gebhart/patrepeval huggingface dataset:
Characterization of proteoglycans synthesized by murine embryonal carcinoma cells (P19) reveals increased expression of perlecan (heparan sulfate proteoglycan) during neuronal differentiation (1994)

Proteoglycans (PGs) incorporated into cell layer and secreted into media were characterized during retinoic acid-induced neuronal differentiation of cultured P19 murine embryonal carcinoma cells. Heparan sulfate significantly increased (P < 0.01) in cell layer following neuronal differentiation of P19 cells by 3.9-fold. CL-4B gel chromatography revealed the major PGs present in cell layer of stem cells eluted as a broad peak with a Kav = 0.65, and was susceptible to chondroitin ABC lyase. The chondroitin ABC lyase resistant material eluted as a broad peak between Kav = 0.40 and Kav = 0.60, and was only partially digested with heparitinase/heparinase (with resistant material eluting at Kav = 0.70). Therefore, the cell layer of stem cells contained primarily chondroitin sulfate/dermatan sulfate (CS/DS) PGs, with lesser amounts of heparan sulfate proteoglycans (HSPGs). This was confirmed by SDS-PAGE. The CS/DS PGs in the cell layer of stem cells had an apparent M(r) of approximately > 200 kDa, and the HSPGs had an apparent M(r) of approximately 140-230 kDa. In contrast, the major PGs in the cell layer of neurons consisted primarily of HSPGs, with only a minor proportion of CS/DS PGs. Furthermore, both gel filtration chromatography and SDS-PAGE analysis revealed a larger HSPG in the cell layer of neurons (Kav = 0.3-0.6 on CL-4B following chondroitin ABC lyase digestion; M(r) 170 kDa- > 400 kDa on SDS-PAGE) in comparison to stem cells (Kav = 0.4-0.6 on CL-4B following chondroitin ABC lyase digestion; M(r) 140-230 kDa on SDS-PAGE). Likewise, the major PGs secreted into media of stem cells consisted almost exclusively of CS/DS PGs, with lesser amounts of HSPGs, whereas an increase in HSPGs in the media of neurons was apparent. Western, Northern, and immunocytochemical analysis demonstrated that mRNA transcript and protein levels for a specific HSPG (i.e., perlecan) markedly increased in cell layer following P19 neuronal differentiation. Perlecan core protein was identified by Western blot analysis using specific monoclonal and polyclonal antibodies, as a large HSPG with a core protein of apparent M(r) approximately 370-400 kDa, and was observed primarily in extracts from neurons. Northern blot analysis with a cDNA to perlecan revealed a significant (P < 0.01) 12.7-fold increase in expression of perlecan in neurons (day 9) in comparison to stem cells. The increase in perlecan message during P19 neuronal differentiation was concomitant with a significant (P < 0.01) 26.3-fold increase in message for beta-amyloid precursor protein (beta PP).(ABSTRACT TRUNCATED AT 400 WORDS)
Amino acid sequence homology among the major outer membrane proteins of Escherichia coli. (1984)

Analysis of amino acid sequences reported for the major outer membrane proteins of Escherichia coli, including the porins (OmpF, OmpC, and PhoE), the phage lambda receptor (LamB), and another protein (OmpA), revealed several regions of local homology that is statistically significant. The implications of this observation are discussed in relation to the evolutionary origins of these proteins, as well as to the mechanism of export of these proteins to the outer membrane.
A neural network approach to the detection of incipient faults on power distribution feeders (1990)

A neural network strategy for the detection of high-impedance faults on electric power distribution feeders is described. This approach consists of collecting samples of substation current during normal and abnormal feeder operation and using these samples to teach a neural network the rules for fault detection. The learning capability utilized in a neural network approach makes it possible to adapt partially trained fault detectors to individual feeders. The data preprocessing required to set up the training cases and the implementation of the neural network itself are described in detail. the potential of the neural network approach is demonstrated by applying the detection scheme to high-impedance faults simulated on a model distribution system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Transplantation of Human Mesenchymal Stems Cells Into Intervertebral Discs in a Xenogeneic Porcine Model (2009)

hMSCs survive in the porcine disc for at least 6 months and express typical chondrocyte markers suggesting differentiation toward disc-like cells. As in autologous animal models the combination with a three-dimensional-hydrogel carrier seems to facilitate differentiation and survival of MSCs in the disc. Xenotransplantation seems to be valuable in evaluating the possibility for human cell therapy treatment for intervertebral discs.
An associative logic matrix (1976)

While retaining the regular interconnection structure of read-only memory and programmable logic array devices, associative logic makes possible the efficient realization of multiple output, multilevel, combinational, and sequential networks. The extreme versatility of associative logic is provided by internal feedback and matrix segmentation, both characteristic features of the new device. Internal feedback permits networks to be realized in two or more logic levels without the need for external output-input connections. It also makes practical the formation of memory circuits within the matrix. Segmentation permits formation of collinear but functionally independent line segments, thereby improving the areal efficiency of monolithic devices. Consideration of associative logic proceeds from a review of logic implementation by means of memory devices and concludes with a description of an associative logic device developed using bipolar technology.
Microfluidic titer plate for stratified 3D cell culture (2013)

Human tissues and organs are inherently heterogeneous. Their functionality is determined by the interplay between different cell types, their secondary architecture, vascular system and gradients of signaling molecules and metabolites. Here we propose a stratified 3D cell culture platform, in which adjacent lanes of gels and liquids are patterned by phaseguides to capture this tissue heterogeneity. We demonstrate 3D cell culture of HepG2 hepatocytes under continuous perfusion, a rifampicin toxicity assay and co-culture with fibroblasts. 4T1 breast cancer cells are used to demonstrate invasion and aggregation models. The platform is incorporated in a microtiter plate format that renders it fully compatible with automation and high-content screening equipment. The extended functionality, ease of handling and full compatibility to standard equipment is an important step towards adoption of Organ-on-a-Chip technology for screening in an industrial setting.
Circulating levels of interleukin-6 in patients with hormone refractory prostate cancer (1999)

Serum IL-6 levels are significantly elevated in hormone-refractory prostate cancer patients and may be a surrogate marker of the androgen independent phenotype.
Peptide Hormone Covalently Bound to Polyelectrolytes and Embedded into Multilayer Architectures Conserving Full Biological Activity (2001)

We report the development of new bioactive coatings of biomaterials based on the alternate deposition of oppositely charged polyelectrolytes. We selected polylysine (PLL) and poly(glutamic acid) (PGA) for the polyelectrolytes and murine melanoma cells as a biological test model system. These cells respond specifically to a small peptide hormone, alpha-melanocortin, which is a potent stimulator of melanogenesis. We show that a synthetic alpha-melanocortin derivative, covalently coupled to PLL forming the outer layer of a multilayer film remains as biologically active as the free hormone. Furthermore, the long time activity of the hormone is maintained when embedded in multilayer architectures whereas its short time activity depends on integration depth. The embedding of bioactive molecules not only anchors them irreversibly on the biomaterial, but opens also the possibility to control their activity. In comparison to conventional coating methods, polyelectrolyte multilayers are easy to prepare and retain their biological activity after storage as dry material. These very flexible systems allow broad medical applications for implant and tissue engineering.
Inhibitor‐induced structural change of the active site of human poly(ADP‐ribose) polymerase (2003)

The crystal structure of human recombinant poly(ADP-ribose) polymerase (PARP) complexed with a potent inhibitor, FR257517, was solved at 3.0 A resolution. The fluorophenyl part of the inhibitor induces an amazing conformational change in the active site of PARP by motion of the side chain of the amino acid, Arg878, which forms the bottom of the active site. Consequently, a corn-shaped hydrophobic subsite, which consists of the side chains of Leu769, Ile879, Pro881, and the methylene chain of Arg878, newly emerges from the well-known active site.
Sucrose biosynthesis in a prokaryotic organism: Presence of two sucrose-phosphate synthases in Anabaena with remarkable differences compared with the plant enzymes (1996)

Biosynthesis of sucrose-6-P catalyzed by sucrose-phosphate synthase (SPS), and the presence of sucrose-phosphate phosphatase (SPP) leading to the formation of sucrose, have both been ascertained in a prokaryotic organism: Anabaena 7119, a filamentous heterocystic cyanobacterium. Two SPS activities (SPS-I and SPS-II) were isolated by ion-exchange chromatography and partially purified. Four remarkable differences between SPSs from Anabaena and those from higher plants were shown: substrate specificity, effect of divalent cations, native molecular mass, and oligomeric composition. Both SPS-I and SPS-II accept Fru-6-P (K(m) for SPS-I = 0.8 +/- 0.1 mM; K(m) for SPS-II = 0.7 +/- 0.1 mM) and UDP-Glc as substrates (K(m) for SPS-I = 1.3 +/- 0.4 mM; K(m) for SPS-II = 4.6 +/- 0.4 mM), but unlike higher plant enzymes, they are not specific for UDP-Glc. GDP-Glc and TDP-Glc are also SPS-I substrates (K(m) for GDP-Glc = 1.2 +/- 0.2 mM and K(m) for TDP-Glc = 4.0 +/- 0.4 mM), and ADP-Glc is used by SPS-II (K(m) for ADP-Glc = 5.7 +/- 0.7 mM). SPS-I has an absolute dependence toward divalent metal ions (Mg2+ or Mn2+) for catalytic activity, not found in plants. A strikingly smaller native molecular mass (between 45 and 47 kDa) was determined by gel filtration for both SPSs, which, when submitted to SDS/PAGE, showed a monomeric composition. Cyanobacteria are, as far as the authors know, the most primitive organisms that are able to biosynthesize sucrose as higher plants do.
High-Throughput Quantitative Polymerase Chain Reaction in Picoliter Droplets (2008)

Limiting dilution PCR has become an increasingly useful technique for the detection and quantification of rare species in a population, but the limit of detection and accuracy of quantification are largely determined by the number of reactions that can be analyzed. Increased throughput may be achieved by reducing the reaction volume and increasing processivity. We have designed a high-throughput microfluidic chip that encapsulates PCR reagents in millions of picoliter droplets in a continuous oil flow. The oil stream conducts the droplets through alternating denaturation and annealing zones, resulting in rapid (55-s cycles) and efficient PCR amplification. Inclusion of fluorescent probes in the PCR reaction mix permits the amplification process to be monitored within individual droplets at specific locations within the microfluidic chip. We show that amplification of a 245-bp adenovirus product can be detected and quantified in 35 min at starting template concentrations as low as 1 template molecule/167 droplets (0.003 pg/microL). The frequencies of positive reactions over a range of template concentrations agree closely with the frequencies predicted by Poisson statistics, demonstrating both the accuracy and sensitivity of this platform for limiting dilution and digital PCR applications.
High Pressure Refolding of Recombinant Human Growth Hormone from Insoluble Aggregates (2001)

Two different types of insoluble, non-native aggregates of recombinant human growth hormone were formed by agitation in buffer or buffer containing 0.75 m guanidine HCl (GdnHCl) and characterized by infrared and second derivative UV spectroscopies. The degree of secondary structural perturbation was greater in the aggregates formed in 0.75 m GdnHCl. Both aggregate types were dissolved and refolded using high hydrostatic pressures in combination with either elevated temperature or non-denaturing levels of guanidine HCl or urea. The effects of a range of temperature, pressure, and chaotrope concentrations were tested and led to optimal conditions that approached 100% yield of native protein. The aggregates formed in 0.75 m GdnHCl required higher concentrations of urea or GdnHCl, or higher temperature or pressure for a yield equivalent to that for aggregates formed in buffer alone. Investigation of the effects of pressure, temperature, and chaotrope on unfolding of rhGH documented that under conditions used for optimal high pressure disaggregation and refolding, the native state is greatly favored thermodynamically (e.g. 25 kJ/mol at 2000 bar and 0.75 m GdnHCl). Dissolution of aggregates under pressure is a kinetically limited process. Comparison of refolding yields in GdnHCl and urea solutions suggest that pressure effects on electrostatic interactions do not dominate pressure effects on disaggregation. We suggest that non-native hydrogen bonds between protein molecules within aggregates of recombinant human growth hormone are responsible for the rate-limiting kinetic barrier in pressure-induced disaggregation.
The Effect of Relaxin on Tissue Expansion (1992)

Relaxin is a 56-amino acid polypeptide that produces relaxation of the pubic ligament. Ten young male pigs were implanted with tissue expanders and osmotic pumps. The pumps in five animals contained recombinant human relaxin to produce a serum relaxin level of 1 ng/mL. The other five pumps contained saline. Repeated measurements of the pressure-volume expansion curves showed a significant decrease in the pressure needed to fill the expanders in the relaxin group compared with the control group. Dermal thickness in the control group and epidermal thickness in both control and experimental groups were increased on histomorphometric measurement. No adverse effects were seen in the relaxin group. Relaxin facilitates tissue expansion in pigs without affecting dermal thickness.
Lensless high-resolution on-chip optofluidic microscopes for Caenorhabditis elegans and cell imaging (2008)

Low-cost and high-resolution on-chip microscopes are vital for reducing cost and improving efficiency for modern biomedicine and bioscience. Despite the needs, the conventional microscope design has proven difficult to miniaturize. Here, we report the implementation and application of two high-resolution (approximately 0.9 microm for the first and approximately 0.8 microm for the second), lensless, and fully on-chip microscopes based on the optofluidic microscopy (OFM) method. These systems abandon the conventional microscope design, which requires expensive lenses and large space to magnify images, and instead utilizes microfluidic flow to deliver specimens across array(s) of micrometer-size apertures defined on a metal-coated CMOS sensor to generate direct projection images. The first system utilizes a gravity-driven microfluidic flow for sample scanning and is suited for imaging elongate objects, such as Caenorhabditis elegans; and the second system employs an electrokinetic drive for flow control and is suited for imaging cells and other spherical/ellipsoidal objects. As a demonstration of the OFM for bioscience research, we show that the prototypes can be used to perform automated phenotype characterization of different Caenorhabditis elegans mutant strains, and to image spores and single cellular entities. The optofluidic microscope design, readily fabricable with existing semiconductor and microfluidic technologies, offers low-cost and highly compact imaging solutions. More functionalities, such as on-chip phase and fluorescence imaging, can also be readily adapted into OFM systems. We anticipate that the OFM can significantly address a range of biomedical and bioscience needs, and engender new microscope applications.
BDNF rescues myosin heavy chain IIB muscle fibers after neonatal nerve injury (2004)

Neonatal sciatic nerve injury is known to result in an extensive loss of lumbar motor neurons as well as the disappearance of their respective muscle fibers in the hindlimb musculature. The loss of motor neurons and muscle fibers can be prevented by immediate administration of target-derived neurotrophic factors to the site of injury. In the present study, we investigated the role of ciliary neurotrophic factor (CNTF) and brain-derived neurotrophic factor (BDNF) in the survival and maturation of a subset of motor neurons innervating the extensor digitorum longus (EDL) and tibialis anterior (TA) muscles. We have shown that combined administration of CNTF and BDNF prevented the loss of motor units after neonatal nerve injury and contributed to the maintenance of muscle mass. Importantly, this combined neurotrophin regimen also prevented the disappearance of muscle fibers that express myosin heavy chain IIB (MyHC IIB) in both EDL and TA muscles 3 mo after neonatal sciatic nerve crush. In parallel studies, we observed a higher level of BDNF in EDL muscle during the critical period of development when motor neurons are highly susceptible to target removal. Given our previous findings that combined administration of CNTF with neurotrophin-3 (NT-3) or neurotrophin-4/5 (NT-4/5) did not result in the rescue of MyHC IIB fibers in EDL, the present results show the importance of muscle-derived BDNF in the survival and maturation of a subpopulation of motor neurons and of MyHC IIB muscle fibers during neonatal development of the neuromuscular system.
Lipid X protects mice against fatal Escherichia coli infection (1988)

Lipid X, the major monosaccharide precursor of lipid A, is nontoxic and has previously been shown to protect mice and sheep from the harmful effects of endotoxin. To test the hypothesis that lipid X could be therapeutic against infections with gram-negative organisms, neutropenic ICR mice were infected by intramuscular inoculation of Escherichia coli and subsequently treated with lipid X alone or in combination with the antibiotic ticarcillin. Lipid X slightly prolonged survival; treated mice had a significantly improved rate of survival 18 h after intramuscular inoculation as compared with controls (P less than 0.025). By 24 h, however, this difference disappeared. When lipid X was combined with ticarcillin, survival differences were both significant and prolonged. Treatment of mice with one to two doses of lipid X for a total dose of 1 mg intravenously and with 1,200 mg of ticarcillin per kg every 6 h improved survival over a 48-h treatment period from 5 to 23% (P less than 0.0025). Treatment with lipid X and ticarcillin over a broad range of antibiotic dosages in 362 mice demonstrated improved survival of two- to fourfold (P less than 0.0001 at 24 h after inoculation, P less than or equal to 0.0005 at 48 h, and P less than or equal to 0.0001 at 5 days). Lipid X enabled the dose of ticarcillin necessary to protect 50% of mice from death to be reduced by two- to fivefold. Pretreatment with lipid X was not necessary to improve survival: 16 of 17 (94%) infected and visibly ill animals that received lipid X and ticarcillin 6 h after thigh inoculation survived versus 30 of 44 (68%) control animals treated with ticarcillin alone (P less than 0.0001). Lipid X had no antimicrobial activity in vitro. Lipid X is a novel agent that enhances survival in an animal model of severe infection with gram-negative organisms.
A Randomized Trial of Itraconazole in Allergic Bronchopulmonary Aspergillosis (2000)

For patients with corticosteroid-dependent allergic bronchopulmonary aspergillosis, the addition of itraconazole can lead to improvement in the condition without added toxicity.
Frequency Selective Surfaces for High-Sensitivity Terahertz Sensors (2007)

We present a frequency selective surface (FSS) of asymmetric split-ring resonators for terahertz (THz) sensor applications. Multiple resonances of the rings combine to sharp edges in the FSS's frequency response to achieve high sensitivity.
Plasma Autoantibodies Associated with Basal-like Breast Cancers (2015)

Our study identifies 13 AAb markers associated specifically with BLBC and may improve detection or management of this deadly disease.
A General Method for the Preparation of Chiral TREN Derivatives (2005)

Abstract A general procedure for the preparation of C 3 ‐symmetric TREN derivatives with backbone chirality has been developed. Stereo‐ and regioselective ring opening by ammonia of ( S )‐ N ‐tosyl‐2‐isopropylaziridine, obtained starting from either the corresponding amino alcohol or amino acid, followed by deprotection of the amino groups afforded the parent chiral TREN compound in high overall yield. In addition to TREN compounds with primary amino groups, the synthetic method employed provides easy access to a variety of N , N' , N'' ‐substituted derivatives. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Organocatalytic Preparation of Simple β-Hydroxy and β-Amino Esters: Low Catalyst Loadings and Gram-Scale Synthesis (2010)

A combined amino- and N-heterocyclic carbene (NHC)-catalyzed one-pot reaction sequence for the synthesis of simple enantioenriched β-hydroxy and β-amino esters using commercially available catalysts at low catalyst loadings has been developed. The desired products were obtained in high yield and excellent enantiopurity. The generation of quaternary stereocenters and application in gram-scale synthesis were also realized, with no requirements of inert or anhydrous reaction conditions, thus making this transformation a highly practical protocol.
Intron Loss and Gain During Evolution of the Catalase Gene Family in Angiosperms (1998)

Angiosperms (flowering plants), including both monocots and dicots, contain small catalase gene families. In the dicot, Arabidopsis thaliana, two catalase (CAT) genes, CAT1 and CAT3, are tightly linked on chromosome 1 and a third, CAT2, which is more similar to CAT1 than to CAT3, is unlinked on chromosome 4. Comparison of positions and numbers of introns among 13 angiosperm catalase genomic sequences indicates that intron positions are conserved, and suggests that an ancestral catalase gene common to monocots and dicots contained seven introns. Arabidopsis CAT2 has seven introns; both CAT1 and CAT3 have six introns in positions conserved with CAT2, but each has lost a different intron. We suggest the following sequence of events during the evolution of the Arabidopsis catalase gene family. An initial duplication of an ancestral catalase gene gave rise to CAT3 and CAT1. CAT1 then served as the template for a second duplication, yielding CAT2. Intron losses from CAT1 and CAT3 followed these duplications. One subclade of monocot catalases has lost all but the 5'-most and 3'-most introns, which is consistent with a mechanism of intron loss by replacement of an ancestral intron-containing gene with a reverse-transcribed DNA copy of a fully spliced mRNA. Following this event of concerted intron loss, the Oryza sativa (rice, a monocot) CAT1 lineage acquired an intron in a novel position, consistent with a mechanism of intron gain at proto-splice sites.