gebhart/patrepeval huggingface dataset:
The Fibroblast Growth Factor Receptor Acid Box Is Essential for Interactions with N-Cadherin and All of the Major Isoforms of Neural Cell Adhesion Molecule (2006)

Interactions between the neural cell adhesion molecules NCAM and N-cadherin with the fibroblast growth factor receptor (FGFR) are important for a number of developmental events and have also been implicated in tumor progression. The factors regulating these interactions are not known. We have used co-immunoprecipitation and co-clustering paradigms to show that both adhesion molecules can interact with the 3Ig IIIC isoform of the FGFR1 in a number of cell types. Interestingly, whereas the interaction can be seen over most of the cell surface, it is not seen at points of cell-cell contact where the adhesion molecules accumulate at stable junctions. We also demonstrate for the first time that all of the major isoforms of NCAM can interact with the FGFR. Using deletion mutagenesis we have found that the adhesion molecule/FGFR interaction can withstand the removal of most of any one of the FGFR immunoglobulin-like domains (D1-D3). In contrast, the FGFR interaction with N-cadherin and NCAM (but not FGF) is absolutely dependant on the presence of the acid box motif that can be found in the linker region between D1 and D2. As this motif can be spliced out of all four FGFRs, it suggests that this is one mechanism that can regulate the interaction of the receptor with different ligand classes.
Expression and Function of Sonic Hedgehog Pathway Components in Pituitary Adenomas: Evidence for a Direct Role in Hormone Secretion and Cell Proliferation (2005)

Our results suggest that Shh might maintain pituitary cells in a nonproliferative state. We conclude that Shh is a newly described hypophysiotropic cytokine and its down-regulation may be involved in the pathogenesis of pituitary adenomas.
Sensitive detection and quantification of particle-associated reverse transcriptase in plasma of HIV-1-infected individuals by the product-enhanced reverse transcriptase (PERT) assay (1996)

Tests for the enzyme reverse transcriptase (RT) should permit the detection of all infectious retroviruses, provided that these are present as extracellular particles. The capability of a new procedure, named product-enhanced reverse transcriptase (PERT) assay, to detect HIV-1 in fresh human plasma was compared with that of the polymerase chain reaction (PCR) for viral RNA. Both procedures had identical dilution endpoints corresponding to 10(2) particles/ml. All 30 samples from HIV-1 positive patients at different stages contained RT activity whose level was significantly correlated with viral RNA and corresponded to 553-417,000 particles/ml. In HIV-1 low titer performance and seroconversion panels, the PERT assay detected more positives than PCR for viral RNA. Three of 160 blood donors exhibited elevated RT activity, indicating a prevalence of 1.9% (95% CI 0.4-5.3%). One positive donor, with laboratory parameters suggesting a mild chronic liver impairment, exhibited RT activity comparable to that of HIV positives, but was consistently negative by various tests for hepatitis viruses, cytomegalovirus, the HIVs and HTLVs. The results suggest that the PERT assay is more sensitive for detection of HIV-1 contamination of plasma than RNA PCR. However, it is not affected adversely by viral sequence variability, and may therefore, also detect HIV-1 subtype O, and additional retroviruses as yet undetectable by PCR.
Acquired immunodeficiency syndrome-associated non-Hodgkin's lymphoma. (1990)

The clinical picture is of aggressive high and intermediate grade lymphoma with extranodal presentation either as the first manifestation or during the course of HIV infection. The dramatic growth of tumors, leukopenia, opportunistic infections, and pre-existing AIDS-related problems of KS and chronic infections have made treatment extremely difficult. New regimens using short courses of chemotherapy, GM-CSF, and antiviral therapy have raised hopes that these measures will lead to improved survival.
Autoimmunity to Chaperonins in the Pathogenesis of Arthritis and Diabetes (1991)

The immunology of the 65 kd heat shock protein (hsp65) is paradoxical. Microbial and mammalian hsp65 molecules are 50% identical in amino acid sequence and immunologically cross-reactive, so microbial hsp65 looks like self; yet hsp65 is a dominant antigen in infection. Immunity to hsp65 can cause autoimmune diabetes in mice and may be related to autoimmune arthritis in rats and humans, so immunity to hsp65 should be forbidden; yet healthy persons manifest T-cell responses to self-hsp65. The aim of this chapter is to explore the immunological dominance of hsp65 and its role in autoimmunity--benign and pernicious.
The Synthesis of (2S, 3R) - Sphingosine from D - Mannitol (1996)

(2E)-4,5-O- Isopropylidene - pentenylic ester (5), obtained in 3 steps from D -mannitol, was subjected to a series of reactions such as asymmetric dihydroxidation, cyclic sulfation and regioselective opening of the cyclic sulfate by NaN3 and finally was transformed into the 2,3- dibenzoate of (2S,3R) - sphingosine. The overall yield from D - mannitol was 7.7%. This work has opened a new route to the synthesis of sphingosine and other sphingolipids.
Memantine leads to behavioral improvement and amyloid reduction in Alzheimer's‐disease‐model transgenic mice shown as by micromagnetic resonance imaging (2008)

Memantine, an N-methyl-D-aspartate (NMDA) receptor antagonist, has been shown to improve learning and memory in several preclinical models of Alzheimer's disease (AD). Memantine has also been shown to reduce the levels of amyloid beta (A beta) peptides in human neuroblastoma cells as well as to inhibit A beta oligomer-induced synaptic loss. In this study, we assessed whether NMDA receptor inhibition by memantine in transgenic mice expressing human amyloid-beta precursor protein (APP) and presenilin 1 (PS1) is associated with cognitive benefit and amyloid burden reduction by using object recognition, micromagnetic resonance imaging (micro MRI), and histology. APP/PS1 Tg mice were treated either with memantine or with vehicle for a period of 4 months starting at 3 months of age. After treatment, the mice were subjected to an object recognition test and analyzed by ex vivo micro MRI, and histological examination of amyloid burden. micro MRI was performed following injection with gadolinium-DTPA-A beta(1-40). We found that memantine-treated Tg mice performed the same as wild-type control mice, whereas the performance of vehicle-treated Tg mice was significantly impaired (P = 0.0081, one-way ANOVA). Compared with vehicle-treated animals, memantine-treated Tg mice had a reduced plaque burden, as determined both histologically and by micro MRI. This reduction in amyloid burden correlates with an improvement in cognitive performance. Thus, our findings provide further evidence of the potential role of NMDA receptor antagonists in ameliorating AD-related pathology. In addition, our study shows, for the first time, the utility of micro MRI in conjunction with gadolinium-labeled A beta labeling agents to monitor the therapeutic response to amyloid-reducing agents.
Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks (2017)

Image-to-image translation is a class of vision and graphics problems where the goal is to learn the mapping between an input image and an output image using a training set of aligned image pairs. However, for many tasks, paired training data will not be available. We present an approach for learning to translate an image from a source domain $X$ to a target domain $Y$ in the absence of paired examples. Our goal is to learn a mapping $G: X \rightarrow Y$ such that the distribution of images from $G(X)$ is indistinguishable from the distribution $Y$ using an adversarial loss. Because this mapping is highly under-constrained, we couple it with an inverse mapping $F: Y \rightarrow X$ and introduce a cycle consistency loss to push $F(G(X)) \approx X$ (and vice versa). Qualitative results are presented on several tasks where paired training data does not exist, including collection style transfer, object transfiguration, season transfer, photo enhancement, etc. Quantitative comparisons against several prior methods demonstrate the superiority of our approach.
Staining Ability and Biocompatibility of Brilliant Blue G (2006)

The BBG contributed to better capsular visualization and caused no apparent complications to the corneal endothelium.Clinical Relevance The BBG is effective and safe capsular staining for continuous curvilinear capsulorrhexis.
A feedforward system for dynamic equalization of a chirped laser source suitable For photonic analog-to-digital conversion (2009)

In this work we present a method for improving the uniformity of the optical spectrum or the temporal intensity profile of a quasi-CW, linearly chirped laser source covering the time interval between subsequent pulses. A novel laser cavity design, referred to as the Theta (&Theta;) cavity, provides linearly chirped pulses directly from the laser oscillator that having non-uniform optical spectrum, that is mapped into the temporal intensity profile of the pulse, due to the frequency-to-time mapping nature of this cavity design. The system developed in this work has been designed to improve the spectral and temporal intensity profile of lasers for photonic signal processing. A fiberized feed-forward system is implemented to reduce variations in the temporal intensity profile, or the optical spectrum due to the time-to-frequency mapping, input to the system. In the feedforward scheme presented, the quasi-CW pulse train generated from the laser is split and part of it is photodetected, while the electrical signal generated alters the transmittance of the second part of the input as it goes through an amplitude modulator, resulting in increase in the uniformity of the signal. The contrast of the optical spectrum of a chirped pulse at input to the system is improved from 51% to 16%, or 3.1 times.
Stimulation of protein tyrosine phosphorylation, phosphoinositide turnover, and multiple previously unidentified serine/threonine-specific protein kinases by the Pan-B-cell receptor CD40/Bp50 at discrete developmental stages of human B-cell ontogeny. (1991)

CD40/Bp50 B-cell receptor has been implicated as having an important function for the regulation of human B-cell growth and maturation as well as antigen-driven selection of tonsillar B-cells in germinal centers. The purpose of the present study was to examine the biochemical events triggered by the engagement of the CD40 receptor in human B-lineage lymphoid cells corresponding to discrete developmental stages of human B-cell ontogeny. The engagement of the CD40 receptor on pro-B-, pre-pre-B-, pre-B-, or activated mature B-cells but not on resting mature B-cells with the agonistic anti-CD40 monoclonal antibody G28-5 resulted in enhanced tyrosine phosphorylation of four distinct phosphoproteins with molecular masses of 67, 72, 96, and 113 kDa and induced a rapid increase in the production of inositol 1,4,5-trisphosphate. Further, we have identified five electrophoretically distinct renaturable CD40-regulated serine/threonine-specific protein kinases (PK120, PK93, PK76, PK55, and PK48) that showed markedly increased in vitro activity after CD40 stimulation. Protein kinase C inhibitor 1-(5-isoquinolinylsulfonyl)-2-methylpiperazine (H7) abrogated the stimulation of the in vitro activity of PK120, PK93, PK55, and PK48 and attenuated the stimulation of the in vitro activity of PK76 in response to the engagement of the CD40 receptor but did not influence the enhanced tyrosine phosphorylation of cellular substrates after CD40 stimulation. Notably, genistein and herbimycin A, two potent inhibitors of tyrosine-specific protein kinases, not only abrogated the CD40-induced enhanced tyrosine phosphorylation on the 67-, 72-, 96-, and 113-kDa substrates, but they also inhibited the CD40-induced stimulation of phosphoinositide turnover as well as the CD40-induced increase of the in vitro activity of renaturable serine/threonine-specific protein kinases.(ABSTRACT TRUNCATED AT 400 WORDS)
Coupling CD28 Co-Stimulation to Immunoglobulin T-Cell Receptor Molecules: The Dynamics of T-Cell Proliferation and Death (2000)

Immunoglobulin T-cell receptor (IgTCR) molecules are potentially potent immune response modifiers because they allow T cells to bypass tolerance. Tolerance to self antigens has been one of the major barriers to the development of effective adoptive immunotherapies for treating cancer. In vitro studies in several laboratories have shown that cross-linking IgTCR molecules with the target antigen leads to cytolytic activity, cytokine release, and T-cell proliferation in model systems. However, many of these studies have used established T-cell lines rather than normal T cells or indirect assays of cytotoxicity, proliferation, and cytokine release. We have sought to establish the validity of these model systems while developing more effective adoptive immunotherapies using normal human T cells. In the present study the activation of T-cell proliferation after IgTCR cross-linking was evaluated. The results show that, in addition to IgTCR signals, CD28 costimulation is required to induce expansions of normal peripheral blood mononuclear cell-derived T cells. Signals from IgTCR alone can induce transient cell division, but they do not induce the prolonged polyclonal expansions that are characteristic of native immune responses. Very strong IgTCR signals could circumvent the CD28 requirement, but only at levels that are unlikely to be physiologically relevant. CD28 costimulation also suppressed the deletion of tumor-reactive subclones by activation-induced cell death. These studies confirm the importance of CD28 costimulation to the proliferation of IgTCR-modified human T cells, a key feature of an effective, reconstructed antitumor response.
The Effect of Discontinuing Treatment With Blosozumab: Follow-up Results of a Phase 2 Randomized Clinical Trial in Postmenopausal Women With Low Bone Mineral Density (2015)

Administration of blosozumab, a humanized monoclonal antibody that binds sclerostin, increases bone formation and bone mineral density (BMD) in postmenopausal women with low BMD. To evaluate the effect of discontinuing blosozumab, we studied women enrolled in a 1-year randomized, placebo-controlled phase 2 trial for an additional year after they completed treatment. Of the 120 women initially enrolled in the study, 106 women completed treatment and continued into follow-up; 88 women completed 1 year of follow-up. At the beginning of follow-up, groups remained balanced for age, race, and body mass index, but lumbar spine and total hip BMD were increased in prior blosozumab groups, reflecting an anabolic treatment effect. At the end of follow-up, 1 year after discontinuing treatment, lumbar spine BMD remained significantly greater than placebo in women initially treated with blosozumab 270 mg every 2 weeks (Q2W) and blosozumab 180 mg Q2W (6.9% and 3.6% above baseline, respectively). Total hip BMD also declined after discontinuation of treatment but at 1 year after treatment remained significantly greater than placebo in women initially treated with blosozumab 270 mg Q2W and blosozumab 180 mg Q2W (3.9% and 2.6% above baseline, respectively). During follow-up, median serum P1NP was not consistently different between the prior blosozumab groups and placebo. A similar pattern was apparent for median serum C-terminal telopeptide of type 1 collagen (CTx) levels, with more variability. Mean serum total sclerostin concentration increased with blosozumab, indicating target engagement, and declined to baseline after discontinuation. There were no adverse events considered related to prior treatment with blosozumab. Anti-drug antibodies generally declined in patients who had detectable levels during prior treatment. These findings support the continued study of blosozumab as an anabolic therapy for treatment of osteoporosis.
Splenic nerve is required for cholinergic antiinflammatory pathway control of TNF in endotoxemia (2008)

The autonomic nervous system maintains homeostasis through its sympathetic and parasympathetic divisions. During infection, cells of the immune system release cytokines and other mediators that cause fever, hypotension, and tissue injury. Although the effect of cytokines on the nervous system has been known for decades, only recently has it become evident that the autonomic nervous system, in turn, regulates cytokine production through neural pathways. We have previously shown that efferent vagus nerve signals regulate cytokine production through the nicotinic acetylcholine receptor subunit alpha7, a mechanism termed "the cholinergic antiinflammatory pathway." Here, we show that vagus nerve stimulation during endotoxemia specifically attenuates TNF production by spleen macrophages in the red pulp and the marginal zone. Administration of nicotine, a pharmacological agonist of alpha7, attenuated TNF immunoreactivity in these specific macrophage subpopulations. Synaptophysin-positive nerve endings were observed in close apposition to red pulp macrophages, but they do not express choline acetyltransferase or vesicular acetylcholine transporter. Surgical ablation of the splenic nerve and catecholamine depletion by reserpine indicate that these nerves are catecholaminergic and are required for functional inhibition of TNF production by vagus nerve stimulation. Thus, the cholinergic antiinflammatory pathway regulates TNF production in discrete macrophage populations via two serially connected neurons: one preganglionic, originating in the dorsal motor nucleus of the vagus nerve, and the second postganglionic, originating in the celiac-superior mesenteric plexus, and projecting in the splenic nerve.
Adenosine‐Sensitive Ventricular Tachycardia: (1996)

Idiopathic ventricular tachycardia (VT) is a term that refers to tachycardia that arises from ventricles devoid of apparent structural abnormalities. This form of VT is now recognized to be related to several distinct entities and includes a reentrant form typically located in the region of the left posterior fascicle, an automatic form that may originate from either ventricle, and a form that originates from the right ventricular outflow tract. This last type can account for up to 80% of cases of idiopathic VT and with few exceptions can be further subdivided into repetitive monomorphic VT and paroxysmal stress-induced VT. Evidence has accumulated suggesting that both forms of VT are related to cAMP-mediated triggered activity. The experimental underpinnings of this conclusion as well as the clinical characteristics of this form of idiopathic VT are elucidated in this review.
A microfluidic ExoSearch chip for multiplexed exosome detection towards blood-based ovarian cancer diagnosis (2015)

Tumor-derived circulating exosomes, enriched with a group of tumor antigens, have been recognized as a promising biomarker source for cancer diagnosis via a less invasive procedure. Quantitatively pinpointing exosome tumor markers is appealing, yet challenging. In this study, we developed a simple microfluidic approach (ExoSearch) which provides enriched preparation of blood plasma exosomes for in situ, multiplexed detection using immunomagnetic beads. The ExoSearch chip offers a robust, continuous-flow design for quantitative isolation and release of blood plasma exosomes in a wide range of preparation volumes (10 μL to 10 mL). We employed the ExoSearch chip for blood-based diagnosis of ovarian cancer by multiplexed measurement of three exosomal tumor markers (CA-125, EpCAM, CD24) using a training set of ovarian cancer patient plasma, which showed significant diagnostic power (a.u.c. = 1.0, p = 0.001) and was comparable with the standard Bradford assay. This work provides an essentially needed platform for utilization of exosomes in clinical cancer diagnosis, as well as fundamental exosome research.
Fluorescence In Situ Hybridization Method Using a Peptide Nucleic Acid Probe for Identification of Salmonella spp. in a Broad Spectrum of Samples (2010)

A fluorescence in situ hybridization (FISH) method for the rapid detection of Salmonella spp. using a novel peptide nucleic acid (PNA) probe was developed. The probe theoretical specificity and sensitivity were both 100%. The PNA-FISH method was optimized, and laboratory testing on representative strains from the Salmonella genus subspecies and several related bacterial species confirmed the predicted theoretical values of specificity and sensitivity. The PNA-FISH method has been successfully adapted to detect cells in suspension and is hence able to be employed for the detection of this bacterium in blood, feces, water, and powdered infant formula (PIF). The blood and PIF samples were artificially contaminated with decreasing pathogen concentrations. After the use of an enrichment step, the PNA-FISH method was able to detect 1 CFU per 10 ml of blood (5 x 10(9) +/- 5 x 10(8) CFU/ml after an overnight enrichment step) and also 1 CFU per 10 g of PIF (2 x 10(7) +/- 5 x 10(6) CFU/ml after an 8-h enrichment step). The feces and water samples were also enriched according to the corresponding International Organization for Standardization methods, and results showed that the PNA-FISH method was able to detect Salmonella immediately after the first enrichment step was conducted. Moreover, the probe was able to discriminate the bacterium in a mixed microbial population in feces and water by counter-staining with 4',6-diamidino-2-phenylindole (DAPI). This new method is applicable to a broad spectrum of samples and takes less than 20 h to obtain a diagnosis, except for PIF samples, where the analysis takes less than 12 h. This procedure may be used for food processing and municipal water control and also in clinical settings, representing an improved alternative to culture-based techniques and to the existing Salmonella PNA probe, Sal23S10, which presents a lower specificity.
Characterizing virtual memory write references for efficient page replacement in NAND flash memory (2009)

Recently, NAND flash memory is being used as the swap space of virtual memory as well as the file storage of embedded systems. Since temporal locality is dominant in page references of virtual memory, LRU and its approximated algorithms are widely used. However, we show that this is not true for write references. We analyze the characteristics of virtual memory read and write references separately, and find that the temporal locality of write references is weak and irregular. Based on this observation, we present a new page replacement algorithm that uses different strategies for read and write operations in predicting the re-reference likelihood of pages. For read operations, temporal locality alone is used, but for write operations, write frequency as well as temporal locality is used. The algorithm partitions the memory space into a read area and a write area to keep track of their reference patterns precisely, and then adjusts their sizes dynamically based on their reference patterns and I/O costs. Though the algorithm has no external parameter to tune, it performs better than CLOCK, CAR, and CFLRU by 20-66%. It also supports optimized implementations for virtual memory systems.