)

Coronary collateral vessels reduce damage to ischemic myocardium after coronary obstruction. Factors that stimulate collateral formation are expected to have ameliorating effects on myocardial infarction. In a canine experimental myocardial infarct model, intracoronary injection of basic fibroblast growth factor (bFGF) improved cardiac systolic function and reduced infarct size. Treatment with bFGF increased the number of arterioles and capillaries in the infarct. Thus, the angiogenic action of bFGF might lead to a reduction in infarct size. The application of bFGF might bring about a therapeutic modality for the salvage of infarcted myocardium.
Serum levels of matrix metalloproteinase-2 and -9 in patients with head and neck squamous cell carcinoma. (2000)

Matrix Metalloproteinases (MMPs) have been implicated as playing an important role in cancer invasion and metastasis. MMPs have been identified in a wide variety of malignancies including head and neck squamous cell carcinomas (HNSCC).We investigated the circulating level of MMP-2 (gelatinase A or 72-kD type IV collagenase) and MMP-9 (gelatinase B or 92-kD type IV collagenase) in sera from patients with various head and neck squamous cell carcinomas (n = 86) as well as from healthy normal controls (n = 47). Serum MMP concentrations were determined as serum immunoreactivity by using a quantitative sandwich enzyme immunoassay technique. For statistical analysis, the t-test and Kruskal-Wallis test were performed.The majority of the patients with HNSCC were found to have high concentrations of serum MMP-9. The levels of MMP-9 in the sera of patients with cancer ranged from 39 to 1547 ng/ml (mean, 417 ng/ml). In contrast, the MMP-9 serum levels in 47 healthy individuals ranged from 30 to 537 ng/ml (mean, 189 ng/ml), MMP-9 serum concentration being significantly higher in HNSCC patients (p = 0.001). MMP-9 serum concentrations of patients with advanced stage HNSCC were significantly higher (p = 0.0449) compared to patients with early stage cancer. No significant difference of MMP-2 serum levels was seen when comparing HNSCC patients and normal controls.The present data indicate that the elevation of serum levels of MMP-9, but not MMP-2, may be a useful marker for clinical monitoring of HNSCC patients.
Encoded simultaneous source full‐wavefield inversion for spectrally shaped marine streamer data (2011)

In this paper, we apply encoded simultaneous source full‐wavefield inversion (FWI) to marine streamer data. FWI of large scale 3D data is a challenging problem, especially constraining the inversion using the high frequencies available in exploration seismic data. Two methodologies that make high‐frequency FWI feasible for field data are: (a) applying encoded simultaneous source full‐wavefield inversion (ESSFWI) and (b) shaping the data to provide a preferential weighting to the low‐frequency components of the data. These two methods in combination provide us with the computational efficiencies needed for large 3D runs. To date, most encoded simultaneous source methods have been applied to fixed‐receiver data; i.e., each receiver records data from all shots in the survey. We developed an approach that enables us to apply ESSFWI to marine streamer data that are non‐fixed spread. The approach uses a normalized cross‐correlation objective function with multiple realizations of the encoded data at each iteration of the nonlinear FWI. The method can be applied to 2D/3D data with any survey geometry. Here we demonstrate the methodology and discuss its details with synthetic examples. Although not presented here our initial investigations on 3D field streamer data look encouraging.