gebhart/patrepeval huggingface dataset:
Structural and mechanical characteristics of silk fibroin and chitosan blend scaffolds for tissue regeneration (2005)

The expanding field of tissue engineering has required the necessity of developing biomaterials that are tissue compatible, biodegradable, and comparable in mechanical properties to that of native tissue. We propose that the blending of two natural polymers, silk fibroin (SF) and chitosan (CS), into a 3D scaffold will provide unique chemical, structural, and mechanical properties that can be utilized for in vivo tissue regeneration. SF is an attractive material for biomedical applications because it is a fibrous protein that has high permeability to oxygen and water, relatively low thrombogenicity, low inflammatory response, protease susceptibility, supports cell adhesion and growth, and, foremost, high tensile strength with flexibility. CS is a crystalline polysaccharide, with structure similar to glycosaminoglycans, that has good wound healing properties, is nontoxic, and has minimal foreign body reactions. We hypothesized that increasing the SF-to-CS ratio would increase the ultimate tensile strength and elastic modulus and decrease the water capacity of the SFCS scaffolds. With increasing content of silk fibroin, it is observed that the ultimate tensile strength and elastic modulus increase significantly. The ultimate tensile strength and the elastic modulus were significantly higher in the short axis direction for 25:75 and 50:50 SFCS blends as compared to the long axis (p<0.05), while they were similar for the 75:25 SFCS blend. However, no differences were observed in the strain at failure among blends or due to directionality of applied strain. Increasing the chitosan content resulted in an increased water capacity of SFCS blends.
Consensus Based Approach for Economic Dispatch Problem in a Smart Grid (2013)

Economic dispatch problem (EDP) is an important class of optimization problems in the smart grid, which aims at minimizing the total cost when generating certain amount of power. In this work, a novel consensus based algorithm is proposed to solve EDP in a distributed fashion. The quadratic convex cost functions are assumed in the problem formulation, and the strongly connected communication topology is sufficient for the information exchange. Unlike centralized approaches, the proposed algorithm enables generators to collectively learn the mismatch between demand and total amount of power generation. The estimated mismatch is then used as a feedback mechanism to adjust current power generation by each generator. With a tactical initial setup, eventually, all generators can automatically minimize the total cost in a collective sense.
Strong Bragg gratings in phosphate glass single mode fiber (2006)

Bragg gratings with reflectivities greater than 99% have been fabricated in phosphate glass single mode fibers by irradiating the fibers with 193nm wavelength, high intensity pulses from an ArF excimer laser through a phase mask. Thermal treatment for 1000h at temperatures up to 170°C did not degrade the gratings and resulted in an increase in grating strength. The refractive index modulation amplitudes obtained exceed 10−4.
Somatic Gene Therapy for Nervous System Disease (2007)

Neurotrophic factors are target-derived molecules that prevent neuronal degeneration during development and, in some cases, during adulthood. They offer substantial promise as therapeutic agents in neurological disease by preventing cell loss and promoting axonal regeneration. However, the optimal means of delivering neurotrophic factors to the nervous system, and the CNS in particular, is an unresolved issue. Neurotrophic factors rarely influence only a single target neuronal population, hence broad delivery of neurotrophic factors to the nervous system may results in effects on multiple non-targeted neuronal populations. Ideally, neurotrophin delivery to the nervous system should be target-specific, regionally restricted, chronic, safe, well-tolerated and of sufficient concentration to elicit responses from target neurons. In this paper we discuss the use of somatic gene transfer methods to deliver neurotrophic factors to the CNS in a manner that seeks to meet the above criteria.
Fast packet classification for two-dimensional conflict-free filters (2002)

Routers can use packet classification to support advanced functions. Routers with packet classification capability can forward packets based on multiple header fields, such as source address, protocol type, or application port numbers. The destination-based forwarding can be thought of as one-dimensional packet classification. While several efficient solutions are known for the one-dimensional IP lookup problem, the multi-dimensional packet classification has proved to be far more difficult. While an O(log w) time scheme is known for the IP lookup, Srinivisan et al. (1999) show a lower bound of /spl Omega/(/spl omega//sup k-1/) for k-dimensional filter lookup, where /spl omega/ is the number of bits in a header field. In particular, this lower bound precludes the possibility of a binary search like scheme even for 2-dimensional filters. In this paper, we examine this lower bound more closely, and discover that the lower bound depends crucially on conflicts in the filter database. We then show that for two-dimensional conflict-free filters, a binary search scheme does work! Our lookup scheme requires O(log/sup 2/ /spl omega/) hashes in the worst-case, and uses O(n log/sup 2/ /spl omega/) memory. Alternatively, our algorithm can be viewed as making O (log /spl omega/) calls to a prefix lookup scheme. It has been observed in practice that filter databases have very few conflicts, and these conflicts can be removed by adding additional filters (one per conflict). Thus, our scheme may also be quite practical. Our simulation and experimental results show that the proposed scheme also performs as good as or better than existing schemes.
Bone and soft tissue changes with oral phosphate supplements (1972)

Oral phosphate supplements in divided doses were given to adult dogs for a period of 10 months. Bone density, bone turnover, serum chemistry values, and the calcium content of soft tissues were determined initially and at the end of the experimental period. Serum calcium remained the same; serum phosphate decreased slightly but significantly. The decrease in phosphate was related to an increase, compared with pre-experimental values, in bone resorption which was seen in the terminal ulna and iliac crest bone samples from all dogs. Serum immunoreactive parathyroid hormone was increased (compared with pre-experimental values) after 5 and 10 months of phosphate supplementation; this increase was related to the bone loss and the decrease in serum phosphate. Soft-tissue calcification could be demonstrated histologically in the kidney and in the lens of the eye where it resulted in cataracts. Calcium content increased in the thoracic aorta, kidney, heart, and tendon but not in skeletal muscle. Phosphate supplements in adult dogs appear to produce secondary hyperparathyroidism, bone loss, and calcification of soft tissues.
Sequence‐based prediction of pathological mutations (2004)

The development of methods to assess the impact of amino acid mutations on human health has become an important goal in biomedical research, due to the growing number of nonsynonymous SNPs identified. Within this context, computational methods constitute a valuable tool, because they can easily process large amounts of mutations and give useful, almost cost-free, information on their pathological character. In this paper we present a computational approach to the prediction of disease-associated amino acid mutations, using only sequence-based information (amino acid properties, evolutionary information, secondary structure and accessibility predictions, and database annotations) and neural networks, as a model building tool. Mutations are predicted to be either pathological or neutral. Our results show that the method has a good overall success rate, 83%, that can reach 95% when trained for specific proteins. The methodology is fast and flexible enough to provide good estimates of the pathological character of large sets of nonsynonymous SNPs, but can also be easily adapted to give more precise predictions for proteins of special biomedical interest.
A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae (2002)

A high-density transposon mutagenesis strategy was applied to the Haemophilus influenzae genome to identify genes required for growth or viability. This analysis detected putative essential roles for the products of 259 ORFs of unknown function. Comparisons between complete genomes defined a subset of these proteins in H. influenzae having homologs in Mycobacterium tuberculosis that are absent in Saccharomyces cerevisiae, a distribution pattern that favors their use in development of antimicrobial therapeutics. Three genes within this set are essential for viability in other bacteria. Interfacing the set of essential gene products in H. influenzae with the distribution of homologs in other microorganisms can detect components of unrecognized cellular pathways essential in diverse bacteria. This genome-scale phenotypic analysis identifies potential roles for a large set of genes of unknown function.
A simple microfluidic system for efficient capillary electrophoretic separation and sensitive fluorimetric detection of DNA fragments using light‐emitting diode and liquid‐core waveguide techniques (2005)

A miniaturized CE system has been developed for fast DNA separations with sensitive fluorimetric detection using a rectangle type light-emitting diode (LED). High sensitivity was achieved by combining liquid-core waveguide (LCW) and lock-in amplification techniques. A Teflon AF-coated silica capillary on a compact 6x3 cm baseplate served as both the separation channel for CE separation and as an LCW for light transmission of fluorescence emission to the detector. An electronically modulated LED illuminated transversely through a 0.2 mm aperture, the detection point on the LCW capillary without focusing, and fluorescence light was transmitted to the capillary outlet. To simplify the optics and enhance collection of light from the capillary outlet, an outlet reservoir was designed, with a light transmission window, positioned directly in front of a photomultiplier tube (PMT), separated only by a high pass filter. Automated sample introduction was achieved using a sequential injection system through a split-flow interface that allowed effective release of gas bubbles. In the separation of a phiX174 HaeIII DNA digest sample, using ethidium bromide as labeling dye, all 11 fragments of the sample were effectively resolved in 400 s, with an S/N ratio comparable to that of a CE system with more sophisticated LIF.
The effects of nitric oxide synthase--versus lipoxygenase inhibition on coronary flow and nitrite outflow in isolated rat heart. (2005)

The aim of this study was to assess the changes of coronary flow (CF) and nitrite outflow under inhibition of nitric oxide synthase (NOS) by Nomega-nitro-L-arginine monomethyl ester (L-NAME) or lipoxygenase (LOX) induced by nordihydroguaiaretic acid (NDGA) in isolated rat heart. The hearts of male Wistar albino rats (n=18, age 8 weeks, body mass 180-200 g) were retrograde perfused according to the Langendorff's technique at gradually increased constant coronary perfusion pressure (CPP) conditions (40-120 cm H2O) which induced flow-dependent nitric oxide (NO) release (nitrite outflow). The experiments were performed during control conditions, in the presence of NO synthesis inhibitor L-NAME (30 micromol/l) or nonspecific LOX inhibitor (NDGA, 0.1 mmol/l) which were administered separately or in combination. CF varied in autoregulatory range from 4.12+/-0.26 ml/min/g wt at 50 cm H2O to 5.22+/-0.26 ml/min/g wt at 90 cm H2O. In autoregulatory range, nitrite outflow varied from 2.05+/-0.17 nmol/min/g wt at 50 cm H2O to 2.52+/-0.21 nmol/min/g wt at 90 cm H2O and was strictly parallel with CPP/CF curve. The autoregulatory range of CF was significantly extended (40-100 cm H2O, 2.22+/-0.12 ml/min/g wt and 2.90+/-0.25 ml/min/g wt, respectively) under the influence of L-NAME. Hemodynamic effects were accompanied by significant decrease in nitrite outflow after L-NAME administration (0.56+/-0.11 nmol/min/g wt at 40 cm H2O to 1.45+/-0.14 nmol/min/g wt at 100 cm H2O). NDGA affected CF in the range of CPP 40-70 cm H2O only (from 42% at 50 cm H2O to 12% at 90 cm H2O, respectively) with no significant changes in nitrite outflow. When L-NAME was applied in combination with NDGA vs. NDGA only, CF was significantly reduced (from 34% at 50 cm H2O to 50% at 90 cm H2O, respectively) with parallel changes in nitrite outflow (from 40% at 50 cm H2O to 51% at 90 cm H2O, respectively). The results showed that CF and nitrite outflow could be decreased under L-NAME administration. Nonselective LOX inhibitor (NDGA) decreased control values of CF only at lower values of CPP but did not change nitrite outflow indicating antioxidant properties of NDGA. In addition, L-NAME decreased the effects induced by NDGA on CF and nitrite outflow indicating the role of NO.
Nomenclature of Proteins of Cow's Milk: Fifth Revision (1984)

This report reviews changes the nomenclature of bovine milk proteins necessitated by recent advances of our knowledge. Identification of a number of milk proteins (as1-, /~-, and K-caseins; alactalbumin and/3-1actoglcbulin) continues to be based upon their primary structures (amino acid sequences). Since our last report, as2-casein and serum albumin can be added to the list of major milk proteins
Characterization of metabolites of the chemopreventive agent curcumin in human and rat hepatocytes and in the rat in vivo, and evaluation of their ability to inhibit phorbol ester-induced prostaglandin E2 production. (2001)

Curcumin, the yellow pigment in turmeric, has been shown to prevent malignancies in a variety of tissues in rodents, especially in the intestinal tract. Pharmacological activities of curcumin in cells in situ germane to chemoprevention, such as inhibition of expression of cyclooxygenase-2 (COX-2), require drug concentrations in the 10(-5) - 10(-4) M range. The systemic bioavailability of curcumin is low, so that its pharmacological activity may be mediated, in part, by curcumin metabolites. To investigate this possibility, we compared curcumin metabolism in human and rat hepatocytes in suspension with that in rats in vivo. Analysis by high-performance liquid chromatography with detection at 420 and 280 nm permitted characterization of metabolites with both intact diferoylmethane structure and increased saturation of the heptatrienone chain. Chromatographic inferences were corroborated by mass spectrometry. The major metabolites in suspensions of human or rat hepatocytes were identified as hexahydrocurcumin and hexahydrocurcuminol. In rats, in vivo, curcumin administered i.v. (40 mg/kg) disappeared from the plasma within 1 h of dosing. After p.o. administration (500 mg/kg), parent drug was present in plasma at levels near the detection limit. The major products of curcumin biotransformation identified in rat plasma were curcumin glucuronide and curcumin sulfate whereas hexahydrocurcumin, hexahydrocurcuminol, and hexahydrocurcumin glucuronide were present in small amounts. To test the hypothesis that curcumin metabolites resemble their progenitor in that they can inhibit COX-2 expression, curcumin and four of its metabolites at a concentration of 20 microM were compared in terms of their ability to inhibit phorbol ester-induced prostaglandin E2 (PGE2) production in human colonic epithelial cells. Curcumin reduced PGE2 levels to preinduction levels, whereas tetrahydrocurcumin, previously shown to be a murine metabolite of curcumin, hexahydrocurcumin, and curcumin sulfate, had only weak PGE2 inhibitory activity, and hexahydrocurcuminol was inactive. The results suggest that (a) the major products of curcumin biotransformation by hepatocytes occur only at low abundance in rat plasma after curcumin administration; and (b) metabolism of curcumin by reduction or conjugation generates species with reduced ability to inhibit COX-2 expression. Because the gastrointestinal tract seems to be exposed more prominently to unmetabolized curcumin than any other tissue, the results support the clinical evaluation of curcumin as a colorectal cancer chemopreventive agent.
Effect of the sun on visible clinical signs of aging in Caucasian skin (2013)

Clinical signs of aging are essentially influenced by extrinsic factors, especially sun exposure. Indeed UV exposure seems to be responsible for 80% of visible facial aging signs.
HUMAN TUMOR SUPPRESSOR GENES (1990)

We have made rapid progress in recent years in identifying the genetic causes of many human diseases. However, despite this recent progress, our mechanistic understanding of these diseases is often incomplete. This is a problem because it limits our ...Read More
Simultaneous optical monitoring and fiber supervising for WDM networks using an OTDR combined with concatenated fiber gratings (2001)

We have proposed a new optical monitoring technique that employs an optical time-domain reflectometer combined with an acoustooptic switch and concatenated fiber Bragg gratings to achieve simultaneous optical monitoring and fiber surveillance for wavelength-division-multiplexed (WDM) networks. The optical power monitoring with dynamic range of 26 dB and accuracy /spl les//spl plusmn/0.1 dB for each WDM channel and the feasibility of simultaneous optical monitoring and fiber surveillance in WDM networks have also been demonstrated by using this technique.
Hypoxia upregulates von Hippel-Lindau tumor-suppressor protein through RhoA-dependent activity in renal cell carcinoma (2004)

A key task for the multifunctional von Hippel-Lindau protein (pVHL) is regulation of the activity of hypoxia-inducible factor-1alpha (HIF-1alpha) by targeting it to the proteasome for degradation under normoxia. pVHL binding to HIF-1alpha is lost under low O2 tension, leading to transcription of several genes involved in the hypoxia response. However, regulation of pVHL by hypoxia remains to be investigated. We evaluated the effects of hypoxia on pVHL expression in carcinoma and endothelial cells. We showed that hypoxia stimulates pVHL levels (2.5-fold) in renal Caki-1 cells expressing wild-type VHL (VHL+/+). This upregulation was independent of VHL status, because hypoxia also increased pVHL expression in renal 786-O cells carrying mutated VHL (VHL-/-). Hypoxia did not affect pVHL expression in endothelial cells. Hypoxia-induced pVHL in Caki-1 cells was RhoA dependent, because inhibition by exotoxin C3 prevented pVHL stimulation. Furthermore, inhibition of Rho kinase by Y-27632 blocked pVHL induction by hypoxia. During normoxia, pVHL expression was also induced in cells transfected with dominant-active RhoA. Furthermore, disruption of actin organization by chemical agents or by hypoxia stimulated pVHL expression in kidney cells. On the other hand, inhibition of MAP kinases p38 and JNK, but not MAP kinase kinase (MEK1/2), reduced pVHL upregulation by 30 and 72%, respectively, during hypoxia, supporting a significant role for these signaling pathways. Expression and phosphorylation of c-Jun were stimulated in cells transfected with dominant-active RhoA. Together, these findings demonstrate that hypoxia induces pVHL expression in renal cancer cells, and this induction is mediated by RhoA-dependent pathways.
Effect of dietary energy level and oil source on broiler performance and response to an inflammatory challenge (1998)

Broiler chicks were fed one of five diets from 3 d of age: a low energy diet containing 7% cellulose (ME 2,714 kcal/kg), or high energy diets containing approximately 7% of either tallow, corn oil, safflower oil, or fish oil (each 3,302 kcal/kg). Half of the chicks were injected intra-abdominally with Salmonella typhimurium lipopolysaccharide (LPS) on Day 11, sephadex on Day 13, and Freund's complete adjuvant on Day 15; samples were collected on Day 16. The uninjected chicks served as controls. In a second experiment, 3-d-old chicks were fed one of eight isocaloric diets containing tallow as the sole supplemental fat source, or tallow plus either 2% corn oil, 1, 1.5, or 2% fish oil, or fish meal at an amount to provide 1, 1.5 or 2% supplemental oil. Half of the chicks were injected intra-abdominally with S. typhimurium LPS on Days 10, 12 and 14; the uninjected chicks served as controls. Samples were taken on Day 15. In Experiment 1, the cellulose diet decreased performance to 10 d of age relative to the other diets, whereas immunogen injection decreased weight gain and feed efficiency and increased indices of inflammation among all dietary groups. Fish oil at approximately 7% of the diet did not improve weight gain. Fish oil diets improved weight gain and feed efficiency in Experiment 2 relative to the other diets, in spite of minimal effects on indices of inflammation. Injection of LPS decreased performance and increased inflammation across dietary treatment, although the second LPS injection was less potent in altering performance responses and inflammation compared to the first injection, indicating that repeated injections of LPS amy cause the chicks to become refractory to that stimulus. The fish meal diets resulted in poorer performance than similar levels of lipid provided as fish oil. Lower levels of dietary fish oil were more efficacious in improving broiler performance than higher levels, and fish oil provided from fish meal was not as efficacious as oil per se, possibly due to nonlipid components of the meal.
Multiplexed direct genomic selection (MDiGS): a pooled BAC capture approach for highly accurate CNV and SNP/INDEL detection (2014)

Despite declining sequencing costs, few methods are available for cost-effective single-nucleotide polymorphism (SNP), insertion/deletion (INDEL) and copy number variation (CNV) discovery in a single assay. Commercially available methods require a high investment to a specific region and are only cost-effective for large samples. Here, we introduce a novel, flexible approach for multiplexed targeted sequencing and CNV analysis of large genomic regions called multiplexed direct genomic selection (MDiGS). MDiGS combines biotinylated bacterial artificial chromosome (BAC) capture and multiplexed pooled capture for SNP/INDEL and CNV detection of 96 multiplexed samples on a single MiSeq run. MDiGS is advantageous over other methods for CNV detection because pooled sample capture and hybridization to large contiguous BAC baits reduces sample and probe hybridization variability inherent in other methods. We performed MDiGS capture for three chromosomal regions consisting of ∼ 550 kb of coding and non-coding sequence with DNA from 253 patients with congenital lower limb disorders. PITX1 nonsense and HOXC11 S191F missense mutations were identified that segregate in clubfoot families. Using a novel pooled-capture reference strategy, we identified recurrent chromosome chr17q23.1q23.2 duplications and small HOXC 5' cluster deletions (51 kb and 12 kb). Given the current interest in coding and non-coding variants in human disease, MDiGS fulfills a niche for comprehensive and low-cost evaluation of CNVs, coding, and non-coding variants across candidate regions of interest.