gebhart/patrepeval huggingface dataset:
Towards an active network architecture (1996)

Active networks allow their users to inject customized programs into the nodes of the network. An extreme case, in which we are most interested, replaces packets with "capsules" - program fragments that are executed at each network router/switch they traverse.Active architectures permit a massive increase in the sophistication of the computation that is performed within the network. They will enable new applications, especially those based on application-specific multicast, information fusion, and other services that leverage network-based computation and storage. Furthermore, they will accelerate the pace of innovation by decoupling network services from the underlying hardware and allowing new services to be loaded into the infrastructure on demand.In this paper, we describe our vision of an active network architecture, outline our approach to its design, and survey the technologies that can be brought to bear on its implementation. We propose that the research community mount a joint effort to develop and deploy a wide area ActiveNet.
Ex vivoregulation of specific gene expression by nanomolar concentration of double-stranded dumbbell oligonucleotides (1993)

Inhibition of specific transcriptional regulatory proteins is a new approach to control gene expression. Transcriptional activity of DNA-binding proteins can be inhibited by the use of double-stranded (ds) oligodeoxynucleotides that compete for the binding to their specific target sequences in promoters and enhancers. As a model, we used phosphodiester dumbbell oligonucleotides containing a binding site for the liver-enriched transcription factor HNF-1 (Hepatocyte Nuclear Factor 1). Binding affinity of HNF-1 to dumbbell oligonucleotides was the same as that to ds oligonucleotides, as determined by gel retardation assays. HNF-1 dumbbells specifically inhibited in vitro transcription driven by the albumin promoter by more than 90%. HNF-1-dependent activation of a CAT reporter plasmid was specifically inhibited when the HNF-1 dumbbell oligonucleotide was added at nM concentration to transiently transfected C33 cells. On the contrary, HNF-1 ds oligonucleotides, which displayed the same activity as the dumbbell oligonucleotides in the in vitro assays, were no more effective in the ex vivo experiments. These results might reflect the increased stability of the circular dumbbell oligonucleotides towards cellular nuclease degradation, as shown in vitro with nucleolytic enzymes. Dumbbell oligonucleotides containing unmodified phosphodiester bonds may efficiently compete for binding of specific transcription factors within cells, then providing a potential therapeutic tool to control disease-causing genes.
Hybrid Gadolinium Oxide Nanoparticles:  Multimodal Contrast Agents for in Vivo Imaging (2007)

Luminescent hybrid nanoparticles with a paramagnetic Gd2O3 core were applied as contrast agents for both in vivo fluorescence and magnetic resonance imaging. These hybrid particles were obtained by encapsulating Gd2O3 cores within a polysiloxane shell which carries organic fluorophores and carboxylated PEG covalently tethered to the inorganic network. Longitudinal proton relaxivities of these particles are higher than the positive contrast agents like Gd-DOTA which are commonly used for clinical magnetic resonance imaging. Moreover these particles can be followed up by fluorescence imaging. This study revealed that these particles suited for dual modality imaging freely circulate in the blood vessels without undesirable accumulation in lungs and liver.
Nanoscale light–matter interactions in atomic cladding waveguides (2013)

Alkali vapours, such as rubidium, are being used extensively in several important fields of research such as slow and stored light nonlinear optics quantum computation, atomic clocks and magnetometers. Recently, there is a growing effort towards miniaturizing traditional centimetre-size vapour cells. Owing to the significant reduction in device dimensions, light-matter interactions are greatly enhanced, enabling new functionalities due to the low power threshold needed for nonlinear interactions. Here, taking advantage of the mature platform of silicon photonics, we construct an efficient and flexible platform for tailored light-vapour interactions on a chip. Specifically, we demonstrate light-matter interactions in an atomic cladding waveguide, consisting of a silicon nitride nano-waveguide core with a rubidium vapour cladding. We observe the efficient interaction of the electromagnetic guided mode with the rubidium cladding and show that due to the high confinement of the optical mode, the rubidium absorption saturates at powers in the nanowatt regime.
Inorganic Polyphosphate in Mammalian Cells and Tissues (1995)

Inorganic polyphosphate (polyP), a linear polymer of hundreds of orthophosphate (Pi) residues linked by high-energy, phosphoanhydride bonds, has been identified and measured in a variety of mammalian cell lines and tissues by unambiguous enzyme methods. Subpicomole amounts of polyP (0.5 pmol/100 micrograms of protein) were determined by its conversion to ATP by Escherichia coli polyphosphate kinase and, alternatively, to Pi by Saccharomyces cerevisiae exopolyphosphatase. Levels of 25 to 120 microM (in terms of Pi residues), in chains 50 to 800 residues long, were found in rodent tissues (brain, heart, kidneys, liver, and lungs) and in subcellular fractions (nuclei, mitochondria, plasma membranes, and microsomes). PolyP in brain was predominantly near 800 residues and found at similar levels pre- and postnatally. Conversion of Pi into polyP by cell lines of fibroblasts, T-cells, kidney, and adrenal cells attained levels in excess of 10 pmol per mg of cell protein per h. Synthesis of polyP from Pi in the medium bypasses intracellular Pi and ATP pools suggesting the direct involvement of membrane component(s). In confluent PC12 (adrenal pheochromocytoma) cells, polyP turnover was virtually complete in an hour, whereas in fibroblasts there was little turnover in four hours. The ubiquity of polyP and variations in its size, location, and metabolism are indicative of a multiplicity of functions for this polymer in mammalian systems.
Biocompatibility of NDGA-polymerized collagen fibers. II. Attachment, proliferation, and migration of tendon fibroblastsin vitro (2001)

The material properties of collagen fibers polymerized with nordihydroguaiaretic acid (NDGA) are equivalent to native tendon, suggesting that NDGA crosslinking may provide a viable approach to stabilizing collagenous materials for use in repairing ruptured, lacerated, or surgically transected fibrous tissues, such as tendons and ligaments (Koob & Hernandez, Biomaterials, in press). The present study evaluated the biocompatibility of these fibers with cultured bovine tendon fibroblasts. Fibroblast attachment, migration, and proliferation on NDGA-crosslinked materials were compared to those on prepolymerized type I tendon collagen constructs as well as on tissue-culture-treated plastic. Fibroblast attachment on NDGA-crosslinked collagen fibrils was equivalent to attachment on plates coated with collagen alone. Over a period of 8 days in culture, attached fibroblasts proliferated on NDGA-crosslinked collagen at a rate identical to that of fibroblasts attached to native collagen. In order for the biomaterial effectively to bridge gaps in fibrous tissues, fibroblasts must be able to migrate and replicate on the bridging fiber. Control and crosslinked fibers were inserted in calf tendon explants, with a portion of the fiber extending out of the sectioned end of the tendon. Explants were cultured for 9 weeks, and the number of cells was measured at weekly intervals. Cells appeared on the fibers after 1 week of culture. By 2 weeks, cells had colonized the entire fiber. The number of cells continued to increase throughout the 9 weeks in culture, forming a layer several cells thick. Histologic analysis indicated that the fibroblasts populating the fibers appeared to originate in the epitenon. There was no difference in the rate of fibroblast migration and replication, nor in the ultimate number of colonizing cells, between control collagen fibers and NDGA-crosslinked fibers. NDGA-crosslinked fibers may provide a means of bridging gaps in ruptured, lacerated, or surgically transected tendons by providing a mechanically competent scaffold on which tendon fibroblasts can migrate, attach, and proliferate.
Swelling of K+, Na+and Ca2+-montmorillonites and hydration of interlayer cations: a molecular dynamics simulation (2010)

This paper performs molecular dynamics simulations to investigate the role of the monovalent cations K, Na and the divalent cation Ca on the stability and swelling of montmorillonite. The recently developed CLAYFF force field is used to predict the basal spacing as a function of the water content in the interlayer. The simulations reproduced the swelling pattern of these montmorillonites, suggesting a mechanism of their hydration different (K+ < Na+ < Ca2+) from that of K+-, Na+-, and Ca2+-montmorillonites. In particular, these results indicate that the valence of the cations has the larger impact on the behaviour of clay-water systems. It also finds that the differences in size and hydration energy of K+, Na+ and Ca2+ ions have strong implications for the structure of interlayer. This leads to the differences in the layer spacings of the simulated K+-, Na+-, and Ca2+-montmorillonites. Furthermore, these simulations show that the K cations interact strongly with the clay sheets for the dehydrated clay sheets, but for the hydrated clays the Ca cations interact clearly strongly with the clay sheets.
Decline in Invasive Pneumococcal Disease after the Introduction of Protein–Polysaccharide Conjugate Vaccine (2003)

The use of the pneumococcal conjugate vaccine is preventing disease in young children, for whom the vaccine is indicated, and may be reducing the rate of disease in adults. The vaccine provides an effective new tool for reducing disease caused by drug-resistant strains.
HOXB6 Protein Is Bound to CREB-binding Protein and Represses Globin Expression in a DNA Binding-dependent, PBX Interaction-independent Process (2004)

Although HOXB6 and other HOX genes have previously been associated with hematopoiesis and leukemias, the precise mechanism of action of their protein products remains unclear. Here we use a biological model in which HOXB6 represses alpha- and gamma-globin mRNA levels to perform a structure/function analysis for this homeodomain protein. HOXB6 protein represses globin transcript levels in stably transfected K562 cells in a DNA-binding dependent fashion. However, the capacity to form cooperative DNA-binding complexes with the PBX co-factor protein is not required for HOXB6 biological activity. Neither the conserved extreme N-terminal region, a polyglutamic acid region at the protein C terminus, nor the Ser(214) CKII phosphorylation site was required for DNA binding or activity in this model. We have previously reported that HOX proteins can inhibit CREB-binding protein (CBP)-histone acetyltransferase-mediated potentiation of reporter gene transcription. We now show that endogenous CBP is co-precipitated with exogenous HOXB6 from nuclear and cytoplasmic compartments of transfected K562 cells. Furthermore, endogenous CBP co-precipitates with endogenous HOXB6 in day 14.5 murine fetal liver cells during active globin gene expression in this tissue. The CBP interaction motif was localized to the homeodomain but does not require the highly conserved helix 3. Our data suggest that the homeodomain contains most or all of the important structures required for HOXB6 activity in blood cells.
Postweaning Multisystemic Wasting Syndrome Induced after Experimental Inoculation of Cesarean-Derived, Colostrum-Deprived Piglets with Type 2 Porcine Circovirus (2001)

Cesarean-derived, colostrum-deprived pigs (n = 23) were inoculated intranasally and subcutaneously with a low cell culture passage of type 2 porcine circovirus. In 11 pigs, a persistent fever that lasted 7-17 days began 12-15 days after inoculation with virus. Additional signs of disease in those 11 pigs included depression (11 of 11 pigs), palpable enlargement of inguinal, prefemoral, and popliteal lymph nodes (11 of 11), icterus (6 of 11), and hyperpnea (2 of 11). The remaining 12 pigs had fever that occurred intermittently for 2-4 days between days 12 and 20 postinoculation. Overt signs of disease in those pigs were limited to palpable enlargement of inguinal and popliteal lymph nodes (9 of 12 pigs). When compared with control pigs of similar age, the average daily rate of weight gain for all pigs inoculated with virus was less over a 2-week period that began 2 weeks post inoculation. At postmortem examination, lymph node enlargement was seen in 14 of 14 pigs euthanized between days 20 and 28 postinoculation. Lymph node enlargement was especially prominent in pigs that developed a persistent fever. Microscopic lesions noted in pigs that developed a persistent fever included cellular depletion in lymphoid tissues; hepatic cell necrosis; and lymphogranulomatous inflammation of lymph nodes, Peyer's patches of the intestine, liver, kidney, and heart. Virus was isolated with varying frequency from nasal, rectal, or tonsil swab specimens, buffy coat, serum, urine, and lung lavage fluid obtained antemortem or postmortem. Virus was isolated from or viral DNA was detected in a variety of tissues obtained postmortem up to 125 days postinoculation. Antibody against type 2 porcine circovirus usually was detected in serum between 15 and 20 days postinoculation; however, antibody against virus was not detected in serum from 4 pigs euthanized 20-24 days postinoculation. Direct contact with pigs inoculated with virus 42 days previously resulted in transmission of virus to 3 of 3 control pigs.
Film thickness constraints for manufacturable strained silicon CMOS (2003)

This paper studies the effect of the strained silicon thickness on the characteristics of strained silicon MOSFETs on SiGe virtual substrates. NMOSFETs were fabricated on strained silicon substrates with various strained silicon thicknesses, both above and below the strained silicon critical thickness. The low field electron mobility and subthreshold characteristics of the devices were measured. Low field electron mobility is increased by about 1.8 times on all wafers and is not significantly degraded on any of the samples, even for a strained silicon thickness far greater than the critical thickness. From the subthreshold characteristics, however, it is shown that the off-state leakage current is greatly increased for the devices on the wafers with a strained silicon thickness that exceeds the critical thickness. The mechanism of the leakage was examined by using photon emission microscopy. Strong evidence is shown that the leakage mechanism is source/drain electrical shorting caused by enhanced dopant diffusion near misfit dislocations.
Interkinetic nuclear migration: A mysterious process in search of a function (2012)

During interkinetic nuclear migration (INM), the nuclei in many epithelial cells migrate between the apical and basal surfaces, coordinating with the cell cycle, and undergoing cytokinesis at the apical surface. INM is observed in a wide variety of tissues and species. Recent advances in time-lapse microscopy have provided clues about the mechanisms and functions of INM. Whether actin or microtubules are responsible for nuclear migration is controversial. How mitosis is initiated during INM is poorly understood, as is the relationship between the cell cycle and nuclear movement. It is possible that the disagreements stem from differences in the tissues being studied, since epithelia undergoing INM vary greatly in terms of cell height and cell fates. In this review we examine the reports addressing the mode and mechanisms that regulate INM and suggest possible functions for this dramatic event.
Pathological Role of Interleukin-6 in Psoriatic Arthritis (2012)

Psoriatic arthritis (PsA) is a clinical manifestation of psoriatic disease. Although the pathogenesis of PsA remains unknown, PsA can be managed by treatments similar to those used for rheumatoid arthritis (RA). Because interleukin-(IL-) 6 has been suggested to have a pathogenic role in PsA, a humanized anti-IL-6 receptor antibody tocilizumab treatment for PsA was recently tried. However, the efficacy of tocilizumab for PsA was not favorable. This suggests that the pathogenic roles of IL-6 in PsA and RA are different. In RA, tumor necrosis factor (TNF) primarily contributes to the arthritis effector phase and IL-6 contributes to the arthritis priming phase. In PsA, the TNF-related effector phase is similar to that in RA, but the IL-6-related priming phase might not be critical. This paper discusses the role of IL-6 in PsA.
Quantification of Radiolabeled Proteins in Polyacrylamide Gels (2009)

Autoradiography is often used to detect and quantify radiolabeled proteins present after separation by polyacrylamide gel electrophoresis (PAGE) (see Chapter 56). The method, however, requires relatively high levels of radioactivity when weak β-emitters, such as tritium, are to be detected. In addition, lengthy exposures requiring the use of fluorescent enhancers are often required. Recent developments in detection of proteins using silver staining (1, 2) have added to the problem because of the fact that tritium emissions are quenched by the silver (2). Since for many metabolic labeling studies, tritium labeled precursors are often the only ones available, it seemed useful to develop a method that would overcome these drawbacks. The method the author developed involves the use of a cleavable crosslinking agent in the polyacrylamide gels that allows the solubilization of the protein for quantification by scintillation counting. Although developed for tritium (3), the method works well with any covalently bound label, as demonstrated here with 35S. Resolution is as good as or better than autoradiography (3 and Fig. 1), turnaround time can be greatly reduced, and quantification is more easily accomplished.
The Amino Acid Following an Asn-X-Ser/Thr Sequon Is an Important Determinant of N-Linked Core Glycosylation Efficiency (1998)

Many eukaryotic proteins are modified by Asn-linked (N-linked) glycosylation. The number and position of oligosaccharides added to a protein by the enzyme oligosaccharyltransferase can influence its expression and function. N-Linked glycosylation usually occurs at Asn residues in Asn-X-Ser/Thr sequons where X not equal Pro. However, many Asn-X-Ser/Thr sequons are not glycosylated or are glycosylated inefficiently. Inefficient glycosylation at one or more Asn-X-Ser/Thr sequons in a protein results in the production of heterogeneous glycoprotein products. These glycoforms may differ from one another in their level of expression, stability, antigenicity, or function. The signals which control the efficiency of N-linked glycosylation at individual Asn residues have not been fully defined. In this report, we use a site-directed mutagenesis approach to investigate the influence of the amino acid at the position following a sequon (the Y position, Asn-X-Ser/Thr-Y). Variants of rabies virus glycoprotein containing a single Asn-X-Ser/Thr sequon at Asn37 were generated. Variants were designed with each of the twenty common amino acids at the Y position, with either Ser or Thr at the hydroxy (Ser/Thr) position. The core glycosylation efficiency of each variant was quantified using a cell-free translation/glycosylation system. These studies reveal that the amino acid at the Y position is an important determinant of core glycosylation efficiency.
Therapeutic impact of toll-like receptors on inflammatory bowel diseases: A multiple-edged sword (2007)

Recent studies have begun to define the mechanisms through which Toll-like receptors (TLRs) regulate intestinal homeostasis in health and disease. Current therapies for inflammatory bowel diseases (IBDs) mostly aim at interrupting the inflammatory cascade through agents that regulate TH1 or TH2 cytokine responses. As recognition grows for TLR dysfunction to play a role in IBD pathogenesis, TLRs could provide another valid interventional target for novel therapy development. However, seemingly contradictory results from studying different murine models of colitis have so far confounded whether therapeutically useful modulation of TLRs is best accomplished by activating, inhibiting, or rather a combination of both at different stages of mucosal disease. This review evaluates potential strategies as well as their rationale and future prospects.
Projection-based spatially adaptive reconstruction of block-transform compressed images (1995)

At the present time, block-transform coding is probably the most popular approach for image compression. For this approach, the compressed images are decoded using only the transmitted transform data. We formulate image decoding as an image recovery problem. According to this approach, the decoded image is reconstructed using not only the transmitted data but, in addition, the prior knowledge that images before compression do not display between-block discontinuities. A spatially adaptive image recovery algorithm is proposed based on the theory of projections onto convex sets. Apart from the data constraint set, this algorithm uses another new constraint set that enforces between-block smoothness. The novelty of this set is that it captures both the local statistical properties of the image and the human perceptual characteristics. A simplified spatially adaptive recovery algorithm is also proposed, and the analysis of its computational complexity is presented. Numerical experiments are shown that demonstrate that the proposed algorithms work better than both the JPEG deblocking recommendation and our previous projection-based image decoding approach.
Simultaneous measurement of nucleolin and estrogen receptor in breast cancer cells by laser scanning cytometry. (2004)

ER and NU expression can be measured simultaneously in the same nuclei of breast cancer cells.
Estimation of Entropy and Mutual Information (2003)

We present some new results on the nonparametric estimation of entropy and mutual information. First, we use an exact local expansion of the entropy function to prove almost sure consistency and central limit theorems for three of the most commonly used discretized information estimators. The setup is related to Grenander's method of sieves and places no assumptions on the underlying probability measure generating the data. Second, we prove a converse to these consistency theorems, demonstrating that a misapplication of the most common estimation techniques leads to an arbitrarily poor estimate of the true information, even given unlimited data. This “inconsistency” theorem leads to an analytical approximation of the bias, valid in surprisingly small sample regimes and more accurate than the usual [Formula: see text] formula of Miller and Madow over a large region of parameter space. The two most practical implications of these results are negative: (1) information estimates in a certain data regime are likely contaminated by bias, even if “bias-corrected” estimators are used, and (2) confidence intervals calculated by standard techniques drastically underestimate the error of the most common estimation methods. Finally, we note a very useful connection between the bias of entropy estimators and a certain polynomial approximation problem. By casting bias calculation problems in this approximation theory framework, we obtain the best possible generalization of known asymptotic bias results. More interesting, this framework leads to an estimator with some nice properties: the estimator comes equipped with rigorous bounds on the maximum error over all possible underlying probability distributions, and this maximum error turns out to be surprisingly small. We demonstrate the application of this new estimator on both real and simulated data.