gebhart/patrepeval huggingface dataset:
Activation of the Myc oncoprotein leads to increased turnover of thrombospondin-1 mRNA (2000)

The Myc oncoprotein is implicated in transcriptional regulation of a variety of genes pertaining to cell cycle and neoplastic transformation. Examples of both positive and negative regulation have been reported that involve E-box and initiator (Inr) promoter elements, respectively. In both cases, Myc is thought to induce changes in transcription initiation. We have previously shown that overexpression of Myc causes down-regulation of the thrombospondin-1 (tsp-1) gene, an important negative modulator of tumor angiogenesis. In this study, we demonstrate that Myc in combination with Max can bind, albeit with low affinity, to an E-box-like element in the tsp-1 promoter. However, the 2.7 kb DNA segment containing both this non-canonical E-box and an Inr-like sequence does not constitute a Myc-responsive element in a transient expression system. Furthermore, Myc does not significantly affect the rate of initiation or elongation of the tsp-1 mRNA. Thus, in this instance Myc does not act as a canonical transcription factor. Instead, as demonstrated by blocking de novo RNA synthesis, down-regulation of the tsp-1 gene by Myc occurs through increased mRNA turnover. To our knowledge, this is the first example of gene regulation by Myc that involves mRNA destabilization.
An optimal low loss HF diplexer using helical resonators (2003)

A diplexer comprising two narrowband closely spaced channels in the 164-175-MHz band having relatively low insertion loss, small size, and light weight is described. The diplexer replaces a device with dimensions of 6*10*18 in. with one of dimensions 2.2*6*6 in. This order-of-magnitude reduction in size is achieved by the use of optimal asymmetric filters each having poles placed in the other passband giving high mutual isolation, combined with the use of helical resonators giving an unloaded Q on the order of 800, which is about twice as high as previous lumped element filters. Additional out-of-band rejection is obtained by the unusual technique of introducing an additional attenuation pole in the output coupling.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Random-Restart Reactive Tabu Search Algorithm for Detection in Large-MIMO Systems (2010)

We present a low-complexity algorithm based on reactive tabu search (RTS) for near maximum likelihood (ML) detection in large-MIMO systems. The conventional RTS algorithm achieves near-ML performance for 4-QAM in large-MIMO systems. But its performance for higher-order QAM is far from ML performance. Here, we propose a random-restart RTS (R3TS) algorithm which achieves significantly better bit error rate (BER) performance compared to that of the conventional RTS algorithm in higher-order QAM. The key idea is to run multiple tabu searches, each search starting with a random initial vector and choosing the best among the resulting solution vectors. A criterion to limit the number of searches is also proposed. Computer simulations show that the R3TS algorithm achieves almost the ML performance in 16 × 16 V-BLAST MIMO system with 16-QAM and 64-QAM at significantly less complexities than the sphere decoder. Also, in a 32 × 32 V-BLAST MIMO system, the R3TS performs close to ML lower bound within 1.6 dB for 16-QAM (128 bps/Hz), and within 2.4 dB for 64-QAM (192 bps/Hz) at 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> BER.
Interleukin-10-based therapy for inflammatory bowel disease (2003)

AbstractIn recent years it has become clear that chronic inflammatory bowel disease (IBD), especially Crohn's disease (CD), is caused by a loss of tolerance against the autologous bacterial flora of the intestine. Tolerance against the indigenous flora requires optimal recognition of antigens by pattern recognition receptors and the presence of important regulatory cells and cytokines. Interleukin-10 (IL-10) has a major role in the regulatory network of cytokines controlling mucosal tolerance, and it is, therefore, not surprising that this cytokine is proposed as a potent anti-inflammatory biological therapy in chronic IBD. This review will discuss the characteristics of IL-10, its immunoregulatory properties in mice and humans, and the use of IL-10 as a treatment for CD. The review will summarise the clinical studies that have taken place and discuss the lessons learned from these trials. Finally, the advantages and disadvantages of promising new strategies of IL-10 treatment, including gene therapy and the use of genetically modified bacteria, will be discussed. Both novel therapies have been shown to be successful in animal models of disease, and clinical testing is currently underway. The future goal of IL-10 treatment should be focused on mucosal delivery and remission maintenance instead of remission induction. In conclusion, it can be said that despite the disappointing results of IL-10 therapy so far, there is still enough rationale for the use of IL-10 as an anti-inflammatory biological treatment in chronic IBD.KeywordsbiologicalsCrohn's diseasegene therapyinflammatory bowel diseaseinterleukin-10
Semivariogram and Kriging Analysis in Developing Sampling Strategies (1990)

The study in this paper loolcs at using the concepts of semivariogram analysis and krigng estimation to develop strategies for corrosion rate estimation in steel plating. This involves determining the number and location of thickness measurements to be taken so that a desired level of confidence is achieved in the estimation of the corrosion rate.
Language, Literature, and Learning. (1993)

Mild UCHL caused localization to deteriorate. HAs significantly improved sound localization, albeit the delay caused by the device processing time. Most of the improvements were seen in high-frequency sounds, representing a beneficial effect of amplification on ILD. Our results have potential clinical value in situations of mild CHL, for instance, otitis media with effusion.
Rapid multipoint linkage analysis of recessive traits in nuclear families, including homozygosity mapping. (1995)

Homozygosity mapping is a powerful strategy for mapping rare recessive traits in children of consanguineous marriages. Practical applications of this strategy are currently limited by the inability of conventional linkage analysis software to compute, in reasonable time, multipoint LOD scores for pedigrees with inbreeding loops. We have developed a new algorithm for rapid multipoint likelihood calculations in small pedigrees, including those with inbreeding loops. The running time of the algorithm grows, at most, linearly with the number of loci considered simultaneously. The running time is not sensitive to the presence of inbreeding loops, missing genotype information, and highly polymorphic loci. We have incorporated this algorithm into a software package, MAPMAKER/HOMOZ, that allows very rapid multipoint mapping of disease genes in nuclear families, including homozygosity mapping. Multipoint analysis with dozens of markers can be carried out in minutes on a personal workstation.
Association of B Cell Antigen Receptor with Protein Tyrosine Kinase Lyn (1991)

Antigen is thought to cross-link membrane-bound immunoglobulins (Igs) of B cells, causing proliferation and differentiation or the inhibition of growth. Protein tyrosine kinases are probably involved in signal transduction for cell proliferation and differentiation. The Src-like protein tyrosine kinase Lyn is expressed preferentially in B cells. The Lyn protein and its kinase activity could be coimmunoprecipitated with IgM from detergent lysates. Cross-linking of membrane-bound IgM induced a rapid increase in tyrosine phosphorylation of at least ten distinct proteins of B cells. Thus, Lyn is physically associated with membrane-bound IgM, and is suggested to participate in antigen-mediated signal transduction.
Review Surfactant protein-D and pulmonary host defense (2000)

Surfactant protein-D (SP-D) participates in the innate response to inhaled microorganisms and organic antigens, and contributes to immune and inflammatory regulation within the lung. SP-D is synthesized and secreted by alveolar and bronchiolar epithelial cells, but is also expressed by epithelial cells lining various exocrine ducts and the mucosa of the gastrointestinal and genitourinary tracts. SP-D, a collagenous calcium-dependent lectin (or collectin), binds to surface glycoconjugates expressed by a wide variety of microorganisms, and to oligosaccharides associated with the surface of various complex organic antigens. SP-D also specifically interacts with glycoconjugates and other molecules expressed on the surface of macrophages, neutrophils, and lymphocytes. In addition, SP-D binds to specific surfactant-associated lipids and can influence the organization of lipid mixtures containing phosphatidylinositol in vitro. Consistent with these diverse in vitro activities is the observation that SP-D-deficient transgenic mice show abnormal accumulations of surfactant lipids, and respond abnormally to challenge with respiratory viruses and bacterial lipopolysaccharides. The phenotype of macrophages isolated from the lungs of SP-Ddeficient mice is altered, and there is circumstantial evidence that abnormal oxidant metabolism and/or increased metalloproteinase expression contributes to the development of emphysema. The expression of SP-D is increased in response to many forms of lung injury, and deficient accumulation of appropriately oligomerized SP-D might contribute to the pathogenesis of a variety of human lung diseases.
UVB Induces IL‐12 Transcription in Human Keratinocytes in vivo and in vitro (1996)

Human epidermal cells produce a wide range of cytokines, including those characteristic of Th2-like responses such as interleukin (IL)-4 and IL-10. As well, keratinocytes have recently been shown to produce Th1-like cytokines such as IL-12. Exposure to UVB has profound effects on the skin and systemic immune system, which is in part mediated by secretion of tumor necrosis factor (TNF)-alpha by epidermal cells. Because IL-12 induces production of TNF-alpha by certain cells of the immune system, we sought to determine whether UVB is an inducer of IL-12 gene expression in epidermal cells. Human epidermal cells were exposed to UVB radiation in vivo, isolated by suction blister technique and trypsinization and transcription of the IL-12 p35 and p40 chains was examined by RT-PCR. We found the p35 chain of IL-12 to be constitutively expressed and the p40 chain inducible by UVB irradiation. Because epidermis consists of a heterogenous cell population with distinct cytokine repertoires, we sought to determine the cellular source of the IL-12 message after UVB exposure. After depleting UVB-exposed epidermal cells for DR+ cells, no reduction in the IL-12 activity was detected, suggesting that keratinocytes are a source of IL-12 transcripts in UVB-exposed human epidermis. This was supported by the up-regulation of IL-12 p40 transcripts in UV-irradiated cultured keratinocytes that were devoid of DR+ cells. Up-regulation of IL-12 p40 gene expression by UVB as demonstrated here, taken together with the finding that keratinocytes also up-regulate IL-10 transcription, suggests that there is a complex interplay between Th1- and Th2-like epidermis-derived cytokines following exposure to UVB.
Structural studies on the non‐toxic lipid A from Rhodopseudomonas sphaeroides ATCC 17023 (1983)

The lipid A isolated from Rhodopseudomonas sphaeroides ATCC 17023 has been investigated. A sequence of analyses indicated beta-D-glucosaminyl-1,6-D-glucosamine as the sugar backbone carrying phosphate groups at C-1 of the reducing glucosamine and C-4 of the non-reducing glucosamine. Both 3-(7-tetradecenoyl)oxytetradecanoic and 3-oxotetradecanoic acid are linked to the NH2 groups. Two residues of 3-hydroxydecanoic acid are linked to hydroxy groups at C-3 of both reducing and non-reducing glucosamine, and the hydroxy group of 3-hydroxydecanoic acid is free. In free lipid A, the hydroxy group at C-4 of the reducing glucosamine and at C-6 of the non-reducing glucosamine are unsubstituted. The latter probably arises from a 3-deoxy-D-manno-octulosonate linkage. The structural similarities and dissimilarities existing between lipid A of R. sphaeroides, which is non-toxic, and lipid A types such as those from Salmonella, which are toxic, are discussed.
All-fiber coherent beam combining of fiber lasers (1999)

One half of a 2x2 fused taper single-mode fiber coupler is used for the all-fiber spatial and spectral beam combining of two fiber lasers.
Prolyl endopeptidase activity in bronchoalveolar lavage fluid: a novel diagnostic biomarker in a guinea pig model of invasive pulmonary aspergillosis (2013)

Improved diagnostics are needed to detect invasive pulmonary aspergillosis, a life-threatening infection caused by the pathogenic fungus Aspergillus fumigatus. We are investigating secreted fungal proteases as novel biomarkers for the diagnosis of this disease. Although the A. fumigatus genome encodes a multitude of secreted proteases, few have been experimentally characterized. Here, we employed an unbiased combinatorial library of internally quenched fluorogenic probes to detect infection-associated proteolysis in the lungs of guinea pigs experimentally infected with A. fumigatus. Comparative protease activity profiling revealed a prolyl endopeptidase activity that is reproducibly induced during infection but is not observed in healthy animals. This proteolytic activity was found in four independent animal experiments involving two A. fumigatus isolates. We synthesized a small, focused fluorogenic probe library to define the substrate specificity of the prolyl endopeptidase substrate motif and to identify optimal Probe sequences. These efforts resulted in the identification of a panel of six individual substrate-based fluorescent probes capable of detecting infection in guinea pigs with high statistical significance (P<0.005 in most cases). Receiver operating characteristic analyses demonstrated that this fluorogenic assay could detect A. fumigatus infection-associated proteolysis with comparable sensitivity and specificity as existing diagnostic procedures, suggesting that further optimization of the methodology may lead to improved diagnostics options for invasive pulmonary aspergillosis.
Gene optimization mechanisms: A multi‐gene study reveals a high success rate of full‐length human proteins expressed in Escherichia coli (2010)

The genetic code is universal, but recombinant protein expression in heterologous systems is often hampered by divergent codon usage. Here, we demonstrate that reprogramming by standardized multi-parameter gene optimization software and de novo gene synthesis is a suitable general strategy to improve heterologous protein expression. This study compares expression levels of 94 full-length human wt and sequence-optimized genes coding for pharmaceutically important proteins such as kinases and membrane proteins in E. coli. Fluorescence-based quantification revealed increased protein yields for 70% of in vivo expressed optimized genes compared to the wt DNA sequences and also resulted in increased amounts of protein that can be purified. The improvement in transgene expression correlated with higher mRNA levels in our analyzed examples. In all cases tested, expression levels using wt genes in tRNA-supplemented bacterial strains were outperformed by optimized genes expressed in non-supplemented host cells.
Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/GcvR interaction and allow GcvA-mediated activation of the Escherichia coli gcvTHP operon (2002)

The Escherichia coli gcvTHP operon is under control of the LysR-type transcriptional regulator GcvA. GcvA activates the operon in the presence of glycine and represses the operon in its absence. Repression by GcvA is dependent on a second regulatory protein, GcvR. Generally, LysR-type transcriptional regulators bind to specific small co-effector molecules which results in either their altered affinity for specific binding sites on the DNA or altered ability to bend the DNA, resulting in either activation or repression of their respective operons. This study shows that glycine, the co-activator for the gcv operon, does not alter either GcvA's ability to bind DNA nor its ability to bend DNA. Rather, glycine binds to GcvR, disrupting a GcvA/GcvR interaction required for repression and allowing GcvA activation of the gcvTHP operon. Amino acid changes in GcvR that reduce glycine binding result in a loss of glycine-mediated activation in vivo.
Myogenic cell formation in regenerating rat skeletal muscle injured by mincing I. A fine structural study (1977)

Abstract The degenerative and early regenerative events following mincing and autotransplantation of rat skeletal muscle were examined at the ultrastructural level. During the first eight hours after injury, myonuclei undergo pyknosis, mitochondria become enlarged and vesiculated, myofilaments appear less distinct than normal and the sarcolemmata either disappear or become extensively fragmented. Further degeneration of the myofibers progresses slowly until macrophages and polymorphonuclear neutrophils invade the degenerating sarcoplasm between one to four days after mincing. Scattered throughout the minced muscle implant during the first 24 hours after injury are small, viable‐appearing, undifferentiated cells located between the external lamina and degenerating sarcoplasm. Such cells, which are structurally similar to satellite cells seen in uninjured muscle, are believed to be regenerating presumptive myoblasts due to their mesenchymal‐like morphology and sublaminar position. External laminae of the injured muscle fibers do not undergo immediate degenerative changes, but rather persist during the first three to six days as laminar tubes within which spindle‐shaped myoblasts and newly formed myotubes are frequently observed. Examples of regenerating myoblasts in the process of budding‐off from damaged muscle fibers were not observed in this study. Therefore, the evidence suggests that satellite cells are the major source of regenerating myoblasts in skeletal muscle of the rat.
Interventional techniques: evidence-based practice guidelines in the management of chronic spinal pain. (2007)

These guidelines include the evaluation of evidence for diagnostic and therapeutic procedures in managing chronic spinal pain and recommendations for managing spinal pain. However, these guidelines do not constitute inflexible treatment recommendations. These guidelines also do not represent a "standard of care."
Systemic Administration of Polymeric Nanoparticle-Encapsulated Curcumin (NanoCurc) Blocks Tumor Growth and Metastases in Preclinical Models of Pancreatic Cancer (2010)

Curcumin or diferuloylmethane is a yellow polyphenol extracted from the rhizome of turmeric (Curcuma longa). A large volume (several hundreds) of published reports has established the anticancer and chemopreventative properties of curcumin in preclinical models of every known major cancer type. Nevertheless, the clinical translation of curcumin has been significantly hampered due to its poor systemic bioavailability, which mandates that patients consume up to 8 to 10 g of the free drug orally each day to achieve detectable levels in circulation. We have engineered a polymeric nanoparticle encapsulated curcumin formulation (NanoCurc) that shows remarkably higher systemic bioavailability in plasma and tissues compared with free curcumin upon parenteral administration. In xenograft models of human pancreatic cancer established in athymic mice, administration of parenteral NanoCurc significantly inhibits primary tumor growth in both subcutaneous and orthotopic settings. The combination of parenteral NanoCurc with gemcitabine results in enhanced tumor growth inhibition versus either single agent, suggesting an additive therapeutic influence in vivo. Furthermore, this combination completely abrogates systemic metastases in orthotopic pancreatic cancer xenograft models. Tumor growth inhibition is accompanied by significant reduction in activation of nuclear factor-kappaB, as well as significant reduction in expression of matrix metalloproteinase-9 and cyclin D1, in xenografts treated with NanoCurc and gemcitabine. NanoCurc is a promising new formulation that is able to overcome a major impediment for the clinical translation of curcumin to cancer patients by improving systemic bioavailability, and by extension, therapeutic efficacy.
First evidence for a restrictionâmodification system in Leptospira sp.1 (2001)

The LE1 leptophage exhibited a host range restricted to the saprophytic Leptospira biflexa [Saint Girons et al., Res. Microbiol. 141 (1990) 1131-1133] and mainly to the Patoc 1 strain (hereafter called PFRA) kept in the Paris, France collection. Results of titration of LE1 lysates indicated the presence of a host-controlled modification and restriction system within PUSA (Patoc 1 strain maintained in the Morgantown, WV, USA collection) that was absent in PFRA. Because genomic DNA of PITAL (Patoc 1 strain maintained in Trieste, Italy) appeared smeared in pulsed field gel electrophoresis (PFGE), this strain is likely to contain nucleases that are activated upon DNA isolation. Moreover, comparative NotI digestions of PUSA and PFRA DNAs, as visualized by PFGE, indicated that PUSA belonged to a different serovar than PFRA. Finally, 16S ribosomal sequence analysis indicated that PUSA belonged to the saprophytic Leptospira meyeri species, while PITAL and PFRA appertained to L. biflexa. The evolutionary significance and the importance of the restriction and modification enzymes or non-specific nucleases within strains for genetic experiments are discussed.
Effects of Power Densities, Continuous and Pulse Frequencies, and Number of Sessions of Low-Level Laser Therapy on Intact Rat Brain (2006)

Long-term safety tests lasting 30 and 70 days at optimal 10x and 100x doses, as well as at multiple doses at the same power densities, indicate that the tested laser energy doses are safe under this treatment regime. Neurological deficits and histopathological damage to 750 mW/cm2 CW laser irradiation are attributed to thermal damage and not due to tissue-photon interactions.
Coup d'Etat: An Orphan Takes Control (2011)

Chicken ovalbumin upstream promoter transcription factors (COUP-TFs) belong to the steroid/thyroid hormone receptor superfamily. Cloning of their cDNAs demonstrated the existence of two distinct but related genes: COUP-TFI (EAR-3, NR2F1) and COUP-TFII (ARP-1, NR2F2). They are referred to as orphan receptors because ligands for COUP-TFs have yet to be identified. Since 1998, extensive studies have demonstrated their physiological importance in cell-fate specification, organogenesis, angiogenesis, and metabolism, as well as a variety of diseases. In this article, we will comprehensively review the biological functions of COUP-TFII and its underlying mechanism in various developmental processes and diseases. In addition, we will briefly summarize some of the current findings of COUP-TFI.