gebhart/patrepeval huggingface dataset:
Generation of Fluorescent IgG Fusion Proteins in Mammalian Cells (2012)

The generation of recombinantly produced fluorescent antibody derivatives that are derived from full-length immunoglobulin G (IgG) has until now been problematic. One major reason for that lies in different and partially incompatible secretion- and folding-requirements of antibodies and green fluorescent protein (GFP) derived fluorescent entities in mammalian cells. The use of citrine as fluorescent fusion entity can overcome this limitation. Citrine is a modified yellow fluorescent protein (YFP) derivative which in contrast to GFP and yellow fluorescent protein (YFP) folds effectively and properly in the endoplasmic reticulum (ER) of mammalian cells. Provided that proper design parameters regarding fusion positions and linker/connector sequences are applied, citrine can be fused to different positions of IgGs and be expressed without interfering with secretion capability or functionality of IgG-citrine derivatives. Because IgG-citrine fusions are stable and retain biophysical properties of IgGs, they can be expressed and purified in the same manner as regular antibodies. IgG-citrine fusions not only retain the binding properties (affinity and specificity) of antibodies but also contain Fc-regions (useful for immunoassay applications), and are fully defined molecules (in contrast to antibody conjugates with fluorophores).
Synthetic anti-BR3 antibodies that mimic BAFF binding and target both human and murine B cells (2006)

BR3, which is expressed on all mature B cells, is a specific receptor for the B-cell survival and maturation factor BAFF (B-cell-activating factor belonging to the tumor necrosis factor [TNF] family). In order to investigate the consequences of targeting BR3 in murine models and to assess the potential of BR3 antibodies as human therapeutics, synthetic antibody phage libraries were employed to identify BAFF-blocking antibodies cross-reactive to murine and human BR3, which share 52% identity in their extracellular domains. We found an antibody, CB1, which exhibits muM affinity for murine BR3 and very weak affinity for the human receptor. CB3s, an affinity-matured variant of CB1, has sub-nM affinity for BR3 from both species. Alanine scanning and crystallographic structural analysis of the CB3s/BR3 complex reveal that CB3s mimics BAFF by interacting with a similar region of the BR3 surface. Despite this similarity in binding epitopes, CB1 variants antagonize BAFF-dependent human B-cell proliferation in vitro and are effective at reducing murine B-cell populations in vivo, showing significant promise as therapeutics for human B-cell-mediated diseases.
Low Molecular Weight Heparin, Therapy With Dalteparin, and Survival in Advanced Cancer: The Fragmin Advanced Malignancy Outcome Study (FAMOUS) (2004)

Purpose In experimental systems, interference with coagulation can affect tumor biology. Furthermore, it has been suggested that low molecular weight heparin therapy may prolong survival in patients with cancer. The primary aim of this study was to assess survival at 1 year of patients with advanced cancer. Patients and Methods Patients with advanced malignancy (N = 385) were randomly assigned to receive either a once-daily subcutaneous injection of dalteparin (5,000 IU), a low molecular weight heparin, or placebo for 1 year. Results The Kaplan-Meier survival estimates at 1, 2, and 3 years after randomization for patients receiving dalteparin were 46%, 27%, and 21%, respectively, compared with 41%, 18%, and 12%, respectively, for patients receiving placebo (P = .19). In an analysis not specified a priori, survival was examined in a subgroup of patients (dalteparin, n = 55; and placebo, n = 47) who had a better prognosis and who were alive 17 months after randomization. In these patients, Kaplan-Meier survival estimates at 2 and 3 years from randomization were significantly improved for patients receiving dalteparin versus placebo (78% v 55% and 60% v 36%, respectively, P = .03). The rates of symptomatic venous thromboembolism were 2.4% and 3.3% for dalteparin and placebo, respectively, with bleeding rates of 4.7% and 2.7%, respectively. Conclusion Dalteparin administration did not significantly improve 1-year survival rates in patients with advanced malignancy. However, the observed improved survival in a subgroup of patients with a better prognosis suggests a potential modifying effect of dalteparin on tumor biology.
Oxygen Doping Modifies Near-Infrared Band Gaps in Fluorescent Single-Walled Carbon Nanotubes (2010)

Controlled chemical modifications of single-walled carbon nanotubes (SWCNTs) that tune their useful properties have been sought for multiple applications. We found that beneficial optical changes in SWCNTs resulted from introducing low concentrations of oxygen atoms. Stable covalently oxygen-doped nanotubes were prepared by exposure to ozone and then light. Treated samples showed distinct, structure-specific near-infrared fluorescence at wavelengths 10 to 15% longer than displayed by pristine semiconducting SWCNTs. Dopant sites harvest light energy absorbed in undoped nanotube regions by trapping mobile excitons. The oxygen-doped SWCNTs are much easier to detect and image than pristine SWCNTs because they give stronger near-infrared emission and do not absorb at the shifted emission wavelength.
Sequence and characterization of an Ehrlichia chaffeensis gene encoding 314 amino acids highly homologous to the NAD A enzyme (2006)

DNA sequence analysis of the nadA gene of Ehrlichia chaffeensis revealed a 942 bp open reading frame with the capacity to encode 314 amino acids. The amino acid sequence of the E. chaffeensis quinolinate synthetase A (NAD/A) has 53.6% identity and 82% similarity to the NAD A of the cyanelle of Cyanophora paradoxa. Portions of the homologous genes of E. canis and E. muris were also sequenced. The amino acid sequences of the NAD A of E. canis and E. muris have 89.2% and 93.2% homology, respectively, to the NAD A of E. chaffeensis. We propose that the nadA gene may be an excellent candidate for a genetic tool for the phylogenetic study of ehrlichiae.
Regeneration following spinal cord injury, from experimental models to humans: where are we? (2006)

Regeneration in the adult CNS following injury is extremely limited. Traumatic spinal cord injury causes a permanent neurological deficit followed by a very limited recovery due to failed regeneration attempts. In fact, it is now clear that the spinal cord intrinsically has the potential to regenerate, but cellular loss and the presence of an inhibitory environment strongly limit tissue regeneration and functional recovery. The molecular mechanisms responsible for failed regeneration are starting to be unveiled. This gain in knowledge led to the design of therapeutic strategies aimed to limit the tissue scar, to enhance the proregeneration versus the inhibitory environment, and to replace tissue loss, including the use of stem cells. They have been very successful in several animal models, although results are still controversial in humans. Nonetheless, novel experimental approaches hold great promise for use in humans.
Targeting Inhibitors of the Tumor Suppressor PP2A for the Treatment of Pancreatic Cancer (2014)

The PP2A inhibitors SET and CIP2A are overexpressed in human pancreatic cancer and are important for pancreatic cancer cell growth and transformation; thus, antagonizing SET and/or CIP2A may be an innovative approach for the treatment of human pancreatic cancer.
A review of anemia as a cardiovascular risk factor in patients with myelodysplastic syndromes. (2011)

Based upon a relatively small body of evidence, there appears to be a strong and clinically significant association between anemia and cardiovascular morbidity and mortality in MDS. While further research is needed, clinicians should seek to actively manage hemoglobin levels in MDS patients before the point of transfusion dependency is reached.
Attraction of polar bears Ursus maritimus to offshore drilling sites in the eastern Beaufort Sea (1988)

Abstract Wildlife observations recorded at several offshore hydrocarbon exploration sites in the Beaufort Sea were examined to evaluate the hypothesis that polar bears Ursus maritimus are attracted to drill rigs, will be judged to represent a threat to humans there, and consequently will have to be deterred or destroyed. When polar bears came south with the pack ice in the autumn, they approached drillships or artificial islands, probably because they became curious or were attracted by unfamiliar smells. However, these bears did not usually remain in the area. In late winter, when most of the natural leads are frozen, the movement of compacted annual ice from east to west past permanent offshore drill rigs creates open cracks on the downstream side. Because of the open water there, seals are more abundant, more accessible, or both, and bears are attracted because of better hunting conditions. In mid to late winter some bears may remain in the area for several days or longer while hunting seals. This positive reinforcement may lead these bears to be attracted to other offshore rigs in the future. In the last five years four bears attracted to offshore rigs have been shot; thus the hypothesis was found to be valid. To date, the population is not under threat, but this could change if the number of offshore drill rigs operating through the winter were to increase.
Potential Therapeutic Strategies for Alzheimer’s Disease Targeting or Beyondβ-Amyloid: Insights from Clinical Trials (2014)

Alzheimer's disease (AD) is a progressive neurodegenerative disorder with two hallmarks: β-amyloid plagues and neurofibrillary tangles. It is one of the most alarming illnesses to elderly people. No effective drugs and therapies have been developed, while mechanism-based explorations of therapeutic approaches have been intensively investigated. Outcomes of clinical trials suggested several pitfalls in the choice of biomarkers, development of drug candidates, and interaction of drug-targeted molecules; however, they also aroused concerns on the potential deficiency in our understanding of pathogenesis of AD, and ultimately stimulated the advent of novel drug targets tests. The anticipated increase of AD patients in next few decades makes development of better therapy an urgent issue. Here we attempt to summarize and compare putative therapeutic strategies that have completed clinical trials or are currently being tested from various perspectives to provide insights for treatments of Alzheimer's disease.
Roles of Specific Amino Acids in the N Terminus of Pseudomonas aeruginosa Flagellin and of Flagellin Glycosylation in the Innate Immune Response (2005)

ABSTRACT The Toll-like receptor 5 (TLR5) binding site has been predicted to be in the N terminus of the flagellin molecule. In order to better define the interaction between the N-terminal amino acids of Pseudomonas aeruginosa flagellin and TLR5, site-specific mutations were generated between residues 88 and 97 of P. aeruginosa PAK flagellin as well as outside of this region. The mutant flagellins were expressed in Escherichia coli BL21(plysS), purified by affinity chromatography, and passed through a polymyxin B column to remove contaminating lipopolysaccharide (LPS). Their ability to stimulate interleukin-8 (IL-8) release from A549 cells was examined. The cloned mutated genes were used to complement a PAK fliC mutant in order to test for effects on motility and on IL-8 release by purified flagellar preparations. All the mutations, single or double, in the predicted TLR5 binding region reduced IL-8 signaling to less than 95% of the wild-type flagellin levels, but the single mutation outside the binding region had no effect. Changes made at two amino acid sites resulted in loss/reduction of motility; however, changes made at single sites, i.e., Q83A, L88A, R90A, M91A, L94A, and Q97A, had no effect on motility. The mutated genes encoding two of the motile but poorly signaling flagellins had no compensatory mutations to allow motility. Thus, while it is speculated that pathogen-associated molecular patterns (PAMPs) have evolved in locations that are essential to maintain function, it appears that there is tolerance for at least single amino acid changes in the PAMP of P. aeruginosa flagellin. The purpose of flagellin glycosylation in P. aeruginosa is unknown. In order to examine its role, if any, in signaling an inflammatory response, we used whole flagella from the motile chromosomal mutant strains PAK rfbC and PAO1 rfbC , which are defective in flagellin glycosylation. IL-8 release from A549 cells stimulated with nonglycosylated flagellar preparations (having less then 1 picogram of LPS/μg) was significantly reduced compared to their respective wild-type flagellar preparations, indicating a role of flagellar glycosylation in the proinflammatory action of Pseudomonas flagellin. The basis of the latter activity is unknown, since the glycosylation sites are found in the D3 domain of flagellins and the TLR5 binding site is located in the D1 domain. Thus, P. aeruginosa flagellin has evolved additional flagellar signaling mechanisms over that described for Salmonella flagellin.
Derivation of Multipotent Mesenchymal Precursors from Human Embryonic Stem Cells (2005)

Our findings will help to elucidate the mechanism of mesoderm specification during embryonic stem cell differentiation and provide a platform to efficiently generate specialized human mesenchymal cell types for future clinical applications.
Output feedback control of a flexible robot arm (1986)

In this paper, a method is proposed to control a flexible robot arm by using a special output feedback control law based on the truncated model. The proposed method is simple and easy to implement, it is robust to modal truncation and to parameter variation. Numerical simulation shows that the performance of the arm is satisfactory.
Electrically tunable diffraction efficiency from gratings in Al-doped ZnO (2017)

Transparent conducting aluminum-doped zinc oxide (AZO) can be used as part of an active plasmonic device due to its electrically tunable permittivity, which is accomplished by changing the carrier concentration with electrical biasing. In this letter, we report a continuous electrical tuning of diffraction efficiency from AZO gratings in the visible range (specifically 532 nm) when the AZO is under bias voltages between −1 V and −3.5 V. The carrier concentration in AZO under negative bias has been measured and simulated. The diffraction efficiency changes have been explained by the carrier concentration variation and induced complex refractive index change at the Al2O3 and AZO interface. The reported results can lead toward the application of post-fabrication tuning of optoelectronic devices using AZO.
Gateway vectors for the production of combinatorially‐tagged His6‐MBP fusion proteins in the cytoplasm and periplasm of Escherichia coli (2005)

Many proteins that accumulate in the form of insoluble aggregates when they are overproduced in Escherichia coli can be rendered soluble by fusing them to E. coli maltose binding protein (MBP), and this will often enable them to fold in to their biologically active conformations. Yet, although it is an excellent solubility enhancer, MBP is not a particularly good affinity tag for protein purification. To compensate for this shortcoming, we have engineered and successfully tested Gateway destination vectors for the production of dual His6MBP-tagged fusion proteins in the cytoplasm and periplasm of E. coli. The MBP moiety improves the yield and solubility of its fusion partners while the hexahistidine tag (His-tag) serves to facilitate their purification. The availability of a vector that targets His6MBP fusion proteins to the periplasm expands the utility of this dual tagging approach to include proteins that contain disulfide bonds or are toxic in the bacterial cytoplasm.
Gamma-carboxyglutamate in a neuroactive toxin. (1984)

The venom of a fish-hunting cone snail (Conus geographus) contains a novel toxin, the "sleeper" peptide, which induces a sleep-like state in mice when injected intracerebrally. We demonstrate that this peptide contains 5 mol of gamma-carboxyglutamate (Gla) in 17 amino acids. The amino acid sequence of the sleeper peptide is Gly-Glu-Gla-Gla-Leu-Gln-Gla-Asn-Gln-Gla-Leu-Ile-Arg-Gla-Lys-Ser-Asn-NH2.
Importance of renal sympathetic tone in the development of DOCA-salt hypertension in the rat. (1980)

In many experimental models, acute increases in sympathetic nervous system activity produce disproportionately greater vasoconstriction in the renal vascular bed than occurs in most other vascular beds. Since increased sympathetic nervous system activity has been implicated in the pathogenesis of DOCA-salt hypertension in the rat, we hypothesized that an attenuation of renal sympathetic tone would delay the development of this form of hypertension. Renal denervation was carried out in 5-week-old uninephrectomized male Sprague-Dawley rats 1 week before beginning DOCA-salt treatment. Systolic blood pressures using the tailcuff method in 32 sham-operated rats were significantly (p less than 0.05) elevated above control by Day five (115 +/- 3 vs 128 +/- 3 mm Hg) of DOCA-salt administration and continued to rise, reaching a plateau by Day 21 (192 +/- 5 mm Hg). In contrast, DOCA-salt administration in 32 renal denervated rats did not result in a significant elevation of blood pressure above control until Day 17 (121 +/- 3 vs 135 +/- 3 mm Hg, p less than 0.05). During the first 2 weeks of DOCA-salt treatment, fractional urinary sodium excretion was significantly greater (p less than 0.05) in renal denervated rats than in sham animals. During the third week of DOCA-salt administration, renal denervated rats had a rapid rise in blood pressure and a fall in fractional urinary sodium excretion to the level of the sham-operated animals. Coincident with the development of hypertension was a threefold increase in renal norepinephrine content (5.3 +/- 0.4 ng/g on Day 14 vs 17.7 +/- 3.0 ng/g on Day 24, p less than 0.01), suggesting reinnervation. These data suggest that increased renal sympathetic tone in the DOCA-salt rat facilitates sodium retention and is necessary for the development of the hypertension.
Angiogenesis Inhibition and Tumor Regression Caused by Heparin or a Heparin Fragment in the Presence of Cortisone (1983)

Heparin or a heparin fragment administered with cortisone inhibited angiogenesis, caused regression of large tumor masses, and prevented metastases. Oral administration of heparin resulted in the release of non-anticoagulant heparin fragments in the serum which, in the presence of cortisone, had similar anti-angiogenic and antitumor effects. Of all the heparin fragments tested, the most potent inhibition of angiogenesis in the presence of cortisone was provided by a hexasaccharide with a molecular weight of about 1600.
Reverse blocking IGBT for matrix converter with ultra-thin wafer technology (2004)

A high performance vertical 600 V–50 A IGBT with reverse blocking capability (RB-IGBT) has been developed for the first time. Ultra-thin wafer technology combined with a deep boron diffusion technique results in a great improvement on trade-off performance. Two RB-IGBTs connected in anti-parallel form a bi-directional switch. These bi-directional switches are necessary to implement a high efficiency matrix converter.
Mechanisms of Electrode Induced Injury. Part 1: Theory (2006)

Electrodes are the essential elements of clinical neurophysiology both in recording of neural activity and in functional electrical stimulation of the nervous system. Therefore it is important to understand the potential complications of using electrodes. In this paper, the factors that influence the chance of electrode related injury are discussed from a theoretical standpoint. The mechanical factors, especially pressure related injury, are discussed first, followed by a discussion of injury that is of chemical origin such as contact dermatitis. Next, the ways in which electrical currents flowing from electrodes can cause injury including: Joule heating, electroporation, electroconformational denaturation, and excitatory neurotoxicity are discussed. The differential effects of constant current and constant voltage stimulation on tissue heating are examined, as are the effects of the conductivity and geometric structure of the stimulated tissue. Finally, the effects of electrochemical reactions are discussed both in the context of surface and implanted electrodes.
Interpenetrating Polymer Networks (1978)

Abstract Besides mechanical blending and copolymerization there is a third possible way in which two polymers can be combined. Each polymer forms its own network, while both networks interpenetrate each other. There are no covalent bonds between the polymers. Such interpenetrating networks have been synthesized sequentially (from polymer A and monomer B) and simultaneously (from monomer A and monomer B). It is preferable that the polymers be of different chemical type; usually, an elastomer and a glass are combined, e.g. a polyurethane and a polyacrylate. Depending upon the ratio of component polymers either a strengthened elastomer or a glass having impact strength is formed. So far, there are no direct methods for establishing the degree of interpenetration.
Powder Rolling of Carbon Nanotube-Reinforced Aluminium (2006)

Powder Rolling is a traditional technique for the fabrication of metal strips in which metal powder is continuously fed into a rolling mill and compacted into strip. Recently, carbon nanotubes (CNTs) have emerged as promising new materials with exceptional properties. This has stimulated interest in their use to reinforce polymer, and ceramic matrices. In spite of their potential technological importance, a few research groups have investigated their use to reinforce metal matrices. In this paper, the powder rolling technique is used for the first time to fabricate aluminium strips reinforced with carbon nanotubes. Mixtures of aluminium powder and various wt% catalytic multi-wall carbon nanotubes (MWCNT) were roll compacted and sintered to form thin strips. CNTs were observed to be aligned in the in-plane direction. Tension tests were conducted on the strips to investigate the effect of the carbon nanotubes on the mechanical properties. Although the yield strength for the 0.5 wt% CNT samples increased, the ultimate strength and strain-to-failure for all samples with CNT were mostly lower than the base metal. This was attributed to the observed clustering of the CNTs, especially in higher wt% CNT samples. Provided the CNT clustering problem is overcome, the process promises many advantages; namely, its low cost, the ease of incorporating the carbon nanotubes and the potential important applications for the carbon nanotube-metal strips.
Genetic variation in the 3’ untranslated region of dengue virus serotype 3 strains isolated from mosquitoes and humans in Brazil (2013)

The phylogeny based on the analysis of the complete genome and 3'UTR characterized the DENV-3 isolated from both vector and human host as belonging to Genotype III (GIII), despite the differences observed on the 3' UTR. Further studies are needed to address the role of those mutations in the transmission of the different viral populations and vector competence.