gebhart/patrepeval huggingface dataset:
Hydrophobin gene deletion and environmental growth conditions impact mechanical properties of mycelium by affecting the density of the material (2018)

Filamentous fungi colonize substrates by forming a mycelium. This network of hyphae can be used as a bio-based material. Here, we assessed the impact of environmental growth conditions and deletion of the hydrophobin gene sc3 on material properties of the mycelium of the mushroom forming fungus Schizophyllum commune. Thermogravimetric analysis showed that Δsc3 mycelium retained more water with increasing temperature when compared to the wild type. The Young's modulus (E) of the mycelium ranged between 438 and 913 MPa when the wild type strain was grown in the dark or in the light at low or high CO<sub>2</sub> levels. This was accompanied by a maximum tensile strength (σ) of 5.1-9.6 MPa. In contrast, E and σ of the Δsc3 strain were 3-4- fold higher with values of 1237-2727 MPa and 15.6-40.4 MPa, respectively. These values correlated with mycelium density, while no differences in chemical composition of the mycelia were observed as shown by ATR-FTIR. Together, genetic modification and environmental growth conditions impact mechanical properties of the mycelium by affecting the density of the mycelium. As a result, mechanical properties of wild type mycelium were similar to those of natural materials, while those of Δsc3 were more similar to thermoplastics.
Improving Sensitivity and Spectral Efficiency in Direct-Detection Optical OFDM Systems (2008)

Analysis and simulations show that boosting the carrier power relative to the sideband just prior to photodetection, using an optical filter, will significantly increase the sensitivity and spectral efficiency of direct-detection optical orthogonal frequency-division multiplexed systems.
Review of Ocular Drug Delivery (2006)

Successful treatment of eye diseases requires effective concentration of drug at the eye for sufficient period of time. Conventional ocular drug delivery including eye drops, systemic administration, ophthalmic ointments, is no longer sufficient to combat ocular diseases. This article reviews the constraints with conventional ocular therapy, and explores various novel approaches, to improve the ocular bioavailability of drugs to the anterior chamber of the eye.
The N-terminal Sequence (Residues 1–65) Is Essential for Dimerization, Activities, and Peptide Binding of Escherichia coli DsbC (2000)

Limited proteolysis of DsbC with trypsin resulted in a compact and stable C-terminal fragment (residues 66-216), fDsbC, which retains the active site sequence, -Cys(98)-Gly-Tyr-Cys(101)-, and shows only minor differences in conformation compared with that of the intact molecule. The pK(a) of active site thiol and the K(SS) with glutathione are very close to that of DsbC, respectively; however, fDsbC is inactive as an isomerase in catalyzing the formation of correct disulfide bonds in scrambled RNase A and denatured and reduced bovine pancreatic trypsin inhibitor and shows only 13% thiol-protein oxidoreductase activity (TPOR) of DsbC. In contrast to the dimeric DsbC, fDsbC exists as a monomer and has no chaperone activity in assisting the reactivation of denatured d-glyceraldehyde-3-phosphate dehydrogenase. The heterodimer of DsbC with the inactive DsbC carboxymethylated at both active site thiols shows about 50% TPOR activity of DsbC but no isomerase activity, indicating that the DsbC subunit in the heterodimer displays full TPOR activity but little, if any, isomerase activity. It is concluded that the N-terminal sequence (residues 1-65) is essential for dimer formation and chaperone activity of DsbC. The active sites in both subunits of the dimeric DsbC appear to be essential for its isomerase activity.
The structure of porcine protegrin genes (1995)

We cloned the genes of three protegrins, a family of cathelin‐associated antimicrobial peptides originally isolated from porcine leukocytes. Each gene comprised 4 exons and 3 introns, wherein Exon I encoded the signal sequence and the first 37 amino acids of cathelin, Exons II and III contained 36 and 24 additional cathelin residues and Exon IV contained the final two cathelin residues followed by the protegrin sequence. This quadripartite gene structure helps explain how structurally diverse antimicrobial peptides can be expressed on common, cathelin‐containing precursors. Southern blot probed with an oligonucleotide specific for protegrin genes suggested that several identical or nearly identical protegrin genes were densely clustered in the pig chromosome.
Metallopharmaceuticals based on silver(I) and silver(II) polydiguanide complexes: activity against burn wound pathogens (2010)

Ag(I)CHX and Ag(II)CHX showed superior antibacterial activity and faster killing kinetics compared with chlorhexidine and AgNO(3). These complexes may serve as new-generation antibacterial agents in wound care.
Mechanisms of nucleoside analog antiviral activity and resistance during human immunodeficiency virus reverse transcription (1996)

Free access1 March 1996 Share on Mechanisms of nucleoside analog antiviral activity and resistance during human immunodeficiency virus reverse transcriptionAuthors: E J Arts, M A WainbergAuthors Info & AffiliationsDOI: https://doi.org/10.1128/AAC.40.3.527 PDF/EPUB
The effect of caffeine on mammary gland development and milk yield in primiparous sows2 (1995)

Pregnant Yorkshire gilts (n = 42) were fed caffeine (6 g/d) or served as controls from d 60 of pregnancy until d 4 postpartum to test the effect of caffeine on mammary gland development, milk yield, and feed consumption. Caffeine reduced voluntary feed intake (P = .001) and body weight gain (P = .001) of gilts from d 60 to 109 of gestation. Pig birth weight in the treated group was less than (P = .01) that in the control group. However, pig viability score at birth was not affected by maternal caffeine ingestion. For assessing mammary gland DNA, RNA, dry fat-free tissue (DFFT), fat, and protein content, four sows from the caffeine group and three controls were slaughtered on the 1st d of lactation. Immediately after slaughter, mammary systems were removed, separated by gland, and dissected free of skin, muscle, and fatty pad, which had not been invaded by glandular tissue. The DNA and RNA content were evaluated in DFFT. Caffeine increased mammary RNA content (P = .023) and milk yield (P = .001) on d 1 of lactation. However, DNA, DFFT, fat, and protein were not significantly increased, although values were somewhat greater in the treatment group (approximately 82%). On d 21 of lactation, milk yield of treated sows did not differ from that of controls. The increased milk yield on d 1 of lactation was due to increased mammary epithelial cell activity and cell numbers. These results indicate that caffeine feeding can have a positive effect on porcine mammary gland development as well as milk yield.
Properties of 5-Hydroxyvalerate CoA-Transferase fromClostridium aminovalericum (1990)

5-Hydroxyvalerate CoA-transferase from Clostridium aminovalericum, strain T2-7, was purified approximately 100-fold to homogeneity. The molecular mass of the native enzyme was determined by three different methods to be 178 +/- 11 kDa; that of the subunit was 47 kDa, indicating a homotetrameric structure. The following CoA esters acted as substrates (decreasing specificity, V/Km): 5-hydroxyvaleryl-CoA greater than propionyl-CoA greater than acetyl-CoA greater than (Z)-5-hydroxy-2-pentenoyl-CoA greater than butyryl-CoA greater than valeryl-CoA. 4-Pentenoate and 3-pentenoate were also activated by acetyl-CoA to the corresponding CoA esters, whereas crotonate, (E)-5-hydroxy-2-pentenoate, (E)-2-pentenoate and 2,4-pentadienoate were not attacked. 5-Hydroxyvalerate CoA-transferase showed ping-pong kinetics and was inactivated by sodium boranate only in the presence of a CoA substrate. This indicated the formation of a thiolester between a specific carboxyl group of the enzyme and CoASH during the course of the reaction. The CoA-transferase was inhibited by ATP and CTP, slightly by ADP, GTP and UTP, but not by AMP. The inhibition by ATP was competitive towards CoA esters and noncompetitive towards acetate.
The effects of domain deletion, glycosylation, and long IgG3 hinge on the biodistribution and serum stability properties of a humanized IgG1 immunoglobulin, hLL2, and its fragments. (1999)

Antibody (Ab) fragments are preferred agents for imaging applications because of their rapid clearance from the blood, thereby providing high tumor:blood ratios within a few hours. Several preclinical studies have also suggested that Ab fragments might be preferred for therapeutic applications over an intact IgG. The purpose of this project was to develop engineered Ab fragments using a humanized anti-carcinoembryonic antigen and anti-CD22 Ab as the parent. Three types of variants were prepared: a deltaCH2 (deletion mutant missing the CH2), a gamma3 F(ab')2 containing the human IgG3 hinge, and three glycosylated variants. The gamma3 F(ab')2 and glycosylated variants were developed because of the potential for site-specific linkage to the Ab in its divalent or monovalent fragment. The gamma3 F(ab')2 variant contains 10 cysteine residues that could be used for direct coupling using thiol chemistry, whereas the glycosylated variants have N-linked glycosylation sites engineered in the CH1 domain (two variants) as well as the VK domain (one variant). All of these variants were successfully prepared and shown to react with the target antigen. All Abs could be purified to a single peak by size-exclusion HPLC, but the deltaCH2 variant showed two distinct peaks, which were believed to be both the divalent and monovalent forms of this fragment. The two CH1 glycosylated variants showed differences in the extent of glycosylation. Modeling studies suggest that one variant would be better suited for site-specific coupling than the other because the carbohydrate chain is extended further away from the antigen-binding site. The Abs were radioiodinated to determine their pharmacokinetic behavior in mice. All of the humanized Ab divalent fragments cleared nearly 20 times faster from the blood than the murine parent F(ab')2 over a 24-h period. The glycosylated fragments showed some added stability compared to the other fragments over 4 h, but by 24 h, they had cleared to the same extent. Size-exclusion high-performance liquid chromatography of blood samples indicated that the humanized Ab fragments were quickly degraded in the blood. Thus, there is an inherent instability of the divalent fragments from these humanized IgG1 constructs that may affect their utility in imaging or therapy applications.
Localization and Induced Expression of Fusion Genes in the Rat Lung (1991)

Liposome-mediated gene transfer is useful for DNA transfection into cells in culture. We wondered whether this method could be used to introduce new DNA into the intact lung. Fusion genes containing either the Rous sarcoma virus (RSV) promoter or the mouse mammary tumor virus (MMTV) promoter (which contains glucocorticoid response elements) were linked to the bacterial gene chloramphenicol acetyltransferase (CAT), an enzyme not present in mammalian cells. Plasmids containing the RSV-CAT fusion gene were mixed with cationic liposomes (Lipofectin; BRL, Inc., Grand Island, NY), and single doses were instilled into the cervical trachea of anesthetized rats. Control rats received either liposomes or plasmid. After 24, 48, and 72 h, lungs were perfused free of blood, homogenized, and analyzed for CAT enzyme activity. Liver and kidney tissue were also obtained. We found that rats given either intratracheal liposomes or plasmid had no detectable CAT activity. By contrast, 24 h after instillation of lipid:DNA complexes, lung CAT expression remained elevated for the next 48 h but was barely detectable in liver or kidney. In another group of rats, MMTV-CAT:liposome complexes were instilled intratracheally and then the rats were injected with either dexamethasone or saline. We found that the dexamethasone-treated rats had a 5- to 10-fold higher level of lung CAT expression at 24 and 48 h than the saline-treated controls had; liver and kidney CAT levels were negligible in both groups. Dexamethasone treatment did not increase RSV-CAT expression, indicating that the dexamethasone effect on MMTV-CAT expression was related to the presence of the MMTV promoter.(ABSTRACT TRUNCATED AT 250 WORDS)
Significance of birth weight for the future (2002)

hat factors determine birth weight and do they have any biological significance for the future health and welfare of the individual? These are important questions for all paediatricians and four groups of experts have been approached to independently give their thoughts on key areas. The aim was for concise pithy comments and opinions, so the length of the articles was rigourously controlled. Firstly, are there genetic factors that . . . . . . . . . . .
ICP34.5 mutants of herpes simplex virus type 1 strain 17syn+ are attenuated for neurovirulence in mice and for replication in confluent primary mouse embryo cell cultures (1994)

In a recent report, the neurovirulence of herpes simplex virus type 1 (HSV-1) was mapped to the ICP34.5 gene (J. Chou, E. R. Kern, R. J. Whitley, and B. Roizman, Science 250:1262-1266, 1990). In this report, specific mutations within ICP34.5 were constructed in HSV-1 strain 17syn+ to determine the effects of these mutations in a fully neurovirulent isolate. It was found that termination of the ICP34.5 gene after the N-terminal 30 amino acids resulted in a mutant, 17termA, which was 25- to 90-fold reduced in neurovirulence. This reduction of neurovirulence was associated with restricted replication of the mutant virus in mouse brain. The reduced replication phenotype was also evident in the trigeminal and dorsal root ganglia following inoculation at the periphery. 17termA was capable of replicating with wild-type kinetics in mouse footpads, and therefore the restriction seen in neural tissues was not due to a generalized replication defect in mouse cells. Significantly, replication of the mutant was also restricted in the mouse cornea in vivo and in confluent primary mouse embryo cells and mouse 10T1/2 cells in vitro. However, 17termA replicated with much greater efficiency in subconfluent mouse embryo cells, suggesting that the physiological state of the cell may be an important factor for productive replication of this mutant. Restoration of the ICP34.5 gene to the mutant resulted in a virus which displayed wild-type neurovirulence and replication kinetics in all cells and tissues tested.
.ALPHA.-Methylene-.GAMMA.-butyrolactones: Synthesis and Vasorelaxing Activity Assay of Coumarin, Naphthalene, and Quinoline Derivatives. (1998)

Certain alpha-methylene-gamma-butyrolactone derivatives of coumarin, naphthalene, and quinoline were synthesized and evaluated for vasorelaxing effects on isolated rat thoracic aorta. The 7-[(2,3,4,5-tetrahydro-2-methyl-4-methylene-5-oxo-2-furanyl)methoxy]-2H- 1- benzopyran-2-ones, which have an aliphatic methyl substituent at the lactone C2, were more active than their C2-phenyl counterparts against high-K+ (80 mM) medium, Ca2+ (1.9 mM)-induced vasoconstriction and the norepinephrine (NE, 3 microM)-induced phasic and tonic constrictions (2a vs. 2b; 2c vs. 2d; 2e vs. 2f; 2g vs. 2h). Although 3-chloro-7-[(2,3,4,5-tetrahydro-2-methyl-4-methylene-5-oxo-2- furanyl)methoxy]-4-methyl-2H-1-benzopyran-2-one (2g) demonstrated the most potent inhibitory activities on the NE-induced phasic and tonic constrictions at concentrations of as low as 10 micrograms/ml, it possesses both affinity for NE-receptor and intrinsic activity to trigger the vasoconstriction. However, 8-[(2,3,4,5-tetrahydro-2-methyl-4-methylene-5-oxo-2- furanyl)methoxy]quinoline (10a) and other quinoline derivatives (11a, 12a) are pure irreversible non-competitive blockers of NE-receptor with no intrinsic activity. The aromatic ring played an important role in the vasorelaxing effects of alpha-methylene-gamma-butyrolactones; naphthalene was inactive, quinolines exhibited only affinity to the alpha-receptor, and coumarins possessed both affinity and intrinsic activity.
Plant Protein Hydrolysates: Preparation of Defined Peptide Fractions Promoting Growth and Production in Animal Cells Cultures (2000)

A new approach was applied with the aim at producing plant protein hydrolysates less heterogeneous and less contaminated with nonpeptide substances than are the presently available digests. A significant reduction of nonprotein contaminants was achieved by extraction of the plant material, soy flour or wheat flour, with acetone prior to isolation of the protein. Enzymes of nonanimal origin, papain or Pronase, were used for protein hydrolysis. The components of the hydrolysates were resolved by low-pressure liquid chromatography. Separation of peptide fractions and of remaining nonpeptide contaminants was achieved using small-pore size-exclusion chromatography matrices, Sephadex G-15 or Biogel P-2. Individual peptide fractions, both from soy protein and from wheat gluten, varied substantially in their growth-promoting and production-enhancing activities when tested on a mouse hybridoma culture in protein-free medium. The highest enhancement of viable cell density in batch cultures was 180% of control, and the highest enhancement of final immunoglobulin concentration was more than 230% of control. The existence of marked differences in activity of individual peptide fractions leads to a suggestion that the hydrolysates may provide peptides exerting specific positive effects on cultured animal cells.
Neurotrophic Effects of Extracellular Guanosine (2008)

Central nervous system (CNS) astrocytes release guanosine extracellularly, that exerts trophic effects. In CNS, extracellular guanosine (GUO) stimulates mitosis, synthesis of trophic factors, and cell differentiation, including neuritogenesis, is neuroprotective, and reduces apoptosis due to several stimuli. Specific receptor-like binding sites for eGUO in the nervous system may mediate its effects through both MAP kinase and PI3-kinase signalling pathways. Extracellular guanine (eGUA) also exerts several effects; the trophic effects of eGUO are likely regulated by conversion of eGUO to eGUA by a membrane located purine nucleoside phosphorylase (ecto-PNP) and by conversion of eGUA to xanthine by guanine deaminase.
Core-scale heterogeneity and dual-permeability pore structure in the Barnett Shale (2014)

I present a stratigraphically layered dual-permeability model composed of thin, alternating, high (~9.2x 10 -20 m 2 ) and low (~3.0 x 10 -22 m 2 ) permeability layers to explain pressure dissipation observed during pulse-decay permeability testing on an intact Barnett Shale core.I combine both layer parallel and layer perpendicular measurements to estimate layer permeability and layer porosity.Micro-computed x-ray tomography and scanning electron microscopy confirm the presence of alternating cm-scale layers of silty-claystone and organic-rich claystone.I interpret that the silty-claystone has a permeability of 9.2 x 10 -20 m 2 (92 NanoDarcies) and a porosity of 1.4% and that the organic-rich claystone has a permeability of 3.0 x 10 -22 m 2 (0.3 NanoDarcies) and a porosity of 14%.A layered architecture explains the horizontal (k H = 107 x 10 -21 m 2 ) to vertical (k V = 2.3 x 10 -21 m 2 ) permeability anisotropy ratio observed in the Barnett Shale.These core-scale results suggest that spacing between high-permeability carrier beds can influence resource recovery in shales at the reservoir-scale.I also illustrate the characteristic pulse-decay behavior of core samples with multiple mutually-orthogonal vii fracture planes, ranging from a single planar fracture to the Warren and Root (1963) "sugar cube" model with three mutually-orthogonal fracture sets.By relating sub corescale matrix heterogeneity to core-scale gas transport, this work is a step towards upscaling experimental permeability results to describe in-situ gas flow through matrix at the reservoir scale.viii
The antiinflammatory mechanism of methotrexate. Increased adenosine release at inflamed sites diminishes leukocyte accumulation in an in vivo model of inflammation. (1993)

Methotrexate, a folate antagonist, is a potent antiinflammatory agent when used weekly in low concentrations. We examined the hypothesis that the antiphlogistic effects of methotrexate result from its capacity to promote intracellular accumulation of 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) that, under conditions of cell injury, increases local adenosine release. We now present the first evidence to establish this mechanism of action in an in vivo model of inflammation, the murine air pouch model. Mice were injected intraperitoneally with either methotrexate or saline for 3-4 wk during induction of air pouches. Pharmacologically relevant doses of methotrexate increased splenocyte AICAR content, raised adenosine concentrations in exudates from carrageenan-inflamed air pouches, and markedly inhibited leukocyte accumulation in inflamed air pouches. The methotrexate-mediated reduction in leukocyte accumulation was partially reversed by injection of adenosine deaminase (ADA) into the air pouch, completely reversed by a specific adenosine A2 receptor antagonist, 3,7-dimethyl-1-propargylxanthine (DMPX), but not affected by an adenosine A1 receptor antagonist, 8-cyclopentyl-dipropylxanthine. Neither ADA nor DMPX affected leukocyte accumulation in the inflamed pouches of animals treated with either saline or the potent antiinflammatory steroid dexamethasone. These results indicate that methotrexate is a nonsteroidal antiinflammatory agent, the antiphlogistic action of which is due to increased adenosine release at inflamed sites.
Blinatumomab, a Bi-Specific Anti-CD19/CD3 BiTEÂ® Antibody for the Treatment of Acute Lymphoblastic Leukemia: Perspectives and Current Pediatric Applications (2014)

Leukemia is the most common childhood malignancy and acute lymphoblastic leukemia (ALL) represents the largest sub-type. Despite remarkable improvements over the last 40 years, standard therapy fails in 10-20% of newly diagnosed patients. Survival for children with relapsed ALL is poor, and the development and implementation of novel therapeutic strategies in pediatric ALL are critical to further advancements. Immunotherapeutic approaches have been central to more novel ALL therapies. However, more recent innovation in antibody engineering has improved potency and efficacy, and antibody-drug conjugates (ADCs) are an especially attractive option in severely immunocompromised patients. An even more sophisticated antibody design is that of bi-specific T-cell engaging or BiTE(®) antibodies, which directly recruit effector T cells to augment the anti-neoplastic effect. This review focuses on blinatumomab, a bi-specific anti-CD19/CD3 antibody that has shown efficacy in adult patients with precursor B-ALL and is currently being evaluated in the pediatric setting.
Role of p38 and p44/42 mitogen‐activated protein kinases in microglia (2002)

Although microglial cells are thought to play a beneficial role in the regeneration and plasticity of the central nervous system (CNS), recent studies have indicated that at least some molecules released by microglia may be harmful in acute brain insults and neurodegenerative diseases. Therefore, the pathways mediating the synthesis and release of these neurotoxic compounds are of importance. p38 and p44/42 families of mitogen-activated protein kinases (MAPKs) in microglia respond strongly to various extracellular stimuli, such as ATP, thrombin, and beta-amyloid, a peptide thought to be responsible for the neuropathology in Alzheimer's disease. In this review we describe in vivo evidence implicating that p38 and p44/42 MAPKs may play a critical role in harmful microglial activation in acute brain injury, such as stroke, and in more chronic neurodegenerative diseases, such as Alzheimer's disease. We also clarify the extracellular signals responsible for activation of p38 and p44/42 MAPK in microglia and review the responses so far reported to be mediated by these kinases.