gebhart/patrepeval huggingface dataset:
Glycosylation and proteolytic processing of 70 kDa C-terminal recombinant polypeptides of Plasmodium falciparum merozoite surface protein 1 expressed in mammalian cells (1999)

The cDNAs that encode the 70 kDa C-terminal portion of Plasmodium falciparum merozoite surface protein 1 (MSP-1), with or without an N-terminal signal peptide sequence and C-terminal glycosylphosphatidylinositol (GPI) signal sequence of MSP-1, were expressed in mammalian cell lines via recombinant vaccinia virus. The polypeptides were studied with respect to the nature of glycosylation, localization, and proteolytic processing. The polypeptides derived from the cDNAs that contained the N-terminal signal peptide were modified with N -linked high mannose type structures and low levels of O -linked oligosaccharides, whereas the polypeptides from the cDNAs that lacked the signal peptide were not glycosylated. The GPI anchor moiety is either absent or present at a very low level in the polypeptide expressed from the cDNA that contained both the signal peptide and GPI signal sequences. Together, these data establish that whereas the signal peptide of MSP-1 is functional, the GPI anchor signal is either nonfunctional or poorly functional in mammalian cells. The polypeptides expressed from the cDNAs that contained the signal peptide were proteolytically cleaved at their C-termini, whereas the polypeptides expressed from the cDNAs that lacked the signal peptide were uncleaved. While the polypeptide expressed from the cDNA containing both the signal peptide and GPI anchor signal was truncated by approximately 14 kDa at the C-terminus, the polypeptide derived from the cDNA with only the signal peptide was processed to remove approximately 6 kDa, also from the C-terminus. Furthermore, the polypeptides derived from cDNAs that lacked the signal peptide were exclusively localized intra-cellularly, the polypeptides from cDNAs that contained the signal peptide were predominantly intracellular, with low levels on the cell surface; none of the polypeptides was secreted into the culture medium to a detectable level. These results suggest that N -glycosylation alone is not sufficient for the efficient extracellular transport of the recombinant MSP-1 polypeptides through the secretory pathway in mammalian cells.
Selective immunosuppressive action of a factor produced by colon cancer cells. (1990)

A soluble substance (HT29 factor) produced by HT29 colon cancer cells markedly suppresses mitogen-induced T-cell proliferation and interleukin-2 production. In this study the range of T-cell functions susceptible to the inhibitory effects of the HT29 factor was evaluated. Serum-free conditioned medium was collected from confluent cultures of HT29 cancer cells, concentrated, and subjected to gel filtration chromatography and anion exchange chromatography, resulting in 24.4-fold purification of the HT29 factor with 31% yield. This factor abolished the development of lymphokine-activated killer cells when present during activation of peripheral blood lymphocytes by interleukin-2 but did not affect the lysis of target cells by normal effectors when added in the lysis stage only. The HT29 factor did not affect the generation of concanavalin A-induced suppressor lymphocytes, even though it markedly inhibited synthesis of DNA, RNA, and protein as well as expression of the CD25 (Tac) antigen during mitogen activation of T-cells. The HT29 factor itself did not induce suppressor cells. These results indicate that the immunosuppressive action of the HT29 factor is selective.
Embryonic Stem Cell Transplantation after Experimental Traumatic Brain Injury Dramatically Improves Neurological Outcome, But May Cause Tumors (2007)

Transplantation of embryonic stem (ES) cells may provide cures for the damaged nervous system. Pre-differentiated ES or neuronal precursor cells have been investigated in various animal models of neurodegenerative diseases including traumatic brain injury (TBI). To our knowledge, no study has yet examined the effects of undifferentiated, murine ES cells on functional recovery and tumorigenity following implantation into injured rat brains. We evaluated the effect of transplantation of undifferentiated, murine embryonic cells on the recovery of motor function following lateral fluid percussion brain injury in Sprague-Dawley rats. At 3 days post-injury, animals received stereotactic injections of either embryonic stem cell suspension or injections of phosphate buffered saline without cells (control) into the injured cortex. Neurological motor function assessments were performed before injury, 72 h, 1, 3, and 6 weeks after transplantation using a Rotatrod and a Composite Neuroscore test. During this time period brain injured animals receiving ES cell transplantation showed a significant improvement in the Rotarod Test and in the Composite Neuroscore Test as compared to phosphate buffered saline (PBS)-treated animals. At 1 week post-transplantation, ES cells were detectable in 100% of transplanted animals. At 7 weeks following transplantation, EScells were detectable in only one animal. Two of 10 xenotransplanted animals revealed tumor formation over the observation period. These findings provide evidence for therapeutic potency of embryonic stem cell transplantation after TBI in rat, but also raise serious safety concerns about the use of such cells in human.
The Naming of Hosts (1997)

This RFC is a commentary on the difficulty of deciding upon an
acceptably distinctive hostname for one's computer, a problem which
grows in direct proportion to the logarithmically increasing size of
the Internet. This memo provides information for the Internet
community. This memo does not specify an Internet standard of any
kind.
Patterns of gene expression that characterize the colonic mucosa in patients at genetic risk for colonic cancer. (1991)

We have used a computer-driven scanning and image-processing system to identify a panel of 30 cDNA clones whose pattern of expression in individual biopsy specimens distinguishes the flat, normal-appearing colonic mucosa of patients in two genetic groups at high risk for development of colorectal cancer from that of normal colonic mucosa in low-risk individuals. The two high-risk groups, familial adenomatous polyposis and hereditary nonpolyposis colon cancer, are indistinguishable based on the pattern of expression of the 30 selected clones. This suggests that the extensive pleiotropic effects of the inherited loci, which may play an important role in the mechanism of increased risk and early onset of the disease, are similar in these populations.
Opiate Analgesia: Evidence for Mediation by a Subpopulation of Opiate Receptors (1980)

Naloxazone, a hydrazone derivative of the opiate antagonist naloxone, has a high affinity for opiate receptor binding sites. Naloxazone injections reduce opiate receptor binding to extensively washed mouse brain membranes for more than 24 hours, suggesting that the effect is irreversible. High-affinity binding sites are abolished by this treatment, whereas low-affinity sites are unaffected. Naloxazone treatment blocks the analgesic effects of morphine for at least 24 hours but does not prevent death from high doses of morphine. Thus analgesic but nonlethal opiate effects may be mediated by the high-affinity subpopulation of opiate receptors.
The fibroblast: Sentinel cell and local immune modulator in tumor tissue (2003)

Development and progression of epithelial malignancies are frequently accompanied by complex phenotypic alterations of resident tissue fibroblasts. Some of these changes, such as myofibroblastic differentiation and an oncofetal extracellular matrix (ECM) expression profile, are also implicated in inflammation and tissue repair. Studies over the past decade revealed the relevance of reciprocal interactions between tumor cells and tumor-associated host fibroblasts (TAF) in the malignant process. In many tumors, a considerable fraction of the inflammatory infiltrate is located within the fibroblast- and ECM-rich stromal compartment. However, while fibroblasts are known as "sentinel cells" in various nonneoplastic diseases, where they often regulate the composition and function of recruited leucocytes, they are hardly considered active participants in the inflammatory host response in tumors. This article focuses on the functional impact of TAF on immune cells. The complex network of immune-modulating effects transduced by TAF and TAF-derived factors is highlighted, and recent reports that support the hypothesis that TAF are involved in the inflammatory response and immune suppression in tumors are reviewed. The role of TAF-dependent ECM remodeling and TAF-derived peptide growth factors, cytokines, and chemokines in the immune modulation is stressed and the idea of TAF as an important therapeutic target is emphasized.
Guidelines for the prevention, detection and management of people with chronic heart failure in Australia 2006 (2006)

Chronic heart failure (CHF) is found in 1.5%-2.0% of Australians. Considered rare in people aged less than 45 years, its prevalence increases to over 10% in people aged >/= 65 years. CHF is one of the most common reasons for hospital admission and general practitioner consultation in the elderly (>/= 70 years). Common causes of CHF are ischaemic heart disease (present in > 50% of new cases), hypertension (about two-thirds of cases) and idiopathic dilated cardiomyopathy (around 5%-10% of cases). Diagnosis is based on clinical features, chest x-ray and objective measurement of ventricular function (eg, echocardiography). Plasma levels of B-type natriuretic peptide (BNP) may have a role in diagnosis, primarily as a test for exclusion. Diagnosis may be strengthened by a beneficial clinical response to treatment(s) directed towards amelioration of symptoms. Management involves prevention, early detection, amelioration of disease progression, relief of symptoms, minimisation of exacerbations, and prolongation of survival.
Gaussian Process Regression for Model Estimation (2008)

Optimal enhancement of the hybridization signal was developed for the detection of porcine circovirus (PCV) 2 in formalin-fixed, paraffin-wax-embedded tissues from pigs with postweaning multisystemic wasting syndrome. The hybridization signal obtained after thermocycler pretreatment was very uniform across the section, whereas the signal obtained after either proteinase K or microwave pretreatment not only was weaker but was of variable intensity across sections. Thermocycler pretreatment combined with brief proteinase K digestion can enhance signal detection for target viral nucleic acid in formalin-fixed, paraffin-wax-embedded tissues. A strong hybridization signal was detected in the cytoplasm of macrophages and multinucleated giant cells in lymph node and spleen without background staining and morphological damage. The technical improvement results, therefore, in an identical background at the same time as an increased signal and, thus, may help detect lower levels of PCV2 DNA in formalin-fixed, paraffin-wax-embedded tissues.
Determination of Aromatic Compounds in Water by Solid Phase Microextraction and Ultraviolet Absorption Spectroscopy. 1. Methodology (1997)

A simple method is described for determining aromatic compounds (i.e., benzene, toluene, ethylbenzene, etc.) in water that combines solid phase microextraction (SPME) and ultraviolet (UV) absorption spectroscopy. The extraction medium consists of a small “chip” of poly(dimethylsiloxane) (total volume of ∼80 μL) that is immersed in a water sample contaminated with an aromatic compound. Equilibrium is first allowed to establish between the analyte in the water and the extraction medium, and the concentration of the aromatic compound is then determined directly in the sorbent chip by UV spectroscopy. Calibration information on this new method was obtained for 11 aromatic compounds commonly found in unleaded gasoline (e.g., benzene, toluene, naphthalene, etc). It was found that equilibrium is established in the range of 30−50 min, with the exception of 1-methylnaphthalene and naphthalene, which equilibrated within 100 min. Detection limits for the aromatic compounds at their equilibration times range from 0.40 to 12 ppb except for benzene (97 ppb). Relative standard deviations of the SPME-UV measurements are 3−12%.
A new RAPD marker for beet necrotic yellow vein virus resistance gene in Beta vulgaris (2009)

RAPD markers linked to beet necrotic yellow vein virus (BNYVV) resistance genes were identified in two Beta vulgaris accessions Holly-1-4 and WB42 using bulked segregant analysis. The polymorphism revealed by the RAPD markers in the F2 generations of WB42 was higher than that of Holly-1-4. The segregation distortion at marker loci was slightly lower in the B. vulgaris Ă B. maritima cross than in the B. vulgaris Ă B. vulgaris cross. For Holly-1-4, a RAPD marker was identified in a long distance from the resistance gene of Rz 1 . However, a RAPD marker tightly linked with Rz 2 gene in repulsion phase was detected with an approximate distance of 0.036 rf. This marker was not generation specific and showed high repeatability. The distance between Rz 1 and Rz 2 genes was estimated as 0.464 rf. After the Rz 2 Rz 2 and Rz 2 rz 2 genotypes were identified using ELISA values and repulsion phase RAPD markers, comparison of their ELISA means revealed lack of the gene dosage effects. Nevertheless, under the field or severe infection conditions, the difference between ELISA mean values of the Rz 2 Rz 2 and Rz 2 rz 2 genotypes might be more than that observed in this study and the gene dosage effects of Rz 2 allele might be important.
Transdermal deferoxamine prevents pressure-induced diabetic ulcers (2014)

There is a high mortality in patients with diabetes and severe pressure ulcers. For example, chronic pressure sores of the heels often lead to limb loss in diabetic patients. A major factor underlying this is reduced neovascularization caused by impaired activity of the transcription factor hypoxia inducible factor-1 alpha (HIF-1α). In diabetes, HIF-1α function is compromised by a high glucose-induced and reactive oxygen species-mediated modification of its coactivator p300, leading to impaired HIF-1α transactivation. We examined whether local enhancement of HIF-1α activity would improve diabetic wound healing and minimize the severity of diabetic ulcers. To improve HIF-1α activity we designed a transdermal drug delivery system (TDDS) containing the FDA-approved small molecule deferoxamine (DFO), an iron chelator that increases HIF-1α transactivation in diabetes by preventing iron-catalyzed reactive oxygen stress. Applying this TDDS to a pressure-induced ulcer model in diabetic mice, we found that transdermal delivery of DFO significantly improved wound healing. Unexpectedly, prophylactic application of this transdermal delivery system also prevented diabetic ulcer formation. DFO-treated wounds demonstrated increased collagen density, improved neovascularization, and reduction of free radical formation, leading to decreased cell death. These findings suggest that transdermal delivery of DFO provides a targeted means to both prevent ulcer formation and accelerate diabetic wound healing with the potential for rapid clinical translation.
Cell surface expression of heat shock protein gp96 enhances cross-presentation of cellular antigens and the generation of tumor-specific T cell memory. (2003)

Gp96 is an endoplasmic reticular heat shock protein (HSP). We have shown previously that surface expression of gp96 (96tm) on tumor cells led to the activation of dendritic cells and increased anti-tumor immunity. In this report, we have found that protective immunity elicited by 96tm+ tumor cells was tumor-specific and long-lasting. Both CD4+ and CD8+ T cell memory were elicited. By immunizing with tumor cells loaded with the chicken ovalbumin (ova) model antigen, we demonstrated that the priming of adoptively transferred ova-specific CD8+ T cells could occur across MHC haplotypes. The efficiency of this cross priming can be significantly increased when mice were immunized with whole cells that express both ova and cell surface gp96 (ova+96tm+). Mere mixture of soluble ova with 96tm-expressing tumor cells (ova-96tm+) was insufficient, arguing for further processing of ova and perhaps the participation of 96tm-ova complexes in this process. We further compared the relative efficiency of two whole cell vaccines based on the manipulation of gp96 expression in one system: 96tm+ whole cells and cells that secrete the gp96-Ig fusion protein. We found that both vaccines are effective in a prophylactic model against tumors. Our study has reinforced the notion that the manipulation of the site of expression of HSPs may be an effective approach for cancer immunotherapy.
A New 2.5D Representation for Lymph Node Detection using Random Sets of Deep Convolutional Neural Network Observations (2014)

Automated Lymph Node (LN) detection is an important clinical diagnostic task but very challenging due to the low contrast of surrounding structures in Computed Tomography (CT) and to their varying sizes, poses, shapes and sparsely distributed locations. State-of-the-art studies show the performance range of 52.9% sensitivity at 3.1 false-positives per volume (FP/vol.), or 60.9% at 6.1 FP/vol. for mediastinal LN, by one-shot boosting on 3D HAAR features. In this paper, we first operate a preliminary candidate generation stage, towards 100% sensitivity at the cost of high FP levels (40 per patient), to harvest volumes of interest (VOI). Our 2.5D approach consequently decomposes any 3D VOI by resampling 2D reformatted orthogonal views N times, via scale, random translations, and rotations with respect to the VOI centroid coordinates. These random views are then used to train a deep Convolutional Neural Network (CNN) classifier. In testing, the CNN is employed to assign LN probabilities for all N random views that can be simply averaged (as a set) to compute the final classification probability per VOI. We validate the approach on two datasets: 90 CT volumes with 388 mediastinal LNs and 86 patients with 595 abdominal LNs. We achieve sensitivities of 70%/83% at 3 FP/vol. and 84%/90% at 6 FP/vol. in mediastinum and abdomen respectively, which drastically improves over the previous state-of-the-art work.
The proper ratio of FtsZ to FtsA is required for cell division to occur in Escherichia coli (1992)

Interactions among cell division genes in Escherichia coli were investigated by examining the effect on cell division of increasing the expression of the ftsZ, ftsA, or ftsQ genes. We determined that cell division was quite sensitive to the levels of FtsZ and FtsA but much less so to FtsQ. Inhibition of cell division due to an increase in FtsZ could be suppressed by an increase in FtsA. Inhibition of cell division due to increased FtsA could be suppressed by an increase in FtsZ. In addition, although wild-type strains were relatively insensitive to overexpression of ftsQ, we observed that cell division was sensitized to ftsQ overexpression in ftsI, ftsA, and ftsZ mutants. Among these, the ftsI mutant was the most sensitive. These results suggest that these gene products may interact and that the proper ratio of FtsZ to FtsA is critical for cell division to occur.
A pore way to die: the role of mitochondria in reperfusion injury and cardioprotection (2010)

In addition to their normal physiological role in ATP production and metabolism, mitochondria exhibit a dark side mediated by the opening of a non-specific pore in the inner mitochondrial membrane. This mitochondrial permeability transition pore (MPTP) causes the mitochondria to breakdown rather than synthesize ATP and, if unrestrained, leads to necrotic cell death. The MPTP is opened in response to Ca(2+) overload, especially when accompanied by oxidative stress, elevated phosphate concentration and adenine nucleotide depletion. These conditions are experienced by the heart and brain subjected to reperfusion after a period of ischaemia as may occur during treatment of a myocardial infarction or stroke and during heart surgery. In the present article, I review the properties, regulation and molecular composition of the MPTP. The evidence for the roles of CyP-D (cyclophilin D), the adenine nucleotide translocase and the phosphate carrier are summarized and other potential interactions with outer mitochondrial membrane proteins are discussed. I then review the evidence that MPTP opening mediates cardiac reperfusion injury and that MPTP inhibition is cardioprotective. Inhibition may involve direct pharmacological targeting of the MPTP, such as with cyclosporin A that binds to CyP-D, or indirect inhibition of MPTP opening such as with preconditioning protocols. These invoke complex signalling pathways to reduce oxidative stress and Ca(2+) load. MPTP inhibition also protects against congestive heart failure in hypertensive animal models. Thus the MPTP is a very promising pharmacological target for clinical practice, especially once more specific drugs are developed.
The in vivo histology of an absorbable suture anchor: a preliminary report (1995)

Suture anchors are playing an increasingly important role in attaching tendons or ligaments to bone. Anchors are usually made of metallic or other nonbioabsorbable materials. The development of an absorbable suture anchor would provide a valuable tool for the surgeon; this characteristic would minimize the problems of anchor loosening, migration, interference with imaging studies, and the potential requirement for later implant removal. This study evaluated the in vivo histological response over time of the first generation Arthrex Expanding Suture Plug (ESP) (Arthrex Inc, Naples, FL). Suture anchors threaded with nonabsorbable No. 2 braided polyester sutures were implanted into ram femurs and removed at various intervals over a period of 12 weeks. After preparation, histological study showed a gradual healing response in the bone tract. There was no evidence of an inflammatory infiltrate or foreign-body reaction during the 12 weeks of implantation. A normal bone callus appeared at the insertion tunnel site consistent with a fracture-healing response. Later, a fibrous membrane appeared at the junction of the implant and the bone tunnel. Over the 12 week interval, there was a decrease in osteoblastic activity and the appearance of cavernous vascular spaces in the superficial portions of the membrane near the periosteum. The ESP anchor composed of poly-L-lactic acid was well tolerated in the in vivo setting. Throughout the study, no substantial acute, chronic, or foreign-body reaction was observed. These observations are consistent with the expected in vivo behavior of poly-L-lactic acid. There is no reason to believe that the ESP composed of poly-L-lactic acid should cause a foreign body reaction.
Isolation and characterization of four major neutral glycosphingolipids from the liver of the English sole (Parophrys vetulus). Presence of a novel branched lacto-ganglio-iso-globo hybrid structure. (1988)

We have previously reported on carbohydrate structures of the major acidic glycosphingolipids from the liver of the English sole, Parophrys vetulus (Ostrander, G. K., Levery, S. B., Hakomori, S., and Holmes, E. H. (1988) J. Biol. Chem. 263, 3103-3110). We have now isolated four major neutral glycosphingolipids from English sole liver. They have been characterized by 1H nuclear magnetic resonance spectroscopy, methylation analysis, and by fast atom bombardment-mass spectrometry. In addition to neutral glycosphingolipids with known structures (CMH, lactosylceramide, and Gg3), a major polar neutral glycosphingolipid was isolated and characterized as having the following novel structure: (formula; see text) The compound represents a novel hybrid of neolacto-, ganglio-, and iso-globo-series glycosphingolipid structures, a combination not previously encountered. Furthermore, the linkage Fuc alpha 1----3GalNac has not been previously reported for a glycosphingolipid. The relationship of these structural elements to known glycoconjugates is discussed.