gebhart/patrepeval huggingface dataset:
Chitosan: Effects on Wound Healing in Urogenital Tissue: Preliminary Report (1988)

We conducted a survey of the effect of chitosan on wounds of the genitourinary system in dogs. Wounds were made in the kidney, ureter and penile foreskin. Chitosan caused no adverse effects on urogenital wound healing. A decrease in fibrosis was seen in the wounds treated with chitosan in all tissues studied. These observations suggest that the morbidity of urogenital surgery may be decreased by treating the wounds with chitosan.
Synthesis of .ALPHA.-thio, .ALPHA.-sulfinyl, and .ALPHA.-sulfonyl-substituted nitrosamines. (1977)

A new route to the preparation of α-alkyl (or aryl) thiosubstituted nitrosamines has been provided by nitrosation of alkylaminomethyl alkyl (or aryl) sulfides obtained simply from primary amine hydrochlorides, formaldehyde, and alkyl (or aryl) thioalcohols. By oxidation with metaperiodate and permanganate the corresponding sulfoxides and sulfones have been obtained, respectively. Compositions of the syn and anti isomers of the nitrosamines are determined by NMR technique.
Nonsense-Mediated Decay of MutantwaxymRNA in Rice (2001)

Two rice (Oryza sativa) waxy mutations of the Japonica background were shown to contain approximately 20% of the fully spliced mRNA relative to the wild type. Sequencing analysis of the entire waxy genes of the two mutants revealed the presence of premature translation termination codons in exon 2 and exon 7. These results indicated that the lower accumulation of fully spliced RNA in the mutants was caused by nonsense-mediated decay (NMD), which is an RNA surveillance system universally found in eukaryotes. It is interesting that levels of RNA retaining intron 1 were not changed by premature nonsense codons, suggesting that splicing may be linked with NMD in plants, as previously found in mammalian cells. Measurements of the half-lives of waxy RNAs in transfected rice protoplasts indicated that the half-life of waxy RNA with a premature nonsense codon was 3.3 times shorter than that without a premature nonsense codon. Because the wild-type waxy transcripts, which are derived from the Wx(b) gene predominantly distributed among Japonica rice, have been shown to be less efficiently spliced and their alternative splicing has been documented, we examined whether these splicing properties influenced the efficiency of NMD. However, no effects were observed. These results established that NMD occurs in rice waxy RNA containing a premature nonsense codon.
Functionalization of DNA nanostructures with proteins (2011)

Proteins possess intrinsic functionalities, which have been optimized in billions of years of natural evolution. The conjugation of proteins with artificial nucleic acids allows one to further functionalize proteins with a synthetically accessible, physicochemically robust tag, which is addressable in a highly specific manner by Watson-Crick hybridization. The resulting DNA-protein conjugates can be advantageously used in a variety of applications, ranging from biomedical diagnostics to DNA-based nanofabrication. This critical review provides an overview on chemical approaches to the synthesis of DNA-protein conjugates and their applications in biomolecular nanosciences (96 references).
Exogenous myristic acid can be partially degraded prior to activation to form acyl-acyl carrier protein intermediates and lipid A in Vibrio harveyi (1994)

To study the involvement of acyl carrier protein (ACP) in the metabolism of exogenous fatty acids in Vibrio harveyi, cultures were incubated in minimal medium with [9,10-3H]myristic acid, and labeled proteins were analyzed by gel electrophoresis. Labeled acyl-ACP was positively identified by immunoprecipitation with anti-V. harveyi ACP serum and comigration with acyl-ACP standards and [3H]beta-alanine-labeled bands on both sodium dodecyl sulfate- and urea-polyacrylamide gels. Surprisingly, most of the acyl-ACP label corresponded to fatty acid chain lengths of less than 14 carbons: C14, C12, C10, and C8 represented 33, 40, 14, and 8% of total [3H]14:0-derived acyl-ACPs, respectively, in a dark mutant (M17) of V. harveyi which lacks myristoyl-ACP esterase activity; however, labeled 14:0-ACP was absent in the wild-type strain. 14:0- and 12:0-ACP were also the predominant species labeled in complex medium. In contrast, short-chain acyl-ACPs (< or = C6) were the major labeled derivatives when V. harveyi was incubated with [3H]acetate, indicating that acyl-ACP labeling with [3H]14:0 in vivo is not due to the total degradation of [3H]14:0 to [3H]acetyl coenzyme A followed by resynthesis. Cerulenin increased the mass of medium- to long-chain acyl-ACPs (> or = C8) labeled with [3H]beta-alanine fivefold, while total incorporation of [3H]14:0 was not affected, although a shift to shorter chain lengths was noted. Additional bands which comigrated with acyl-ACP on sodium dodecyl sulfate gels were identified as lipopolysaccharide by acid hydrolysis and thin-layer chromatography. The levels of incorporation of [3H] 14:0 into acyl-ACP and lipopolysaccharide were 2 and 15%, respectively, of that into phospholipid by 10 min. Our results indicate that in contrast to the situation in Escherichia coli, exogenous fatty acids can be activated to acyl-ACP intermediates after partial degradation in V. harveyi and can effectively label products (i.e., lipid A) that require ACP as an acyl donor.
Tour the world: Building a web-scale landmark recognition engine (2009)

Modeling and recognizing landmarks at world-scale is a useful yet challenging task. There exists no readily available list of worldwide landmarks. Obtaining reliable visual models for each landmark can also pose problems, and efficiency is another challenge for such a large scale system. This paper leverages the vast amount of multimedia data on the Web, the availability of an Internet image search engine, and advances in object recognition and clustering techniques, to address these issues. First, a comprehensive list of landmarks is mined from two sources: (1) ~20 million GPS-tagged photos and (2) online tour guide Web pages. Candidate images for each landmark are then obtained from photo sharing Websites or by querying an image search engine. Second, landmark visual models are built by pruning candidate images using efficient image matching and unsupervised clustering techniques. Finally, the landmarks and their visual models are validated by checking authorship of their member images. The resulting landmark recognition engine incorporates 5312 landmarks from 1259 cities in 144 countries. The experiments demonstrate that the engine can deliver satisfactory recognition performance with high efficiency.
1RAP: An End-to-end Rate-based Congestion Control Mechanism for Realtime Streams in the Internet (1998)

Abstract-End-to-end congestion control mechanisms have been critical to the robustness and stability of the Internet. Most of today’s Internet trafftc is TCP, and we expect this to remain so in the future. Thus, having “TCP-friendly ” behavior is crucial for new applications. However, the emergence of non-congestion-controlled realtime applications threatens unfairness to competing TCP traffic and possible congestion collapse. We present an end-to-end TCP-friendly Rate Adaptation Protocol (RAP), which employs an additive-increase, multiplicativedecrease (AIMD) algorithm. It is well suited for unicast playback of realtime streams and other semi-reliable rate-based applications. Its primary goal is to be fair and TCP-friendly while separating network congestion control from application-level reliability. We evaluate RAP through extensive simulation, and conclude that bandwidth is usually evenly shared between TCP and RAP traffic. Unfairness to TCP traffic is directly determined by how TCP diverges from the AIMD algorithm. Basic RAP behaves in a TCPfriendly fashion in a wide range of likely conditions, but we also devised a fine-grain rate adaptation mechanism to extend this range further. Finally, we show that deploying RED queue management can result in an ideal fairness between TCP and RAP traffic. I.
Preparation and characterization of flexible nanoliposomes loaded with daptomycin, a novel antibiotic, for topical skin therapy (2013)

The purpose of this study was to investigate flexible nanoliposomes for mediating topical delivery of daptomycin, and to document permeation rates and bacteriostatic activity towards skin infections. Response surface methodology was used to optimize the daptomycin-loaded flexible nanoliposomes (DAP-FL), and the amount of drug loaded into the particles was evaluated as the investigation index. The optimal lipid ratio was lecithin to sodium cholate 17:1 (w/w) and the lipid to drug ratio was 14:1 (w/w). The hydration temperature was set at 37°C and the duration of treatment with ultrasound was 20 minutes. The DAP-FL obtained had a small mean particle size (55.4 nm) with a narrow size distribution (polydispersity index 0.15). The mean entrapment efficiency was 87.85% ± 2.15% and the mean percent drug loading was 5.61% ± 0.14%. Using skin mounted between the donor and receptor compartments of a modified Franz diffusion cell, the percentage and quantity of cumulative daptomycin permeation from DAP-FL within 12 hours were measured at 96.28% ± 0.70% and (132.23 ± 17.73) μg/cm(2) *5 = 661.15 ± 88.65 μg/cm(2), directly, showing rapid and efficient antibacterial activity against Staphylococcus aureus. Following local administration of DAP-FL, daptomycin was detected in multilayer tissues within the skin and underlying structures in the dorsal skin of the mouse. Effective therapeutic concentrations were maintained for several hours, and significantly inhibited bacterial growth and injury-induced biofilms. These results demonstrate that the DAP-FL can enhance the ability of daptomycin to permeate the skin efficiently, where it has a powerful antibacterial action and activity against biofilms. This novel formulation of daptomycin has potential as a new approach in the clinical application of daptomycin.
Fabrication and characterization of graphene hydrogel via hydrothermal approach as a scaffold for preliminary study of cell growth (2011)

Guided filopodia protrusions of MG63 on the hydrogel were observed on the third day of cell culture, demonstrating compatibility of the graphene hydrogel structure for bioapplications.
Expression of ST2 in Helper T Lymphocytes of Malignant Pleural Effusions (2002)

The objective of this study was to test the hypothesis that accumulated helper T lymphocytes in malignant pleural effusions may shift to T-helper type 2 (Th2) and produce soluble ST2 protein. We took samples of serum and pleural effusions (p-) from patients with carcinomatous pleurisy (CA, n = 17), tuberculous pleurisy (TB, n = 8), and congestive heart failure (HF, n = 5) and compared the concentration of cytokines or ST2. Ex vivo production of interleukin (IL)-4 and IL-10, though not that of interferon (IFN)-gamma or IL-12, from CD4+ T cells isolated from pleural effusions was higher in the CA group than in the TB or HF group. The p-ST2 concentrations were significantly higher in the CA group than in the TB or HF group, positively correlated with the percentage of pleural effusion CD4+ T cells (r = 0.432, p = 0.016) and inversely correlated with p-IFN-gamma concentrations (r = -0.423, p = 0.019). Furthermore, mRNA expression of ST2 in CD4+ T cells isolated from group CA was upregulated, compared with that in those isolated from the TB group. These results suggest that CD4+ T cells in CA shift to Th2, which can produce soluble ST2 protein, resulting in increased concentrations of p-ST2 in malignant pleural effusion.
Myofibroblasts differentiate from fibroblasts when plated at low density. (1996)

Myofibroblasts, defined by their expression of smooth muscle alpha-actin, appear at corneal and dermal incisions and promote wound contraction. We report here that cultured fibroblasts differentiate into myofibroblasts by a cell density-dependent mechanism. Fibroblasts seeded at low density (5 cells per mm2) produced a cell culture population consisting of 70-80% myofibroblasts, 5-7 days after seeding. In contrast, fibroblasts seeded at high density (500 cells per mm2) produced cultures with only 5-10% myofibroblasts. When the myofibroblast-enriched cultures were subsequently passaged at high density, the smooth muscle alpha-actin phenotype was lost within 3 days. Furthermore, initially 60% of the low density-cultured cells incorporated BrdUrd compared to 30% of cells passaged at high density. Media from myofibroblast-enriched cultures had more latent and active transforming growth factor beta (TGF-beta) than did media from fibroblast-enriched cultures. Although there was a trend towards increased numbers of myofibroblasts after addition of exogenous TGF-beta, the results did not reach statistical significance. We conclude that myofibroblast differentiation can be induced in fibroblasts by plating at low density. We propose a cell density-dependent model of myofibroblast differentiation during wounding and healing in which at least two factors interact: loss of cell contact and the presence of TGF-beta.
Characterization of a gene encoding survival motor neuron (SMN)-related protein, a constituent of the spliceosome complex (1998)

Mutations in the gene encoding the Survival Motor Neuron (SMN) protein are responsible for autosomal recessive proximal spinal muscular atrophy (SMA). SMN orthologues have been identified in the nematode worm Caenorhabditis elegans and the yeast Schizosaccharomyces pombe but, to date, no human paralogues have been described. Here we describe identification and characterization of an SMN-related protein (SMNrp) gene that encodes a novel protein of 239 amino acids, which has recently been identified as a constituent of the spliceosome complex and designated SPF30. Significant similarity to the SMN protein is apparent only within a central region of SMNrp that represents a tudor domain. The SMNrp/SPF30 gene has been mapped to chromosome 10q23. It is differentially expressed, with abundant levels in skeletal muscle. An exclusively nuclear localization for SMNrp in cultured cells and muscle sections was revealed using GFP fusion constructs and thereafter confirmed with a polyclonal antibody raised against SMNrp. Overexpression of SMNrp as a fusion protein in HeLa cells in culture induced dose-dependent apoptosis with positive TUNEL staining. In addition to a possible role for this protein as a pro-apoptotic factor, SMN and its related protein share significant similarities in sequence and cellular function.
The Retinoblastoma Susceptibility Gene Product Represses Transcription When Directly Bound to the Promoter (1995)

Rb represses E2F-mediated transcription in part by blocking the trans-activation domain of E2F. In addition, Rb can convert an E2F binding site from a positive to a negative element. To examine the effect of a Rb-DNA-bound complex on transcription, full-length Rb was fused to the DNA binding domain of GAL4. Here, we report that GAL4-Rb can repress transcription mediated by either Sp1, AP-1, or p53, dependent upon the presence of both the GAL4 DNA binding domain and GAL4 binding sites. Moreover, GAL4-Rb inhibited the activity of the herpes simplex virus tk promoter from GAL4 binding sites located at a distance from the promoter. In contrast, GAL4-Rb was unable to repress basal transcription. Cotransfection of specific cyclins and cyclin-dependent kinases or SV40 T-antigen abolished the repressive activity of GAL4-Rb. The domains of Rb involved in mediating the repression of transcription were mapped to regions that are overlapping, but not identical, to those required for the interaction with E2F. We propose that Rb can function as a general repressor of transcription when bound to the promoter region.
Selective Ablation of Pillar and Deiters' Cells Severely Affects Cochlear Postnatal Development and Hearing in Mice (2013)

Mammalian auditory hair cells (HCs) are inserted into a well structured environment of supporting cells (SCs) and acellular matrices. It has been proposed that when HCs are irreversibly damaged by noise or ototoxic drugs, surrounding SCs seal the epithelial surface and likely extend the survival of auditory neurons. Because SCs are more resistant to damage than HCs, the effects of primary SC loss on HC survival and hearing have received little attention. We used the Cre/loxP system in mice to specifically ablate pillar cells (PCs) and Deiters' cells (DCs). In Prox1CreER(T2)+/-;Rosa26(DTA/+) (Prox1DTA) mice, Cre-estrogen receptor (CreER) expression is driven by the endogenous Prox1 promoter and, in presence of tamoxifen, removes a stop codon in the Rosa26(DTA/+) allele and induces diphtheria toxin fragment A (DTA) expression. DTA produces cell-autonomous apoptosis. Prox1DTA mice injected with tamoxifen at postnatal days 0 (P0) and P1 show significant DC and outer PC loss at P2-P4, that reaches ∼70% by 1 month. Outer HC loss follows at P14 and is almost complete at 1 month, while inner HCs remain intact. Neural innervation to the outer HCs is disrupted in Prox1DTA mice and auditory brainstem response thresholds in adults are 40-50 dB higher than in controls. The hearing deficit correlates with loss of cochlear amplification. Remarkably, in Prox1DTA mice, the auditory epithelium preserves the ability to seal the reticular lamina and spiral ganglion neuron counts are normal, a key requirement for cochlear implant success. In addition, our results show that cochlear SC pools should be appropriately replenished during HC regeneration strategies.
Viewpoint shifting in Korean and Bulgarian (2015)

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Phase I Study of Single-Agent Anti–Programmed Death-1 (MDX-1106) in Refractory Solid Tumors: Safety, Clinical Activity, Pharmacodynamics, and Immunologic Correlates (2010)

Blocking the PD-1 immune checkpoint with intermittent antibody dosing is well tolerated and associated with evidence of antitumor activity. Exploration of alternative dosing regimens and combinatorial therapies with vaccines, targeted therapies, and/or other checkpoint inhibitors is warranted.
Specific DNA sequence amplification in human neuroblastoma cells. (1983)

Southern blot analysis of a number of EcoRI-digested human neuroblastoma DNAs has revealed the presence of a family of discrete restriction fragments, the majority of which are amplified in most, but not all, of the neuroblastoma cell lines tested. None of these sequences is abundantly present in DNA from other human tumors of different tissue origins, including several either known or presumed to contain amplified DNA. Hence, these sequences appear to be specifically amplified by neuroblastoma cells. Hybridization with metaphase chromosomes in situ has localized these sequences to either the homogeneously staining regions or double-minute chromosomes of different neuroblastoma cell lines, indicating that these chromosomal structures, although present in cell lines established from different patients, share many sequences and may have a common, but as yet unknown, function.
Semiautomated method for noise reduction and background phase error correction in MR phase velocity data (1993)

Background phase distortion and random noise can adversely affect the quality of magnetic resonance (MR) phase velocity measurements. A semiautomated method has been developed that substantially reduces both effects. To remove the background phase distortion, the following steps were taken: The time standard deviations of the phase velocity images over a cardiac cycle were calculated. Static regions were identified as those in which the standard deviation was low. A flat surface representing an approximation to the background distortion was fitted to the static regions and subtracted from the phase velocity images to give corrected phase images. Random noise was removed by setting to zero those regions in which the standard deviation was high. The technique is demonstrated with a sample set of data in which the in-plane velocities have been measured in an imaging section showing the left ventricular outflow tract of a human left ventricle. The results are presented in vector and contour form, superimposed on the conventional MR angiographic images.
GaN Nanobelt-Based Strain-Gated Piezotronic Logic Devices and Computation (2013)

Using the piezoelectric polarization charges created at the metal-GaN nanobelt (NB) interface under strain to modulate transport of local charge carriers across the Schottky barrier, the piezotronic effect is utilized to convert mechanical stimuli applied on the wurtzite-structured GaN NB into electronic controlling signals, based on which the GaN NB strain-gated transistors (SGTs) have been fabricated. By further assembling and integrating GaN NB SGTs, universal logic devices such as NOT, AND, OR, NAND, NOR, and XOR gates have been demonstrated for performing mechanical-electrical coupled piezotronic logic operations. Moreover, basic piezotronic computation such as one-bit binary addition over the input mechanical strains with corresponding computation results in an electrical domain by half-adder has been implemented. The strain-gated piezotronic logic devices may find applications in human-machine interfacing, active flexible/stretchable electronics, MEMS, biomedical diagnosis/therapy, and prosthetics.
DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus (2004)

Escherichia coli Dps (DNA-binding proteins from starved cells) is the prototype of a DNA-protecting protein family expressed by bacteria under nutritional and oxidative stress. The role of the lysine-rich and highly mobile Dps N-terminus in DNA protection has been investigated by comparing the self-aggregation and DNA-condensation capacity of wild-type Dps and two N-terminal deletion mutants, DpsDelta8 and DpsDelta18, lacking two or all three lysine residues, respectively. Gel mobility and atomic force microscopy imaging showed that at pH 6.3, both wild type and DpsDelta8 self-aggregate, leading to formation of oligomers of variable size, and condense DNA with formation of large Dps-DNA complexes. Conversely, DpsDelta18 does not self-aggregate and binds DNA without causing condensation. At pH 8.2, DpsDelta8 and DpsDelta18 neither self-aggregate nor cause DNA condensation, a behavior also displayed by wild-type Dps at pH 8.7. Thus, Dps self-aggregation and Dps-driven DNA condensation are parallel phenomena that reflect the properties of the N-terminus. DNA protection against the toxic action of Fe(II) and H2O2 is not affected by the N-terminal deletions either in vitro or in vivo, in accordance with the different structural basis of this property.