gebhart/patrepeval huggingface dataset:
Experimental evaluation of cryopreservative solutions to maintain in vitro and in vivo infectivity of P. berghei sporozoites (2017)

The rodent malaria parasite Plasmodium berghei is an excellent model organism for laboratory-based experimental evaluation of anti-malarial therapeutics prior to studies with human malaria parasites. The rodent model is especially important for evaluation of pre-erythrocytic (PE) stage therapies, especially as current efforts to develop new PE vaccines and drugs is limited by access to P. falciparum and P. vivax sporozoites. Developing a more effective method for cryopreservation of sporozoites would help improve access to sporozoites for laboratories lacking suitable insectary facilities. In this study, P. berghei GFP-expressing sporozoites were purified from infected mosquitoes by manual dissection of salivary glands and different commercially-available, serum-free cryopreservative solutions were evaluated for efficient cryopreservation of the sporozoites. The cryopreservative solutions evaluated included CryoStor CS2, CryoSolutions DX5, CryoSolutions MC, Hestar 200, Voluven, Hetastarch, and Glycerolyte 57. The viability of fresh and post-thaw cryopreserved sporozoites was determined as a function of the relative sporozoite infectivity by infecting HC-04 cells in vitro, monitoring invasion and growth and development of liver stage parasites. Flow cytometer-based counting provided unbiased and fast quantitative assessment of parasite in vitro infection in infected HC-04 and in vivo infectivity was validated by injecting sporozoites IV into mice. CryoStor CS2 delivered the highest post-thaw recovery and infectivity of cryopreserved sporozoites. Sporozoites cryopreserved in CryoStor CS2 achieved 38% complete development of hepatic stages in HC-04 and 100% infectivity in mice. The cryopreservation method described here demonstrates a viable alternative for fresh Plasmodium sporozoites. The use of cryopreserved sporozoites should facilitate greater access to sporozoites for chemotherapeutic and vaccine research.
Detection and Quantification of Cannabinoids in Extracts of Cannabis sativa Roots Using LC-MS/MS (2018)

A liquid chromatography-tandem mass spectrometry single-laboratory validation was performed for the detection and quantification of the 10 major cannabinoids of cannabis, namely, (-)-<i>trans</i>-Δ<sup>9</sup>-tetrahydrocannabinol, cannabidiol, cannabigerol, cannabichromene, tetrahydrocannabivarian, cannabinol, (-)-<i>trans</i>-Δ<sup>8</sup>-tetrahydrocannabinol, cannabidiolic acid, cannabigerolic acid, and Δ<sup>9</sup>-tetrahydrocannabinolic acid-A, in the root extract of <i>Cannabis sativa</i>. Acetonitrile : methanol (80 : 20, v/v) was used for extraction; d<sub>3</sub>-cannabidiol and d<sub>3</sub>- tetrahydrocannabinol were used as the internal standards. All 10 cannabinoids showed a good regression relationship with <i>r</i><sup>2</sup> > 0.99. The validated method is simple, sensitive, and reproducible and is therefore suitable for the detection and quantification of these cannabinoids in extracts of cannabis roots. To our knowledge, this is the first report for the quantification of cannabinoids in cannabis roots.
Synthesis and Performance of Acyloxy-diene-Fe(CO)<sub>3</sub> Complexes with Variable Chain Lengths as Enzyme-Triggered Carbon Monoxide-Releasing Molecules (2013)

Novel η4-acyloxy-cyclohexadiene-Fe(CO)3 complexes (with variable length of the acyloxy chain) were synthesized as potential enzyme-triggered carbon monoxide (CO)-releasing molecules (ET-CORMs). The molecular structure of two complexes was additionally confirmed by X-ray crystallography. The enzyme-triggered CO-releasing activity of the compounds was assessed under physiological conditions (37 °C, 0.1 M phosphate buffer, pH = 7.4) by headspace gas chromatography (GC) and additionally by means of a myoglobin assay (UV). The relative rate of CO release and the amount of liberated CO were found to depend on the length of the acyloxy chain and its position at the diene unit (outer or inner position). Some of the new ET-CORMs exhibited very good biological activity as assessed in different cellular assays (cytotoxicity, protective effect against hypothermia-associated cell damage, and inhibition of TNF-α-mediated VCAM-1 expression).
Isolation of human O6-alkylguanine-DNA alkyltransferase mutants highly resistant to inactivation by O6-benzylguanine. (1998)

The activity of O6-alkylguanine-DNA alkyltransferase (AGT) protects cells from killing by methylating or chloroethylating agents. AGT is strongly inhibited by O6-benzylguanine (ED50, 0.2 microM), and this drug is presently undergoing clinical trials to enhance chemotherapy by alkylating agents. Point mutations such as P140A (ED50, 5 microM) render AGT resistant to O6-benzylguanine (BG). Selection for such mutants may prove to be a problem in the use of BG, and a better knowledge of the factors underlying resistance to BG will enable the rational design of improved inhibitors able to inactivate these mutants. BG-resistant AGT mutants may also be valuable for expression in bone marrow stem cells to reduce myelosuppression brought about by alkylating agents, to increase the therapeutic index of therapies including BG, and for use as a selectable marker to allow other genes to be expressed in such stem cells. We have therefore set up a general screen to obtain such mutants by using the ability of AGT to protect Escherichia coli GWR109 lacking endogenous AGT from killing by N-methyl-N'-nitro-N-nitrosoguanidine. When the cells were rendered permeable to BG by mutating the lipopolysaccharide membrane component forming strain TRG8, the protection by AGT expression was abolished by treating the cells with BG. The known P140A mutant was used to test the system and was highly selected for by treatment with 50 microM BG and 40 microg/ml N-methyl-N'-nitro-N-nitrosoguanidine. The sequence coding for PVP at positions 138-140 in AGT was replaced with a random nucleotide sequence, and this library was used to transform TRG8. All of the 59 colonies analyzed having AGT activity that survived the selection from the pool of 36,000 transformants were resistant to BG. Many (69%) of these mutants contained lysine at position 140, and all of these showed the highest level of resistance with <10% loss of activity when crude cell extracts were incubated with 1.2 mM BG. This result was confirmed with three mutants (P138K/V139L/P140K, P138M/V139L/P140K, and P140K), which were purified to homogeneity. The next most common residues found at position 140 were arginine (7%) and asparagine (7%). Studies carried out with purified preparations of mutants P140R and P140N revealed that these mutations also provided resistance to BG but to a lesser extent than P140K (ED50s of 190 and 7 microM, respectively). These results indicate that: (a) this screening method can be used to evaluate BG resistance of single or multiple changes throughout the AGT sequence; and (b) replacement of proline-140 with lysine is the most effective point mutation at this site causing BG resistance and is more than 200 times more effective than replacement with alanine.
Silyl resveratrol derivatives as potential therapeutic agents for neurodegenerative and neurological diseases (2021)

Natural phenolic compounds found in food have demonstrated interesting preventive and therapeutic effects on a large variety of pathologies. Indeed, some of them, such as resveratrol (RES), have been examined in clinical trials. Nevertheless, their success has been scarce mainly due to their low bioavailability. In this study, we found serendipitously that O-silyl RES derivatives exerted a better neuroprotective activity than resveratrol itself and decided to explore them as potential drugs for neurodegenerative and neurological diseases. We have also designed and prepared a series of O-silyl RES prodrugs to improve their bioavailability. We found that di-triethylsilyl and di-triisopropylsilyl RES derivatives were better in vitro neuroprotective and anti-inflammatory agents than RES. Among these derivatives and their corresponding acyl-, glycosyl- and carbamoyl-prodrugs, 3,5-triethylsilyl-4'-(6″-octanoylglucopyranosyl) resveratrol 26 showed the best profile on toxicity and neuroprotective activity in zebra fish embryo. Compound 26 was also capable of reducing the loss of motor coordination in a 3-nitropropionic acid mice model of Huntington's disease, in a similar way to RES. However, 26 diminished pro-inflammatory cytokine IL-6 to a higher extent than RES and improved the latency to fall in the rotarod test by 10% with respect to RES. Finally, we investigated 26 and RES as potential treatments on an experimental autoimmune encephalomyelitis (EAE) multiple sclerosis mice model. We observed that, in a therapeutic regimen, 26 significantly diminished the progression of EAE severity and reduced the percentage of animals with moderate to severe clinical score, whereas RES showed no improvement.
DPP IV resistance and insulin releasing activity of a novel di‐substituted analogue of glucose‐dependent insulinotropic polypeptide, (Ser<sup>2</sup>–Asp<sup>13</sup>)GIP (2003)

Structure-function studies suggest that preservation of the N-terminus and secondary structure of glucose-dependent insulinotropic polypeptide (GIP) is important for biological activity. Therefore, a novel di-substituted analogue of GIP, (Ser(2)-Asp(13))GIP, containing a negatively charged Asp residue in place of an Ala in position 13, was synthesised and evaluated for in vitro biological activity. Incubation with dipeptidyl peptidase IV (DPP IV) showed the half-lives of GIP and (Ser(2)-Asp(13))GIP to be 2.3 and >4h, respectively. Insulin releasing studies in clonal pancreatic BRIN-BD11 cells demonstrated that (Ser(2)-Asp(13))GIP (10(-12)to 10(-7)mol/l) was significantly less potent (60-90%; P<0.05 to P<0.001) than native GIP. The peptide failed to display antagonistic properties as it did not significantly alter insulin secretion when incubated in the presence of GIP (10(-7)mol/l). These results demonstrate that despite increased resistance to DPP IV, substituting Ala in position 13 with a negatively charged Asp, thus producing the di-substituted analogue (Ser(2)-Asp(13))GIP, significantly reduces biological activity, most likely due to modifications within the secondary structure.
Characterization of the Branched-Photocycle Intermediates <b>P</b> and <b>Q</b> of Bacteriorhodopsin (2002)

The bacteriorhodopsin branched-photocycle intermediates P and Q are studied with respect to chromophore isomeric content, photochemical origin, kinetic heterogeneity, and photoreversibility. These blue-shifted species are compared to products with similar spectroscopic properties generated via thermal denaturation. We observe that the thermal and photochemical species differ in both isomeric content and binding site environment. Sequential two-photon activation of glycerol suspensions of bacteriorhodopsin containing low concentrations of water (<15% v/v water/glycerol) form high yields of P state but almost no Q state. This observation is attributed to the role that water plays in the hydrolysis reaction that converts the P state to Q. Relatively large photostationary state populations of both intermediates can be generated in both 85% v/v glycerol suspensions and polyacrylamide gels. At ambient temperature, both intermediates can be fully converted back to bR with blue light. Chromophore extraction and HPLC analysis reveal that P, Q, and the spectrally similar thermal products have a 9-cis retinal chromophore. The thermal products are also found to contain small amounts of the 7-cis isomer. Time-resolved spectroscopy reveals that the P state is actually comprised of two components with maximum absorptivities at 445 and 525 nm. The molar absorptivities of the chromophore band maxima of the P and Q states in an 85% v/v glycerol/water suspension at pH 7 are ε(P445) = 47 000, ε(P525) = 39 000, and ε(Q) = 33 000 M-1 cm-1. Kinetic analyses support previous studies indicating that the P state is formed predominantly from the O state, which is consistent with the branched-photocycle model. However, other paths to the P state are possible, including direct excitation of the small population of blue membrane present in solution. We examine the hypothesis that the branched-photocycle evolved as a photochromic sunscreen for UVA and UVB protection.
Free‐breathing post‐contrast three‐dimensional T<sub>1</sub> mapping: Volumetric assessment of myocardial T<sub>1</sub> values (2014)

The proposed sequence enables high-resolution 3D T1 mapping after contrast injection during free-breathing with volumetric left ventricle coverage.
Synergistic antitumor activity observed for a fixed ratio liposome formulation of Cytarabine (Cyt):Daunorubicin (Daun) against preclinical leukemia models (2005)

Proc Amer Assoc Cancer Res, Volume 46, 2005

1405 

We have previously demonstrated that the in vitro and in vivo activity of anticancer drug combinations is dependent on the drug:drug ratio, where some ratios act synergistically while others can interact additively or antagonistically. We examined here the influence of drug ratio on the in vitro and in vivo anti-tumor effects of Cyt:Daun, a drug combination used for the treatment of acute myeloid leukemia. The median-effect analysis method (Chou and Talalay, Adv Enzyme Regul, 22: 27-55, 1984) provided a quantitative measure of synergy for MTT cytotoxicity assays with Cyt:Daun molar ratios ranging from 10:1 to 1:10. This combination exhibited drug ratio and concentration dependent synergy when tested against P388 and L1210 leukemia cells in vitro. Subsequently, Cyt:Daun was encapsulation inside liposomes engineered to maintain the 5:1 molar ratio in the plasma compartment over 24h post i.v. injection. When administered i.v. to mice bearing ascitic P388 tumors, this fixed ratio liposome formulation (hereafter referred to as CPX-351) provided 90% long-term survivors (60 day), whereas the free drug cocktail at its MTD achieved only a modest increase in life span (22 day median survival time). CPX-351 was also therapeutically superior to individual free drugs and individual liposomal drugs administered at their respective MTDs. Similar results were obtained in the L1210 leukemia model. Quantitative comparisons of in vivo tumor cell kill for CPX-351 vs. individual liposomal drugs were performed based on tumor doubling time values and treatment-induced increases in survival. This analysis demonstrated that CPX-351 therapeutic activity was approximately 500-fold greater than predicted based on additive efficacy contributions of the individual liposomal drugs in the P388 tumor model, indicating strong in vivo synergy. These results demonstrate that fixing synergistic drug:drug ratios in carriers such as liposomes can lead to dramatic improvements of in vivo therapeutic activity. Furthermore, this approach provides an avenue whereby in vitro information on drug:drug interactions can be directly translated in vivo , thus facilitating the optimization of drug combinations based on efficacy in preclinical development.
Derivation of Hematopoietic Stem Cells from Embryonic Stem Cells. (2004)

Abstract Despite the significant in vitro blood-forming potential of murine embryonic stem cells (ESCs), deriving hematopoietic stem cells (HSCs) that can reconstitute irradiated mice has proven to be challenging. Previously, we successfully engrafted lethally irradiated adult mice with ESCs engineered to ectopically express the homeodomain gene hoxB4. In engrafted animals, blood reconstitution showed a myeloid predominance, likely due to an inability to fully pattern the adult HSC from these embryonic populations. Recently, we have investigated cdx4, a caudal-related homeobox gene whose function has been linked to blood development in the zebrafish. During in vitro differentiation of murine ESCs, cdx4 is expressed during a very narrow time interval on day 3, coincident with the specification of hematopoietic mesoderm. To further characterize the function of cdx4 in mouse hematopoiesis, we have established a tetracycline-inducible murine embryonic stem cell line. When cdx4 expression is conditionally induced over a protracted period from day 2 and 6, we observe a marked enhancement of hemangioblast formation as well as significant increases in primitive and definitive hematopoietic colonies. Cdx4 acts to induce a broad array of hox genes, including a modest elevation in hoxb4. Co-expression of cdx4 and hoxb4 promotes robust expansion of hematopoietic blasts on supportive OP9 stromal cultures. When injected intravenously into lethally-irradiated mice, these cell populations provide robust radio-protection, and reconstitute high-level lymphoid-myeloid donor chimerism. Marrow from engrafted primary animals can be transplanted into irradiated secondary mice. B220+ splenic lymphoid cells and Mac-1/Gr-1+ marrow myeloid cells purified from primary and secondary mice show multiple common sites of retroviral integration, thereby proving the derivation of long-term hematopoietic stem cells from embryonic stem cells in vitro. Our data support a central role for the cdx4-hox gene pathway in specifying murine HSC development, and establish a robust system for hematopoietic reconstitution from ESCs. We have coupled techniques for generating ESCs by nuclear transfer with these methods for blood reconstitution to model the treatment of genetic disorders of the bone marrow.
Approach to enhance deuterium incorporation for improved hot carrier reliability in metal-oxide-semiconductor devices (2000)

The deuterium isotope effect has been widely demonstrated to improve hot-carrier reliability in metal-oxide-semiconductor transistors. Most of the interface traps, however, may have been passivated by hydrogen before the final deuterium anneal due to the ubiquitous presence of hydrogen in modern complementary metal-oxide-semiconductor processing technology. Therefore, effective deuteration requires both deuterium diffusion to the SiO2–Si interface and displacement of the previously bonded hydrogen. We have introduced a “prestress” process in which hydrogen is depassivated before deuterium annealing. We found that the prestressed transistors are more robust to hot-carrier stress than control transistors without the prestress. We have also found that the replacement of hydrogen with deuterium is the rate-limiting step for deuterium incorporation at the SiO2–Si interface. With the prestress, a lower deuterium annealing temperature can be applied without compromising the reliability improvement.
Advanced Reservoir and Tar Mat Evaluation Using Downhole Fluid Analysis and Asphaltene Flory-Huggins-Zuo EoS (2013)

Abstract Advances in asphaltene science and a new generation of downhole fluid analysis (DFA) technology have been integrated to yield powerful new insights to reservoir dynamics. The Yen-Mullins model of asphaltene nanoscience has enabled development of the industry's first predictive equation of state (EOS) for asphaltene concentration gradients - the Flory-Huggins-Zuo (FHZ) EOS in oil reservoirs. The FHZ EOS along with DFA measurements has successfully addressed a variety of reservoir concerns including reservoir connectivity, viscosity gradients, and fluid disequilibrium. The model shows that asphaltene concentration gradients can be large owing to both the gravity term and gas/oil ratio (GOR) gradients. The FHZ EOS is reduced to a very simple form for low GOR black oils and heavy oils, and heavy oils are shown to exhibit enormous asphaltene concentration gradients compared to conventional black oil. In this paper, the FHZ EOS has been applied not only to calculate asphaltene concentration gradients but also to predict asphaltene phase instability in oil reservoirs and potential flow assurance issues. Two categories of tar mats are addressed, one with a large discontinuous increase in asphaltene concentration versus depth typically at the base of an oil column (corresponding to asphaltene phase transition); the second with a continuous increase in asphaltene content at the base of a mobile heavy oil column due to an exponential increase in viscosity with asphaltene content. The discontinuous type of tar mat is show to occur in two distinct setting, one more common tar mat at the base of the column and a second unusual tar mat that occurs upstructure and is permeable. The predictions are in good agreement with the laboratory and field data and the mechanisms of forming these two kinds of tar mats are also discussed. This methodology establishes a powerful new approach for conducting the analyses of asphaltene concentration grading, flow assurance and tar mat formation in oil reservoirs by integrating the Yen-Mullins model, and the FHZ EOS with DFA technology.
Late onset Pompe disease: Rescue of acid alpha-glucosidase expression by splice modification (2018)

A deficiency of the enzyme acid alpha‐glucosidase leads to Pompe disease, also known as glycogen storage disease II (GSDII). It is an autosomal recessive disorder, and affected individuals are unable to degrade glycogen stored within lysosomes, leading to an accumulation of glycogen in tissue. Clinically, GSDII may manifest with a broad spectrum of severity, ranging from severe/infantile to a milder late onset adult form. The most common GAA mutation associated with the latter form is IVS1‐13T>G, found in over two thirds of adult onset GSDII patients. The consequence of this mutation is production of a non-functional GAA transcript because exon 2 is excluded during pre-RNA splicing. \n\nCurrent enzyme replacement therapy for Pompe disease has drawbacks, including immune reaction and poor delivery to target tissues. Therefore an efficient alternative therapy is needed. We sought to restore inclusion of GAA exon 2 using splice switching antisense oligomers (AO) directed at splice silencer elements to promote recognition and retention of exon 2 in the mature GAA mRNA, thereby restoring enzyme function. Screen of the best AO sequences that promote exon 2 inclusion in GAA transcript was carried out in fibroblasts derived from adult Pompe patients. Phosphorodiamidate morpholino oligomers (PMOs) were transfected into patient cells and RT‐PCR and acid‐alpha‐glucosidase enzyme activitywere performed. Several PMOs showed an increase in full‐length amplicon and increase inGAAactivity. These results show thatPMOmediatedmodification of GAA transcript could have therapeutic potential for a large portion of adult onset Pompe patients.
Bad Data Detection Algorithm for PMU Based on Spectral Clustering (2020)

Phasor measurement units (PMUs) can provide real-time measurement data to construct the ubiquitous electric of the Internet of Things. However, due to complex factors on site, PMU data can be easily compromised by interference or synchronization jitter. It will lead to various levels of PMU data quality issues, which can directly affect the PMU-based application and even threaten the safety of power systems. In order to improve the PMU data quality, a data-driven PMU bad data detection algorithm based on spectral clustering using single PMU data is proposed in this paper. The proposed algorithm does not require the system topology and parameters. Firstly, a data identification method based on a decision tree is proposed to distinguish event data and bad data by using the slope feature of each data. Then, a bad data detection method based on spectral clustering is developed. By analyzing the weighted relationships among all the data, this method can detect the bad data with a small deviation. Simulations and results of field recording data test illustrate that this data-driven method can achieve bad data identification and detection effectively. This technique can improve PMU data quality to guarantee its applications in the power systems.