gebhart/patrepeval huggingface dataset:
Anti-inflammatory Activity of a High-molecular-weight Cranberry Fraction on Macrophages Stimulated by Lipopolysaccharides from Periodontopathogens (2006)

Periodontitis is a chronic inflammatory disease affecting oral tissues. The continuous, high production of cytokines by host cells triggered by periodontopathogens is thought to be responsible for the destruction of tooth-supporting tissues. Macrophages play a critical role in this host inflammatory response to periodontopathogens. The aim of this study was to investigate the effect of non-dialyzable material prepared from cranberry juice concentrate on the pro-inflammatory cytokine response of macrophages induced by lipopolysaccharides (LPS) from Actinobacillus actinomycetemcomitans, Fusobacterium nucleatum subsp. nucleatum, Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Escherichia coli. Interleukin-1 beta (IL-1beta), IL-6, IL-8, tumor necrosis factor alpha (TNF-alpha), and Regulated on Activation Normal T-cell Expressed and Secreted (RANTES) production by macrophages treated with the cranberry fraction prior to stimulation by LPS was evaluated by ELISA. Our results clearly indicate that the cranberry fraction was a potent inhibitor of the pro-inflammatory cytokine and chemokine responses induced by LPS. This suggests that cranberry constituents may offer perspectives for the development of a new therapeutic approach to the prevention and treatment of periodontitis.
Diffusible signals and interspecies communication in bacteria (2008)

Many bacteria use cell-cell communication mediated by diffusible signal molecules to monitor their population density or confinement to niches and to modulate their behaviour in response to these aspects of their environment. Work on signalling systems within individual species has formed a platform for studies of interspecies interactions that can occur within polymicrobial communities in nature. In addition to signalling between organisms that synthesize the same or related signal molecules, it is becoming evident that bacteria can sense signal molecules that they do not synthesize, thereby eavesdropping on signalling by other organisms in their immediate environment. Furthermore, molecules such as antibiotics that are considered not to be signals for the producing species can have effects on gene expression in other bacteria that indicate a signalling function. Interspecies signalling can lead to alteration in factors contributing to the virulence or persistence of bacterial pathogens as well as influencing the development of beneficial microbial communities. Here we review our current understanding of interspecies signalling in bacteria and the signals involved, what is known of the underlying signal transduction mechanisms and their influences on bacterial behaviour.
A proteolytic pathway that controls the cholesterol content of membranes, cells, and blood (1999)

The integrity of cell membranes is maintained by a balance between the amount of cholesterol and the amounts of unsaturated and saturated fatty acids in phospholipids. This balance is maintained by membrane-bound transcription factors called sterol regulatory element-binding proteins (SREBPs) that activate genes encoding enzymes of cholesterol and fatty acid biosynthesis. To enhance transcription, the active NH(2)-terminal domains of SREBPs are released from endoplasmic reticulum membranes by two sequential cleavages. The first is catalyzed by Site-1 protease (S1P), a membrane-bound subtilisin-related serine protease that cleaves the hydrophilic loop of SREBP that projects into the endoplasmic reticulum lumen. The second cleavage, at Site-2, requires the action of S2P, a hydrophobic protein that appears to be a zinc metalloprotease. This cleavage is unusual because it occurs within a membrane-spanning domain of SREBP. Sterols block SREBP processing by inhibiting S1P. This response is mediated by SREBP cleavage-activating protein (SCAP), a regulatory protein that activates S1P and also serves as a sterol sensor, losing its activity when sterols overaccumulate in cells. These regulated proteolytic cleavage reactions are ultimately responsible for controlling the level of cholesterol in membranes, cells, and blood.
MR imaging of adrenal masses: value of chemical-shift imaging for distinguishing adenomas from other tumors. (1995)

Our results show that chemical-shift MR imaging is an important new technique that enables the differentiation of adrenal adenomas from other adrenal masses, reducing the need for biopsy and prolonged imaging follow-up in patients with adrenal tumors.
Deconstructing the Cell Wall (1994)

Any microorganism that attempts to colonize a plant must contend with the cell wall. One of the most conspicuous effects of microorganisms on plant cell walls is enzymic degradation. Our interpretation of the significance of this depends on our concept of the plant cell wall, which, however, is paradoxical. On the one hand, the wall is an inert mechanical support and barrier; on the other hand, the wall is a dynamic, metabolically active organelle (Robinson, 1991, and refs. therein). The wall is a nutritional source for microorganisms and animals, yet it contains noxious peroxidases, phenolics, and activated oxygen (Cooper, 1984). The wall is mainly carbohydrate, yet its proteins are disproportionately studied (Showalter, 1993). Degradation poses another paradox. On the one hand, plant cell walls are the world's most abundant source of Glc and other sugars; on the other hand, parts of it are resistant to degradation. Since all the polymers of a plant cell wall are eventually degraded by microorganisms, for every type of chemical bond in the wall there must be an enzyme that can cleave it. Some polysaccharidases such as a-amylase are widespread in nature; others, such as ligninase, are very restricted in their distribution.
Oral prodrug of remdesivir parent GS-441524 is efficacious against SARS-CoV-2 in ferrets (2021)

Remdesivir is an antiviral approved for COVID-19 treatment, but its wider use is limited by intravenous delivery. An orally bioavailable remdesivir analog may boost therapeutic benefit by facilitating early administration to non-hospitalized patients. This study characterizes the anti-SARS-CoV-2 efficacy of GS-621763, an oral prodrug of remdesivir parent nucleoside GS-441524. Both GS-621763 and GS-441524 inhibit SARS-CoV-2, including variants of concern (VOC) in cell culture and human airway epithelium organoids. Oral GS-621763 is efficiently converted to plasma metabolite GS-441524, and in lungs to the triphosphate metabolite identical to that generated by remdesivir, demonstrating a consistent mechanism of activity. Twice-daily oral administration of 10 mg/kg GS-621763 reduces SARS-CoV-2 burden to near-undetectable levels in ferrets. When dosed therapeutically against VOC P.1 gamma γ, oral GS-621763 blocks virus replication and prevents transmission to untreated contact animals. These results demonstrate therapeutic efficacy of a much-needed orally bioavailable analog of remdesivir in a relevant animal model of SARS-CoV-2 infection.
Inhibition of Alzheimer β-Fibrillogenesis by Melatonin (1998)

It is generally postulated that the amyloid beta protein (Abeta) plays a central role in the progressive neurodegeneration observed in Alzheimer's disease. Important pathologic properties of this protein, such as neurotoxicity and resistance to proteolytic degradation, depend on the ability of Abeta to form beta-sheet structures or amyloid fibrils. We report that melatonin, a hormone recently found to protect neurons against Abeta toxicity, interacts with Abeta1-40 and Abeta1-42 and inhibits the progressive formation of beta-sheets and amyloid fibrils. These interactions between melatonin and the amyloid peptides were demonstrated by circular dichroism and electron microscopy for Abeta1-40 and Abeta1-42 and by nuclear magnetic resonance spectroscopy for Abeta1-40. Inhibition of beta-sheets and fibrils could not be accomplished in control experiments when a free radical scavenger or a melatonin analog were substituted for melatonin under otherwise identical conditions. In sharp contrast with conventional anti-oxidants and available anti-amyloidogenic compounds, melatonin crosses the blood-brain barrier, is relatively devoid of toxicity, and constitutes a potential new therapeutic agent in Alzheimer's disease.
Novel determinant (comA) essential for natural transformation competence in Neisseria gonorrhoeae and the effect of a comA defect on pilin variation (1993)

A novel genetic determinant (comA) has been identified and found to be required for the transformation of piliated Neisseria gonorrhoeae. Mutants in comA of strain MS11 grow normally and are DNA-uptake proficient but blocked in the translocation of DNA into the cytoplasm. Here we show by site-specific mutagenesis and genetic complementation that only one of two open reading frames identified in comA is essential for competence: it encodes a protein (ComA) with a predicted size of 74 kDa. The comA gene maps upstream of the iga locus and is transcribed in the opposite orientation, probably under the control of a putative sigma 54-type promoter. While DNA probes specific for the N. gonorrhoeae iga locus reveal only a little cross-reactivity with commensal Neisseria species, the neighbouring comA gene appears to be present in most of them. ComA fusion proteins were obtained by in vitro translation. The synthesized gene products migrated atypically in SDS gels indicating its strong hydrophobicity. Several transmembrane alpha-helices were predicted from the amino acid sequence of ComA which, in the context of an observed sequence similarity with other inner membrane proteins, suggests a location for the protein in the inner membrane. Using piliated and non-piliated comA mutants the consequences of transformation deficiency on pilin phase variation were assessed. We show that the comA defect affects some but not all types of DNA rearrangements associated with pilE variation. The results are in agreement with previous observations supporting the notion that multiple recombination pathways contribute to the variability of pilE.
Cloning and sequencing of the genes for Shiga toxin from Shigella dysenteriae type 1 (1988)

The structural genes for Shiga toxin, designated stx A and stx B, were cloned from Shigella dysenteriae type 1 3818T, and a nucleotide sequence analysis was performed. Both stx A and stx B were present on a single transcriptional unit, with stx A preceding stx B. The molecular weight calculated for the processed A subunit was 32,225, while the molecular weight of the processed B subunit was 7,691. Comparison of the nucleotide sequences for Shiga toxin and Shiga-like toxin I (SLT-I) from Escherichia coli revealed that the genes for Shiga toxin and SLT-I were greater than 99% homologous; three nucleotide changes were detected in three separate codons of the A subunits. Only one of these codon differences resulted in a change in the amino acid sequence: a threonine in Shiga toxin at position 45 of the A subunit compared with a serine in the corresponding position in SLT-I. Furthermore, Shiga toxin and SLT-I had identical signal peptides for the A and B subunits, as well as identical ribosome-binding sites, a putative promoter, and iron-regulated operator sequences. These findings indicate that Shiga and SLT-I are essentially the same toxin. Southern hybridization studies with total cellular DNA from several Shigella strains and internal toxin probes for SLT-I and its antigenic variant SLT-II showed that a single fragment in S. dysenteriae type 1 hybridized strongly with the internal SLT-I probe. Fragments with weaker homology to the SLT-I probe were detected in S. flexneri type 2a but no other shigellae. No homology between the Shiga-like toxin II (SLT-II) probe and any of the Shigella DNAs was detected. Whereas SLT-I and SLT-II are phage encoded, no phage could be induced from S. dysenteriae type 1 or other Shigella spp. tested. These results suggest that the Shiga (SLT-I) toxin genes responsible for high toxin production are present in a single copy in S. dysenteriae type 1 but not in other shigellae. The findings further suggest that SLT-II genes are absent in shigellae, as are toxin-converting phages.
Faculty Disclosures (2010)

Funding for this monograph has been provided through an unrestricted educational grant from Novartis Oncology. Sponsorship of this monograph does not imply the sponsor's agreement with the views expressed herein. Every effort has been made to ensure that drug usage and other information are presented accurately; however, the ultimate responsibility rests with the prescribing physician. ERS, Akita Biomedical Consulting and its editorial staff, Cancer Control Journal, and Alan F. List, MD, shall not be held responsible for errors or for any consequences arising from the use of information contained herein. Readers are strongly urged to consult any relevant primary literature. No claims or endorsements are made for any drug or compound at present under clinical investigation.
Synthesis and polymerization of the acrylamide derivatives of fatty compounds (2005)

Abstract The Ritter reaction of plant oil triglycerides (such as soybean and sunflower oil) with acrylonitrile was used to introduce acrylamide functionality on the triglyceride. Acrylonitrile and triglycerides were reacted in the presence of H 2 SO 4 , and acrylamide derivatives were obtained in yields of 45 and 50% for sunflower oil and soybean oil, respectively. Radical initiated copolymerization of the acrylamide derivatives of the triglycerides with styrene produced semirigid polymers. Characterization of new monomers and polymers was done by 1 H‐NMR, 13 C‐NMR, IR, and MS. The swelling behavior of the crosslinked network polymers was determined in different solvents. Glass transiton temperature ( T g ) of the cured resin was also determined by differential scanning calorimeter to be 40°C for soybean based polymer and 30°C for sunflower‐based polymer. Homo‐ and copolymerization behavior of acrylamide derivatives of methyl oleate (MOA) and methyl 10‐undecenoate (MUA) were also investigated. The reactivity ratios of these monomers with respect to styrene were determined by the Fineman–Ross method using 1 H‐NMR spectroscopic data. The reactivity ratios were r sty = 1.776; r moa = 0512 for MOA, and r sty = 1.142; r mua = 0.507 for MUA, respectively. Photopolymerization behaviors of MOA and MUA were also investigated using the photoDSC technique and the rate of polymerization of MUA is higher than that of MOA under the same conditions. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 97: 2264–2272, 2005
The Effect of Trace Mineral Fortification Level and Source on Performance of Dairy Cattle (2006)

Five hundred seventy-three cows, balanced by parity and 305-d mature equivalent at dry off, were assigned to 1 of 4 treatments: 1) 75% complexed trace minerals (CTM; 75C): Zn, Mn, Cu, and Co supplied at 75% of NRC (2001) guidelines by Zn-, Mn-, and Cu-specific AA complexes, and cobalt glucoheptonate; 2) 100% inorganic (100I): Zn, Mn, Cu, and Co supplied at 100% of NRC (2001) requirements by sulfate sources; 3) 100% complexed (100C): Zn, Mn, Cu, and Co supplied at 100% of NRC (2001) requirements by CTM; and 4) complexed/ inorganic (C/I): Zn and Cu supplied at 100% of NRC (2001) requirements using a combination of CTM and sulfates and Co and Mn supplied with sources at 9.1 and 3.3 times NRC (2001) requirements using a combination of CTM and sulfates. All percentages of Zn, Cu, Mn, and Co relative to NRC (2001) reflect supplemental contributions and do not include basal diet contributions. Experimental periods were dry period 1, full lactation 1, dry period 2, and 200 d into the subsequent lactation. Reproductive, health, and production information was collected during both lactations. Claw evaluations were conducted at trial start, 150 d into lactation 1, at the end of lactation 1, and 150 d into lactation 2. During lactation 1, C/I cows produced more milk, fat-corrected milk, energy-corrected milk, and fat than 100I cows. During lactation 2, yields of milk, fat-corrected milk, energy-corrected milk, fat, and protein were higher for 100C and C/I cows than for 75C or 100I cows. Fat percentage was highest for 100C cows with no treatment effect on protein content. During lactations 1 and 2, C/I cows had fewer days to first estrus than cows receiving the other treatments. During lactation 2, C/ I cows had fewer services per conception and days open. There were no significant effects of treatment on health. White line separation incidence was lower for 100I cows than 75C cows, whereas heel erosion was higher for the 100I cows than for the C/I cows. Fortification of trace elements with inorganic and complexed sources at or above NRC requirements improved reproductive and productive performance. In addition, cows can be supplemented with CTM at 75% of NRC requirements with no reduction in performance compared with supplementing at 100% of NRC requirements using only sulfate sources of Zn, Mn, Cu, and Co.
Chlamydia pneumoniae Infection of the Central Nervous System Worsens Experimental Allergic Encephalitis (2002)

Experimental allergic encephalitis (EAE) is considered by many to be a model for human multiple sclerosis. Intraperitoneal inoculation of mice with Chlamydia pneumoniae, after immunization with neural antigens, increased the severity of EAE. Accentuation of EAE required live infectious C. pneumoniae, and the severity of the disease was attenuated with antiinfective therapy. After immunization with neural antigens, systemic infection with C. pneumoniae led to the dissemination of the organism into the central nervous system (CNS) in mice with accentuated EAE. Inoculation with Chlamydia trachomatis did not worsen EAE and infectious organisms were not seen in the CNS. These observations suggest that dissemination of C. pneumoniae results in localized infection in CNS tissues in animals with EAE. We propose that infection of the CNS by C. pneumoniae can amplify the autoreactive pool of lymphocytes and regulate the expression of an autoimmune disease.
Leukocyte adhesion in angiogenic blood vessels. Role of E-selectin, P-selectin, and beta2 integrin in lymphotoxin-mediated leukocyte recruitment in tumor microvessels. (1997)

Interaction of circulating leukocytes with tumor microvasculature is a critical event in the recruitment of effector cells into the tumor stroma. We have examined the ability of lymphotoxin (TNF-beta), to stimulate rolling, adhesion, and transmigration of leukocytes in angiogenic blood vessels induced by tumor spheroids of Lewis lung carcinoma (LLC) implanted in dorsal skinfold chambers of nude mice. In the absence of cytokine stimulation, circulating leukocytes failed to appreciably interact with tumor microvessels (TMV), although significant rolling and adhesion was observed in normal vessels. However, stimulation with lymphotoxin (LT) resulted in a rapid increase in the number of fast and slow rolling leukocytes in TMV. Treatment with anti-P-selectin mAb 5H1 resulted in inhibition of fast rollers alone, while combination treatment with anti-P-selectin and anti-E-selectin (9A9) mAbs effectively blocked slow rolling of leukocytes. Superfusion of the lymphotoxin-stimulated neovasculature with leukotriene B4 (LTB4) resulted in stable cell adhesion followed by emigration of leukocytes into the tumor stroma. LTB4-mediated adhesion and transmigration was significantly inhibited by treatment with anti-beta2 mAb 2E6. These studies delineate a multistep cascade of leukocyte adhesion in TMV and demonstrate that stimulation of the neovasculature with cytokines and chemoattractants can result in P- and E-selectin-dependent rolling and beta2-dependent stable adhesion followed by transmigration into the tumor stroma.
An introduction to the geology of central Scotland (1991)

Abstract The first public event of the Silver Jubilee meeting was a lecture introducing the geological background to the seven technical excursions. The text of the talk, which was recorded, is presented with the minimum of amendment but with selected references also included.
Characterization and quantitation of differential Tsix transcripts: implications for Tsix function (2003)

In dosage compensation of female mammals, the accumulation of Xist RNA initiates silencing of one X-chromosome. Xist action is repressed by the antisense gene, Tsix, whose full-length RNA product is complementary to Xist RNA in mice. While previous work showed that Tsix transcription blocks the accumulation of Xist RNA, it is still unclear whether this repression requires the antisense RNA product or whether the antisense transcriptional movement is sufficient. A better understanding of potential mechanisms requires elucidation of Tsix RNA structure and determination of Tsix RNA copy number relative to that of Xist RNA. Previous work indicated that at least some of murine Tsix is spliced and that human TSIX truncates within the 3' end of XIST. Here, further characterization and quantitation of murine Tsix RNA reveal three new findings: first, in undifferentiated embryonic stem cells, Tsix RNA is present at 10-100-fold molar excess over Xist RNA. Second, only 30-60% of Tsix RNA is spliced at known exon-intron junctions. The nearly equal abundance of spliced and unspliced species leaves open possible roles for both isoforms. Finally, Tsix is spliced heterogeneously at the 5' end and most detectable splice variants exhibit only a 1.9 kb region of complementarity between sense and antisense RNAs. Implications for Tsix's possible mechanisms of action are discussed.
Incorporation of a laser range scanner into an image-guided surgical system (2003)

Laser range scanners provide rapid and accurate non-contact methods for acquiring 3D surface data, offering many advntages over other techniques currently available during surgery. The range scanner was incorporated into our image-guided surgery system to augment registration and deformation compensation. A rigid body, embedded with IR diodes, was attached to the scanner for tracking in physical space with an optical localization system. The relationship between the scanner's coordinate system and the tracked rigid body was determined using a calibration phantom. Tracking of the scanner using the calibration phantom resulted in an error of 1.4&plusmn;0.8 mm. Once tracked, data acquired intraoperatively from the range scanner data is registered with preoperative tomographic volumes using the Iterative Closest Point algorithm. Sensitivity studies were performed to ensure that this algorithm effectively reached a global minimum. In cases where tissue deformation is significant, rigid registrations can lead to inaccuracy during surgical navigation. Methods of non-rigid compensation may be necessary, and an initial study using a linearly elastic finite element model is presented. Differences between intraoperative and preoperative surfaces after rigid registration are used to formulate boundary conditions, and the resulting displacement field deforms the preoperative image volume. To test this protocol, a phantom was built, consisting of fiducial points and a silicone liver model. Range scan and CT data were captured both before and after deforming the organ. The pre-deformed images, after registration and modeling, were compared to post-deformation, although there is a noticeable improvement by implementing the finite element model. To improve accuracy, more elaborate surface registration and deformation compensation strategies will be investigated. To improve accuracy, more elaborate surface registration and deformation compensation strategies will be investigated. The ragne scanner is an innovative, uncumbersome, and relatively inexpensive method of collecting intraoperative data. It has been integrated into our image-guided surgical system and software with virtually no overhead.