gebhart/patrepeval huggingface dataset:
Antiviral Activity of Various 1-(2′-Deoxy-β-d-lyxofuranosyl), 1-(2′-Fluoro-β-d-xylofuranosyl), 1-(3′-Fluoro-β-d-arabinofuranosyl), and 2′-Fluoro-2′,3′-didehydro-2′,3′-dideoxyribose Pyrimidine Nucleoside Analogues against Duck Hepatitis B Virus (DHBV) and Human Hepatitis B Virus (HBV) Replication (2010)

Despite the existence of successful vaccine and antiviral therapies, infection with hepatitis B virus (HBV) continues to be a major global cause of acute and chronic liver disease and high mortality. We synthesized and evaluated several lyxofuranosyl, 2'-fluoroxylofuranosyl, 3'-fluoroarabinofuranosyl, and 2'-fluoro-2',3'-didehydro-2',3'-dideoxyribose pyrimidine nucleoside analogues for antiviral activities against hepatitis B virus. Among the compounds examined, 1-(2-deoxy-β-d-lyxofuranosyl)thymine (23), 1-(2-deoxy-β-d-lyxofuranosyl)-5-trifluoromethyluracil (25), 1-(2-deoxy-2-fluoro-β-d-xylofuranosyl)uracil (38), 1-(2-deoxy-2-fluoro-β-d-xylofuranosyl)thymine (39), 2',3'-dideoxy-2',3'-didehydro-2'-fluorothymidine (48), and 2',3'-dideoxy-2',3'-didehydro-2'-fluoro-5-ethyluridine (49) were found to possess significant anti-HBV activity against DHBV in primary duck hepatocytes with EC(50) values of 4.1, 3.3, 40.6, 3.8, 0.2, and 39.0 μM, respectively. Compounds 23, 25, 39, 48, and 49 (EC(50) = 41.3, 33.7, 19.2, 2.0-4.1, and 39.0 μM, respectively) exhibited significant activity against wild-type human HBV in 2.2.15 cells. Intriguingly, 25, 39, 48, and 49 retained sensitivity against lamivudine-resistant HBV containing a single mutation (M204I) and 48 emerged as an effective inhibitor of drug-resistant HBV with an EC(50) of 4.1 μM. In contrast, 50% inhibition could not be achieved by lamivudine at 44 μM concentration in the drug-resistant strain. The compounds investigated did not show cytotoxicity to host cells up to the highest concentrations tested.
Survival of freeze-dried bacteria (2008)

The aim of this study was to investigate the survival of freeze-dried bacterial species stored at the International Patent Organism Depository (IPOD) and to elucidate the characteristics affecting survival. Bacterial strains were freeze-dried, sealed in ampoules under a vacuum (<1 Pa), and stored in the dark at 5 degrees C. The survival of a variety of species following storage for up to 20 years was analyzed. The survival of freeze-dried species was analyzed in terms of two stages, freeze-drying and storing. Nonmotile genera showed relatively high survival after freeze-drying. Motile genera with peritrichous flagella showed low survival rates after freeze-drying. Vibrio and Aeromonas, which produce numerous flagella, showed very low survival rates. In Lactobacillus, non-trehalose-fermenting species showed better survival rates after freeze-drying than did fermenting species, and those species with teichoic acid in the cell wall showed lower survival rates during storage than species with teichoic acid in the cell membrane. Human pathogenic species of Corynebacterium, Bacillus, Streptococcus, and Klebsiella showed lower survival rates during storage than nonpathogenic species within the same genus. Among Pseudomonas species, P. chlororaphis, the only species tested that forms levan from sucrose, showed the lowest survival rate during storage in the genus. Survival rates of Gram-negative species during storage tended to be lower than those of Gram-positive species, though Chryseobacterium meningosepticum had stable survival during storage. The conclusion is that smooth cell surfaces (i.e., no flagella) and lack of trehalose outside the cytoplasm improved survival rates after freeze-drying. Because desiccation is important for survival during storage, the presence of extracellular polysaccharides or teichoic acids is disadvantageous for long-term survival. The lower survival rates of freeze-dried Gram-negative bacteria compared with those of Gram-positive bacteria may be attributed to the thinner peptidoglycan layer and the presence of lipopolysaccharides on the cell wall in the former species.
Linear least‐squares method for unbiased estimation of T1 from SPGR signals (2008)

The longitudinal relaxation time, T(1), can be estimated from two or more spoiled gradient recalled echo images (SPGR) acquired with different flip angles and/or repetition times (TRs). The function relating signal intensity to flip angle and TR is nonlinear; however, a linear form proposed 30 years ago is currently widely used. Here we show that this linear method provides T(1) estimates that have similar precision but lower accuracy than those obtained with a nonlinear method. We also show that T(1) estimated by the linear method is biased due to improper accounting for noise in the fitting. This bias can be significant for clinical SPGR images; for example, T(1) estimated in brain tissue (800 ms < T(1) < 1600 ms) can be overestimated by 10% to 20%. We propose a weighting scheme that correctly accounts for the noise contribution in the fitting procedure. Monte Carlo simulations of SPGR experiments are used to evaluate the accuracy of the estimated T(1) from the widely-used linear, the proposed weighted-uncertainty linear, and the nonlinear methods. We show that the linear method with weighted uncertainties reduces the bias of the linear method, providing T(1) estimates comparable in precision and accuracy to those of the nonlinear method while reducing computation time significantly.
Syncytium-inducing (SI) phenotype suppression at seroconversion after intramuscular inoculation of a non-syncytium-inducing/SI phenotypically mixed human immunodeficiency virus population (1995)

Two distinct biological phenotypes of human immunodeficiency virus (HIV) have been described: the non-syncytium-inducing (NSI) phenotype, best characterized by the inability to infect MT-2 cells, and the syncytium-inducing (SI) phenotype, with the ability to infect MT-2 cells. The earliest virus population observed following HIV transmission is generally of the NSI phenotype, even after exposure to inocula of mixed NSI/SI phenotype. In this study, the issue of intrapatient selection of virus phenotype following transmission was addressed by studying two cases of accidental transmission. A comparison of the sequences of the V1-V2 and the V3 coding regions of the envelope gene and the p17 region of the gag gene showed that the donor-recipient pairs were tightly clustered in all gene segments, but away from local and published transmission controls. The intrasample variation of the p17 sequence was greater in the recipients and smaller in the donors than that of the V3 region sequence, indicating selection of V3 at transmission. In these transmission cases, the effects of an intravenous inoculation of a small quantity of blood containing predominantly SI V3 sequences (6 of 8 clonal sequences) were compared with those of an intramuscular inoculation of a large quantity of blood containing predominantly NSI viruses (14 of 16 clonal sequences). Both SI and NSI V3 regions were demonstrated to be phenotypic expressions of genetically related viral strains. The inoculation of the predominantly SI virus population resulted in the persistence of an SI virus population in the recipient and a rapid CD4+ T-cell decline. The inoculation of the predominantly NSI population resulted in a selective amplification of SI viruses before seroconversion, followed by a suppression of SI viruses at seroconversion and a rapid decline of CD4+ T-cell numbers. These data suggest that the suppression of SI viruses can be accomplished following the development of HIV-specific immunity and that the ability to suppress SI viruses does not prevent the development of immunodeficiency.
Hypersensitivity and Loss of Disease Site Targeting Caused by Antibody Responses to PEGylated Liposomes (2005)

The systemic application of nucleic acid drugs requires delivery systems that overcome the poor pharmacokinetics, limited biodistribution, and inefficient uptake of nucleic acids. PEGylated liposomes show considerable promise because of their intrinsic ability to accumulate at disease sites and facilitate transfection of target cells. Unlike many viral vectors, PEGylated liposomes are generally considered to be nonimmunogenic. We have developed a PEGylated liposome for the systemic administration of plasmid DNA that achieves high levels of selective gene expression at distal tumor sites. Here we report that the in vivo efficacy and safety of these systems can be severely compromised following repeat administration. This phenomenon is characterized by a loss of disease site targeting, accelerated clearance from the blood, and acute hypersensitivity. These effects are fully attributable to a surprisingly robust, long-lived antibody response generated against polyethylene glycol (PEG) that results from the strong adjuvant effect of the plasmid payload. Importantly, immunogenicity may be substantially reduced by modifying the alkyl chain of the PEG-lipid conjugate, thereby allowing successful repeat dosing of the modified plasmid formulations without adverse side effects. Immunogenicity is a relevant concern for a number of nonviral delivery systems given the potent immunostimulatory properties of many nucleic acid drugs.
Androgen-specific gene activation via a consensus glucocorticoid response element is determined by interaction with nonreceptor factors. (1992)

A fundamental issue in steroid hormone regulation is the question of how specific transcription is attained in vivo when several receptors can bind the same DNA sequence in vitro. We report an enhancer of the mouse sex-limited protein (Slp) gene that, unlike previously characterized enhancers, is activated by androgens but not by glucocorticoids or progestins. Potent androgen induction requires both a consensus glucocorticoid (hormone) response element and auxiliary elements also present within a 120-base-pair DNA fragment. Cotransfection assays with wild-type and mutant receptors reveal that glucocorticoid receptor can bind, but not transactivate from, the hormone response element within the enhancer. The positive effect of androgen and the null effect of glucocorticoid appear to require the amino-terminal domains of the respective receptors. Thus, exclusive transcriptional response to androgens, and lack of response to glucocorticoids, derives from factor interactions that are determined by the context of the receptor binding site rather than by its distinct sequence.
Selectivity Assessment of Noninvasive Glucose Measurements Based on Analysis of Multivariate Calibration Vectors (2007)

Glucose-specific spectral information is present within noninvasive near-infrared spectra collected from a rat model using a transmission geometry. Apparently functional, yet incorrect, calibration models can be generated, and the propensity to create such false PLS calibration models calls into question the validity of past reports. An analysis of calibration vectors can provide valuable insight into the chemical basis of selectivity for multivariate calibration models of complex systems.
Non-destructive, whole wafer assessment of optoelectronic epitaxial materials (1992)

Two optical techniques, high-spatial-resolution scanning photoluminescence spectroscopy (sPL) and scanning reflectance spectroscopy (sRS), have been developed to provide rapid, non-destructive, whole wafer assessment of III-V materials grown by molecular beam epitaxy (MBE) and metal organic chemical vapour deposition (MOCVD). These techniques have been combined in a single measurement system which is used to evaluate epitaxial layer quality, composition (or emission wavelength) and thickness. The combination of low excitation power density and high data density in the sPL intensity maps produced by this measurement system has been shown to be important in revealing those defects that control the performance of minority carrier devices such as p-i-n detectors. High-resolution sPL wavelength maps may also be generated. These can be used to infer spatial variation in ternary composition and quantum well (QW) thickness. High-density thickness maps of non-QW epitaxial layers are produced by this instrument in the sRS mode. Thickness variations of less than 20 nm are clearly distinguishable. Examples from MOCVD and MBE growth experiments demonstrate the utility of sPL wavelength and sRS thickness maps in the optimisation of epitaxial reactor designs.
Evaluation of quantitative magnetic resonance imaging as a noninvasive technique for measuring renal scarring in a rabbit model of antiglomerular basement membrane disease. (1994)

Renal function tests are an insensitive means of detecting progressive scarring of the kidney such as occurs in chronic allograft rejection and lupus nephritis. Alternative approaches for the measurement of small progressive changes in renal structure on a repetitive basis are needed. Quantitative magnetic resonance imaging (proton T1 relaxation time) was assessed for this purpose. A rabbit model of antiglomerular basement membrane disease that develops glomerular and interstitial inflammation followed by scarring of the renal cortex was used. Longitudinal studies of cortical T1 showed a marked prolongation of T1 during the initial inflammation and edema associated with glomerular crescent formation (Day 7). The T1 remained prolonged up to Day 120 in animals with significant fibrosis and crescent formation when the wet/dry weight ratio (a measure of edema) had returned to baseline. T1 was a more sensitive index of renal injury than was serum creatinine for all of the end points measured (cortical hydroxyproline per dry weight, percent crescent formation, or histologic fibrosis score). It was concluded from these studies that measurement of renal cortical T1 is quite a sensitive index of renal injury, probably more sensitive than the measurement of serum creatinine, but that this method does not discriminate between edema and scarring.
Experimental Hydrostatic Pulmonary Edema in Rabbit Lungs: Morphology (1993)

To study the accumulation and distribution of edema fluid and the associated changes in alveolar microarchitecture, edema was induced in excised rabbit lungs perfused with 6% albumin solution. The lungs, including the edema fluid, were then fixed by vascular perfusion with glutaraldehyde, osmium tetroxide, and uranyl acetate. Tissue samples were analyzed by light microscopy and transmission and scanning electron microscopy. We found (1) fixation was successful in that the albumin in the edema fluid formed coherent webs indicating the location and arrangement of the extravascular fluid accumulations; (2) regardless of the filtration pressure (about 29 mm Hg in one set of experiments and about 14 mm Hg in the other), an apical to basal gradient of fluid accumulation was found. This gradient was absent in lungs held in the inverse position, suggesting that the regional distribution of pulmonary edema is not simply gravity dependent. At the same lung height, there was a remarkable inhomogeneity of interstitial and alveolar edema. (3) Both the inhomogeneous distribution of fluid and the resulting changes in surface tension affected the entire alveolar architecture. (4) Within interstitial and alveolar spaces, there were striking inequalities in the density of the proteinaceous fluid pools that suggest local differences in the sieving properties of the barriers, that is, in the reflection coefficients for albumin. In conclusion, our findings suggest that the formation of pulmonary edema cannot be explained solely by uniform membrane models for fluid exchange.
Beneficial effects of two forms of NO administration in feline splanchnic artery occlusion shock (1990)

We studied the effects of nitric oxide (NO) solution and acidified sodium nitrite (NaNO2), which produces NO, in splanchnic artery occlusion (SAO) shock in cats. NO is thought to be endothelium-derived relaxing factor (EDRF), a labile substance having several potentially valuable biological effects. Anesthetized cats subjected to total occlusion of the celiac, superior mesenteric, and inferior mesenteric arteries for 120 min, followed by reperfusion, usually died approximately 60 min after reperfusion. NO infusion significantly improved survival time in SAO-shock cats compared with those receiving vehicle (P less than 0.005). Administration of NO also attenuated the increase in plasma activities of the lysosomal hydrolase cathepsin D (P less than 0.05), total amino-nitrogen (P less than 0.001), and of the cardiotoxic peptide, myocardial depressant factor (MDF) (P less than 0.001). SAO-shock cats treated with NaNO2 at pH 2.0 also exhibited lower plasma cathepsin D (P less than 0.001), amino-nitrogen (P less than 0.05), and MDF activities (P less than 0.01), and survival time was also significantly improved (P less than 0.02). The same dose of NaNO2 infused at pH 7.4 failed to exert any significant protective effect. These results indicate that NO exerts beneficial effects in SAO shock in cats and suggest that exogenously administered NO may be a potentially useful therapeutic agent in splanchnic ischemic shock, probably via a cytoprotective rather than a vasodilator effect.
Epigenetics: DNA demethylation promotes skeletal myotube maturation (2011)

Mesenchymal progenitor cells can be differentiated in vitro into myotubes that exhibit many characteristic features of primary mammalian skeletal muscle fibers. However, in general, they do not show the functional excitation-contraction coupling or the striated sarcomere arrangement typical of mature myofibers. Epigenetic modifications have been shown to play a key role in regulating the progressional changes in transcription necessary for muscle differentiation. In this study, we demonstrate that treatment of murine C2C12 mesenchymal progenitor cells with 10 μM of the DNA methylation inhibitor 5-azacytidine (5AC) promotes myogenesis, resulting in myotubes with enhanced maturity as compared to untreated myotubes. Specifically, 5AC treatment resulted in the up-regulation of muscle genes at the myoblast stage, while at later stages nearly 50% of the 5AC-treated myotubes displayed a mature, well-defined sarcomere organization, as well as spontaneous contractions that coincided with action potentials and intracellular calcium transients. Both the percentage of striated myotubes and their contractile activity could be inhibited by 20 nM TTX, 10 μM ryanodine, and 100 μM nifedipine, suggesting that action potential-induced calcium transients are responsible for these characteristics. Our data suggest that genomic demethylation induced by 5AC overcomes an epigenetic barrier that prevents untreated C2C12 myotubes from reaching full maturity.
Subcutaneous delivery of daratumumab in relapsed or refractory multiple myeloma (2019)

Daratumumab, a human monoclonal antibody targeting CD38, is approved as monotherapy and in combination regimens for patients with multiple myeloma (MM). Currently, daratumumab is administered IV. The phase 1b PAVO (MMY1004) study evaluated subcutaneously administered daratumumab in combination with the recombinant human hyaluronidase PH20 enzyme (rHuPH20) in patients with relapsed or refractory MM. Part 1 of the study, reported here, evaluated a mix-and-deliver (MD) formulation of daratumumab and rHuPH20 (DARA-MD) administered by subcutaneous infusion. Patients received subcutaneous daratumumab according to the approved IV monotherapy dosing schedule at 1200 mg (n = 8) or 1800 mg (n = 45). Primary end points were safety and pharmacokinetic (PK) variables. The most common treatment-emergent adverse events with DARA-MD 1200 mg were thrombocytopenia, upper respiratory tract infection, insomnia, and decreased appetite (37.5% each). Anemia (33.3%), upper respiratory tract infection, pyrexia, and diarrhea (26.7% each) were the most common treatment-emergent adverse events with DARA-MD 1800 mg. One patient in the 1200-mg dose group (12.5%) and 11 patients in the 1800-mg dose group (24.4%) experienced infusion-related reactions, which were generally grade 1/2 and typically occurred at the first infusion. The 1800 mg dose achieved similar or greater serum concentrations compared with the 16 mg/kg IV dose. Overall response rates of 25.0% and 42.2% were achieved with 1200-mg and 1800-mg DARA-MD, respectively. Subcutaneous administration of DARA-MD was well tolerated in patients with relapsed or refractory MM, with the 1800-mg dose exhibiting PK concentrations and responses consistent with IV daratumumab in a similar patient population. This study was registered at www.clinicaltrials.gov as #NCT02519452.
Expression of Kinesin in Escherichia coli (2001)

Kinesin can generally be expressed to high levels in Escherichia coli and this provides an excellent means for obtaining significant amounts of purified constructs. For detailed work, it is essential to have a native construct uncompromised by extraneous tags, and this can readily be obtained. See refs. 1–3 for examples of vector construction using the T7 RNA polymerase system.
Endogenous ligands for C‐type lectin receptors: the true regulators of immune homeostasis (2009)

C-type lectin receptors (CLRs) have long been known as pattern-recognition receptors implicated in the recognition of pathogens by the innate immune system. However, evidence is accumulating that many CLRs are also able to recognize endogenous 'self' ligands and that this recognition event often plays an important role in immune homeostasis. In the present review, we focus on the human and mouse CLRs for which endogenous ligands have been described. Special attention is given to the signaling events initiated upon recognition of the self ligand and the regulation of glycosylation as a switch modulating CLR recognition, and therefore, immune homeostasis.
CAD/CAM–designed 3D-printed electroanalytical cell for the evaluation of nanostructured gas-diffusion electrodes (2016)

The ability to effectively screen and validate gas-diffusion electrodes is critical to the development of next-generation metal-air batteries and regenerative fuel cells. The limiting electrode in a classic two-terminal device such as a battery or fuel cell is difficult to discern without an internal reference electrode, but the flooded electrolyte characteristic of three-electrode electroanalytical cells negates the prime function of an air electrode-a void volume freely accessible to gases. The nanostructured catalysts that drive the energy-conversion reactions (e.g., oxygen reduction and evolution in the air electrode of metal-air batteries) are best evaluated in the electrode structure as-used in the practical device. We have designed, 3D-printed, and characterized an air-breathing, thermodynamically referenced electroanalytical cell that allows us to mimic the Janus arrangement of the gas-diffusion electrode in a metal-air cell: one face freely exposed to gases, the other wetted by electrolyte.
Indanylidenes. 1. Design and Synthesis of (E)-2-(4,6-Difluoro-1-indanylidene)acetamide, a Potent, Centrally Acting Muscle Relaxant with Antiinflammatory and Analgesic Activity (2002)

The design of rigid cyclic analogues derived from cinnamamide 1, (E)-N-cyclopropyl-3-(3-fluorophenyl)prop-2-enamide, and beta-methylcinnamamide 2, (E)-N-cyclopropyl-3-(3-fluorophenyl)but-2-enamide, has led to the discovery of the potent, centrally acting muscle relaxant (E)-2-(4,6-difluoro-1-indanylidene)acetamide, 17. Compound 17 also possesses potent antiinflammatory and analgesic activity. This paper describes the synthesis and the muscle relaxant, antiinflammatory, and analgesic structure-activity relationships of 17 and 67 of its analogues. Compound 17 has been taken into phase I clinical trials.