gebhart/patrepeval huggingface dataset:
Cell surface binding site for Clostridium difficile enterotoxin: evidence for a glycoconjugate containing the sequence Gal alpha 1-3Gal beta 1-4GlcNAc (1986)

This study was undertaken to determine whether a binding site for Clostridium difficile enterotoxin (toxin A) exists in the brush border membranes (BBMs) of the hamster, an animal known to be extremely sensitive to the action of the toxin. Toxin A was the only antigen adsorbed by the BBMs from the culture filtrate of C. difficile. The finding that binding activity could not be destroyed by heat indicated that a carbohydrate moiety might be involved. We therefore examined erythrocytes from various animal species for binding activity since erythrocytes provide a variety of carbohydrate sequences on their cell surfaces. Only rabbit erythrocytes bound the toxin, and the cells agglutinated. A binding assay based on an enzyme-linked immunosorbent assay method for quantifying C. difficile toxin A was used to compare binding of the toxin to hamster BBMs, rabbit erythrocytes, and BBMs from rats, which are less susceptible to the action of C. difficile toxin A than hamsters. Results of this comparison indicated the following order of toxin-binding frequency: rabbit erythrocytes greater than hamster BBMs greater than rat BBMs. Binding of toxin A to hamster BBMs at 37 degrees C was comparable to what has been observed with cholera toxin, but binding was enhanced at 4 degrees C. A similar binding phenomenon was observed with rabbit erythrocytes. Examination of the cell surfaces of hamster BBMs and rabbit erythrocytes with lectins and specific glycosidases revealed a high concentration of terminal alpha-linked galactose. Treatment of both membrane types with alpha-galactosidase destroyed the binding activity. The glycoprotein, calf thyroglobulin, also bound the toxin and inhibited toxin binding to cells. Toxin A did not bind to human erythrocytes from blood group A, B, or O donors. However, after fucosidase treatment of human erythrocytes, only blood group B erythrocytes, which possess the blood group B structure Gal alpha 1-3[Fuc alpha 1-2]Gal beta 1-4GlcNAc-R, bound the toxin. This indicated that toxin A was likely binding to Gal alpha 1-3Gal beta 1-4GlcNAc, a carbohydrate sequence also found on calf thyroglobulin and rabbit erythrocytes. All of the results indicate that hamster BBMs contain a carbohydrate-binding site for toxin A that has at least a Gal alpha 1-3Gal beta 1-4GlcNAc nonreducing terminal sequence.
Plastid Division Is Driven by a Complex Mechanism That Involves Differential Transition of the Bacterial and Eukaryotic Division Rings (2001)

Shin-ya Miyagishima, Manabu Takahara, Toshiyuki Mori, Haruko Kuroiwa, Tetsuya Higashiyama, Tsuneyoshi Kuroiwa, Plastid Division Is Driven by a Complex Mechanism That Involves Differential Transition of the Bacterial and Eukaryotic Division Rings, The Plant Cell, Vol. 13, No. 10 (Oct., 2001), pp. 2257-2268
Frequent and specific immunity to the embryonal stem cell–associated antigen SOX2 in patients with monoclonal gammopathy (2007)

Specific targets of cellular immunity in human premalignancy are largely unknown. Monoclonal gammopathy of undetermined significance (MGUS) represents a precursor lesion to myeloma (MM). We show that antigenic targets of spontaneous immunity in MGUS differ from MM. MGUS patients frequently mount a humoral and cellular immune response against SOX2, a gene critical for self-renewal in embryonal stem cells. Intranuclear expression of SOX2 marks the clonogenic CD138(-) compartment in MGUS. SOX2 expression is also detected in a proportion of CD138(+) cells in MM patients. However, these patients lack anti-SOX2 immunity. Cellular immunity to SOX2 inhibits the clonogenic growth of MGUS cells in vitro. Detection of anti-SOX2 T cells predicts favorable clinical outcome in patients with asymptomatic plasmaproliferative disorders. Harnessing immunity to antigens expressed by tumor progenitor cells may be critical for prevention and therapy of human cancer.
Cellular Localization of Membrane-type Serine Protease 1 and Identification of Protease-activated Receptor-2 and Single-chain Urokinase-type Plasminogen Activator as Substrates (2000)

Membrane-type serine protease 1 (MT-SP1) was recently cloned, and we now report its biochemical characterization. MT-SP1 is predicted to be a type II transmembrane protein with an extracellular protease domain. This localization was experimentally verified using immunofluorescent microscopy and a cell-surface biotinylation technique. The substrate specificity of MT-SP1 was determined using a positional scanning-synthetic combinatorial library and substrate phage techniques. The preferred cleavage sequences were found to be (P4-(Arg/Lys)P3-(X)P2-(Ser)P1-(Arg)P1'-(Ala)) and (P4-(X)P3-(Arg/Lys)P2-(Ser)P1(Arg) P1'(Ala)), where X is a non-basic amino acid. Protease-activated receptor 2 (PAR2) and single-chain urokinase-type plasminogen activator are proteins that are localized to the extracellular surface and contain the preferred MT-SP1 cleavage sequence. The ability of MT-SP1 to activate PARs was assessed by exposing PAR-expressing Xenopus oocytes to the soluble MT-SP1 protease domain. The latter triggered calcium signaling in PAR2-expressing oocytes at 10 nm but failed to trigger calcium signaling in oocytes expressing PAR1, PAR3, or PAR4 at 100 nm. Single-chain urokinase-type plasminogen activator was activated using catalytic amounts of MT-SP1 (1 nm), but plasminogen was not cleaved under similar conditions. The membrane localization of MT-SP1 and its affinity for these key extracellular substrates suggests a role of the proteolytic activity in regulatory events.
Vascular Endothelial Growth Factor Polymorphisms in Relation to Breast Cancer Development and Prognosis (2005)

Although none of the polymorphisms studied in the VEGF gene was found to influence susceptibility to breast cancer significantly, some of the VEGF genotypes and haplotypes may influence tumor growth through an altered expression of VEGF and tumor angiogenesis.
Tissue Inhibitor of Metalloproteinase-1 and -3 Improves Cardiac Function in an Ischemic Cardiomyopathy Model Rat (2014)

Matrix metalloproteinases (MMPs) and a family of tissue inhibitors of metalloproteinases (TIMPs) may contribute to myocardial remodeling in heart failure. TIMPs are the main inhibitors of MMPs and have other MMP-independent functions. Because little is known of the role of TIMPs in the heart, we examined the effects of TIMPs on cardiac fibroblasts (CFs) and cardiomyocytes. In vitro, TIMP-1-4 enhanced smooth muscle actin (SMA) expression in CFs, and TIMP-1 and TIMP-3 enhanced the expression of phosphorylated Smad-3 and phosphorylated transforming growth factor (TGF)-β type 1 receptor in CFs; this effect was inhibited by TGF-β receptor blocker SB-505124. TIMPs-1, -3, and -4 also inhibited the FAK, AKT, and ERK pathways that induce cardiac hypertrophy. TIMP-1 and TIMP-2 suppressed apoptosis in cardiomyocytes; in contrast, TIMP-4 induced apoptosis in CFs. TIMP-2 stimulated collagen synthesis. Collagen gels containing TIMP-1 or TIMP-3, which exhibit cardioprotective effects in vitro, were transplanted to the left ventricular anterior wall of a rat heart model of myocardial infarction. Gel-released TIMP-1 and TIMP-3 significantly improved cardiac function and myocardial remodeling and enhanced SMA expression in the infarcted area in ischemic cardiomyopathy model rats. Further, the transplantation of TIMP-1 or TIMP-3 gels inhibited apoptosis in the ischemic myocardium and reduced MMP-2 activity. TIMPs may be an ideal target of cardiac regeneration therapy.
The biologic window for chimeric l6 radioimmunotherapy (1994)

The clinical importance of understanding these mechanisms is emphasized by the occurrence of measurable tumor regressions in five of the first nine advanced metastatic breast cancer patients treated in this manner. Absence of pulmonary edema and delayed release of dose-dependent IL-2R suggest that targeting of the pulmonary endothelium by L6 or ChL6 is not the major cause of the observed biologic effects. This unique response of a solid tumor to radioimmunoconjugate therapy may be secondary to both the increased delivery of the radioimmunoconjugate to tumor cells caused by enhanced vascular permeability, and to synergistic effects of radiation and activated effector cell mechanisms.
Use of Market Segmentation to Identify Untapped Consumer Needs in Vision Correction Surgery for Future Growth (2003)

There exists a large untapped opportunity for vision correction surgery within the low myope population. Market segmentation analysis helped determine how to best meet this opportunity through repositioning existing procedures or developing new vision correction technology, and could also be applied to identify opportunities in other vision correction populations.
A glucocerebrosidase fusion gene in Gaucher disease. Implications for the molecular anatomy, pathogenesis, and diagnosis of this disorder. (1990)

The molecular diagnosis of Gaucher disease has been difficult due to the existence of several different point mutations in the glucocerebrosidase gene and due to the presence of a tightly linked, highly homologous pseudogene. We now report the occurrence of a "Lepore-like" glucocerebrosidase fusion gene in which the 5' end is the functional gene and the 3' end is the pseudogene. This further complicates the molecular diagnosis of Gaucher disease but sheds light on the molecular anatomy of the glucocerebrosidase gene complex and on the pathogenesis of this important storage disease.
Semi-supervised Lyrics and Solo-singing Alignment (2018)

We propose a semi-supervised algorithm to align lyrics to the corresponding singing vocals. The proposed method transcribes and aligns lyrics to solo-singing vocals using the imperfect transcripts from an automatic speech recognition (ASR) system and the published lyrics. The ASR provides time alignment between vocals and hypothesized lyrical content, while the non-aligned published lyrics correct the hypothesized lyrical content. The effectiveness of the proposed method is validated through three experiments. First, a human listening test shows that 73.32% of our automatically aligned sentence-level transcriptions are correct. Second, the automatically aligned sung segments are used for singing acoustic model adaptation, which reduces the word error rate (WER) of automatic transcription of sung lyrics from 72.08% to 37.15% in an open test. Third, another iteration of decoding and model adaptation increases the amount of reliably decoded segments from 44.40% to 91.96% and further reduces the WER to 36.32%. The proposed framework offers an automatic way to generate reliable alignments between lyrics and solosinging. A large-scale solo-singing and lyrics aligned corpus can be derived with the proposed method, which will be beneficial for music and singing voice related research.
A Robust Passive Damping Method for LLCL-Filter-Based Grid-Tied Inverters to Minimize the Effect of Grid Harmonic Voltages (2013)

In order to minimize the effect of the grid harmonic voltages, harmonic compensation is usually adopted for a grid-tied inverter. However, a large variation of the grid inductance challenges the system stability in case a high-order passive filter is used to connect an inverter to the grid. Although in theory, an adaptive controller can solve this problem, but in such a case the grid inductance may need to be detected online, which will complicate the control system. This paper investigates the relationship between the maximum gain of the controller that still keeps the system stable and the Q-factor for a grid-tied inverter with an RL series or an RC parallel damped high-order power filter. Then, a robust passive damping method for LLCL-filter-based grid-tied inverters is proposed, which effectively can suppress the possible resonances even if the grid inductance varies in a wide range. Simulation and experimental results are in good agreement with the theoretical analysis.
Cell wall anchoring of the Streptococcus pyogenes M6 protein in various lactic acid bacteria (1997)

The M6 protein from Streptococcus pyogenes is the best-characterized member of a family of cell envelope-associated proteins. Based on the observation that the C-terminal sorting signals of these proteins can drive cell wall anchoring of heterologous unanchored proteins, we have cloned and expressed the emm6 structural gene for the M6 protein in various lactic acid bacteria (LAB). The emm6 gene was successfully expressed from lactococcal promoters in several Lactococcus lactis strains, an animal-colonizing Lactobacillus fermentum strain, Lactobacillus sake, and Streptococcus salivarius subsp. thermophilus. The M6 protein was efficiently anchored to the cell wall in all strains tested. In lactobacilli, essentially all detectable M6 protein was cell wall associated. These results suggest the feasibility of using the C-terminal anchor moiety of M6 for protein surface display in LAB.
Epidermal growth factor and platelet‐derived growth factor promote translocation of phospholipase C‐γ from cytosol to membrane (1990)

Treatment of HER 14 cells with epidermal growth factor (EGF) or platelet-derived growth factor (PDGF) induced a translocation of phospholipase C-gamma (PLC-gamma) from cytosol to membrane. In such growth factor-treated cells, cytosolic PLC-gamma was found to contain more phosphotyrosine than membrane-associated enzyme. Because these growth factors have been shown to promote both the physical association of PLC-gamma with their receptors and the subsequent phosphorylation of the enzyme directly by the membrane-bound receptor tyrosine kinases, the membrane association of PLC-gamma may simply be due to the formation of transient enzyme (receptor)-substrate (PLC-gamma) complexes. If this is the case, membrane-associated PLC-gamma would be expected to be released from membrane after undergoing tyrosine phosphorylation. However, tyrosine phosphorylation of membrane-associated PLC-gamma by the EGF receptor in vitro did not result in the release of PLC-gamma from membrane. Thus, the association of PLC-gamma with membrane would appear to involve more than enzyme-substrate complex.
Vagus Nerve Stimulation (2008)

Vagus nerve stimulation (VNS) is a safe and reliable treatment adjunct for patients with medically intractable epilepsy. It is both a preventive and an abortive form of therapy, potentially effective against both partial and generalized seizures in adults and children. VNS also has a number of serendipitous effects on mood, memory, and attention and has been approved for the treatment of refractory depression. Because of its pleiotropic effects, it holds promise for several other diseases as well. Its principal limitations are its unknown mechanism of action, the low likelihood of complete cure, and the inability to predict which patients will derive substantial benefit. This paper reviews the theoretical rationale, practical background, and clinical applications of VNS therapy.
Mutations of human myristoyl-CoA:protein N-myristoyltransferase cause temperature-sensitive myristic acid auxotrophy in Saccharomyces cerevisiae. (1992)

We have isolated cDNAs encoding human myristoyl-CoA:protein N-myristoyltransferase (NMT, EC 2.3.1.97) by complementing the nmtl-181 mutation of Saccharomyces cerevisiae, which causes temperature-sensitive myristic acid auxotrophy. Human NMT is derived from a single-copy gene, contains 416 amino acids, is 44% identical to S. cerevisiae NMT (yeast NMT), and can complement the lethal phenotype of an nmtl null mutation. Human and yeast NMTs have overlapping yet distinct protein substrate specificities as judged by a coexpression system that reconstitutes protein N-myristoylation in Escherichia coli. Both enzymes contain a glycine five residues from the C terminus. Gly----Asp or Lys mutagenesis in these orthologous NMTs produces marked reductions in their activities in E. coli as well as temperature-sensitive myristic acid auxotrophy in S. cerevisiae. These results indicate highly conserved structure-function relationships in vivo and underscore the usefulness of these functional assays for identifying factors that regulate protein N-myristoylation in mammalian systems.
Kupffer cells are central in the removal of nanoparticles from the organism (2007)

Our results suggest that: (1) inert gold nanoparticles do not penetrate cell membranes by non-endocytotic mechanisms, but are rather taken up by endocytosis; (2) gold nanoparticles, independent of size, are taken up primarily by Kupffer cells in the liver and secondarily by macrophages in other places; (3) gold nanoparticles do not seem to penetrate the placenta barrier; (4) the blood-brain barrier seems to protect the central nervous system from gold nanoparticles; (5) 2 nanometer gold particles seem to be removed not only by endocytosis by macrophages, and we hypothesize that part of these tiny nanoparticles are released into the urine as a result of simple filtration in the renal glomeruli.
Structural and functional conservation of the human homolog of the Schizosaccharomyces pombe rad2 gene, which is required for chromosome segregation and recovery from DNA damage. (1994)

The rad2 mutant of Schizosaccharomyces pombe is sensitive to UV irradiation and deficient in the repair of UV damage. In addition, it has a very high degree of chromosome loss and/or nondisjunction. We have cloned the rad2 gene and have shown it to be a member of the Saccharomyces cerevisiae RAD2/S. pombe rad13/human XPG family. Using degenerate PCR, we have cloned the human homolog of the rad2 gene. Human cDNA has 55% amino acid sequence identity to the rad2 gene and is able to complement the UV sensitivity of the rad2 null mutant. We have thus isolated a novel human gene which is likely to be involved both in controlling the fidelity of chromosome segregation and in the repair of UV-induced DNA damage. Its involvement in two fundamental processes for maintaining chromosomal integrity suggests that it is likely to be an important component of cancer avoidance mechanisms.
Antibody conjugates mimic specific B cell presentation of antigen: relationship between T and B cell specificity. (1987)

We developed antibody conjugates by covalently coupling antibodies against mouse mu-chain and monoclonal antibodies against nominal antigen, myoglobin, as a tool for antigen presentation and as a model of specific presentation of antigen by antigen-specific B cells and T-B interaction. In the presence of the antibody conjugates, myoglobin-specific Iad-restricted cloned T cells proliferated at 1000-fold lower concentration of myoglobin than the stimulatory concentration without the conjugates. This enhanced presentation was observed only when Iad spleen cells were 1000 R-irradiated but not 3300 R-irradiated, consistent with B cell presentation. The simple mixture of each component of the conjugates had no enhancement effects. The conjugates per se had no mitogenic effects on either splenic B cells or the cloned T cells at concentrations employed for antigen presentation. The conjugates reduced the number of antigen-presenting cells required for the maximal response but did not change the kinetics of response. The enhanced presentation by the conjugates required a genetically restricted interaction with B cells. Antigen specificity of the enhanced presentation was confirmed by using various T cell clones or lines with different antigen specificities and different conjugates constructed with monoclonal antibodies of known epitope specificity. The enhanced presentation was significantly inhibited by competition with exogenous mouse IgM or anti-mouse mu-chain but was not significantly inhibited by monoclonal antibodies against Fc receptor. Thus, conjugate-coated B cells serve as models for myoglobin-specific B cells in that they can take up specific antigens at extremely low concentration and can present the antigen to specific T cells. This model system can be applied to any antigen and any species without the need to develop antigen-specific B cell clones, which is not yet possible for most antigens and species of experimental animals. This system allowed us to investigate the relationship between T cell epitope and B cell epitope when these cells interact with each other in an antigen-specific and Ia-restricted manner. Experiments using antibody conjugates of different monoclonal antibodies against myoglobin and various myoglobin-specific cloned T cells of known antigen specificity revealed that there are some particular combinations in which much more limited enhancement of antigen presentation is observed.(ABSTRACT TRUNCATED AT 400 WORDS)
Playful bottle (2009)

This study of mobile persuasion system explores the use of a mobile phone, when attached to an everyday object used by an everyday behavior, becomes a tool to sense and influence that behavior. This mobile persuasion system, called Playful Bottle system, makes use of a mobile phone attached to an everyday drinking mug and motivates office workers to drink healthy quantities of water. A camera and accelerometer sensors in the phone are used to build a vision/motion-based water intake tracker to detect the amount and regularity of water consumed by the user. Additionally, the phone includes hydration games in which natural drinking actions are used as game input. Two hydration games are developed: a single-user TreeGame with automated computer reminders and a multi-user ForestGame with computer-mediated social reminders from members of the group playing the game. Results from 7-week user study with 16 test subjects suggest that both hydration games are effective for encouraging adequate and regular water intake by users. Additionally, results of this study suggest that adding social reminders to the hydration game is more effective than system reminders alone.
Relief as a Reward: Hedonic and Neural Responses to Safety from Pain (2011)

Relief fits the definition of a reward. Unlike other reward types the pleasantness of relief depends on the violation of a negative expectation, yet this has not been investigated using neuroimaging approaches. We hypothesized that the degree of negative expectation depends on state (dread) and trait (pessimism) sensitivity. Of the brain regions that are involved in mediating pleasure, the nucleus accumbens also signals unexpected reward and positive prediction error. We hypothesized that accumbens activity reflects the level of negative expectation and subsequent pleasant relief. Using fMRI and two purpose-made tasks, we compared hedonic and BOLD responses to relief with responses during an appetitive reward task in 18 healthy volunteers. We expected some similarities in task responses, reflecting common neural substrates implicated across reward types. However, we also hypothesized that relief responses would differ from appetitive rewards in the nucleus accumbens, since only relief pleasantness depends on negative expectations. The results confirmed these hypotheses. Relief and appetitive reward task activity converged in the ventromedial prefrontal cortex, which also correlated with appetitive reward pleasantness ratings. In contrast, dread and pessimism scores correlated with relief but not with appetitive reward hedonics. Moreover, only relief pleasantness covaried with accumbens activation. Importantly, the accumbens signal appeared to specifically reflect individual differences in anticipation of the adverse event (dread, pessimism) but was uncorrelated to appetitive reward hedonics. In conclusion, relief differs from appetitive rewards due to its reliance on negative expectations, the violation of which is reflected in relief-related accumbens activation.