gebhart/patrepeval huggingface dataset:
NMR imaging techniques and applications: A review (1982)

Over the past ten years, a variety of techniques have been proposed and demonstrated that enable the spatial discrimination and mapping of nuclear-magnetic-resonance (NMR) signals in heterogeneous objects. These NMR imaging techniques are currently finding useful application in clinical medicine and physiological chemistry, where their noninvasive, apparently hazard-free nature, and the sensitivity of the NMR signal to the state of biological tissue, are key advantages. This article reviews the historical development, the conceptual basis, and the applications of the various NMR imaging techniques. Qualitative descriptions and illustrations of each technique and an outline of imaging instrumentation are provided. Proton NMR imaging, in medicine, of pathological states such as cancer, imaging of relaxation time, chemical shift and flow parameters, imaging of nuclei other than hydrogen, and potential hazards are discussed and demonstrated with examples.
A possible role of sphingosine in induction of apoptosis by tumor necrosis factor‐α, in human neutrophils (1994)

Treatment of human neutrophils with tumor necrosis factor-alpha (TNF-alpha) resulted in an increase in concentration of ceramide and its catabolite, sphingosine. Sphingosine, a potent endogenous protein kinase C (PKC) inhibitor, as well as TNF-alpha, induced internucleosomal DNA fragmentation and morphological changes characteristic of apoptotic cells. Ceramide and sphingosine-1-phosphate, the initial product of sphingosine catabolism, did not cause apoptosis under our experimental conditions. In addition, 1-(5-isoquinolinesulfonyl)-2-methylpiperazine (H7) and N,N-dimethylsphingosine (DMS), known as PKC inhibitors, also induced apoptosis, suggesting that induction of apoptosis by sphingosine may be related to inhibition of PKC activity. These results indicate that sphingosine deacylated from ceramide may be an endogenous modulator mediating apoptotic signals by TNF-alpha in neutrophils.
Differential Roles of N- and C-Terminal Immunoreceptor Tyrosine-Based Inhibition Motifs During Inhibition of Cell Activation by Killer Cell Inhibitory Receptors (1999)

Killer cell inhibitory receptors (KIRs) inhibit NK and T cell cytotoxicity when recognizing MHC class I molecules on target cells. They possess two tandem intracytoplasmic immunoreceptor tyrosine-based inhibition motifs (ITIMs) that, when phosphorylated, each bind to the two Src homology 2 domain-bearing protein tyrosine phosphatases SHP-1 and SHP-2 in vitro. Using chimeric receptors having an intact intracytoplasmic KIR domain bearing both ITIMs (N + C-KIR), a deleted domain containing the N-terminal ITIM only (N-KIR), or a deleted domain containing the C-terminal ITIM only (C-KIR), we examined the respective contributions of the two ITIMs in the inhibition of cell activation in two experimental models (a rat mast cell and a mouse B cell line) that have been widely used to analyze KIR functions. We found that the two KIR ITIMs play distinct roles. When coaggregated with immunoreceptor tyrosine-based activation motif-bearing receptors such as high-affinity IgE receptors or B cell receptors, the N + C-KIR and the N-KIR chimeras, but not the C-KIR chimera, inhibited mast cell and B cell activation, became tyrosyl-phosphorylated, and recruited phosphatases in vivo. The N + C-KIR chimera recruited SHP-1 as expected, but also SHP-2. Surprisingly, the N-KIR chimera failed to recruit SHP-1; however, it did recruit SHP-2. Consequently, the N-terminal ITIM is sufficient to recruit SHP-2 and to inhibit cell activation, whereas the N-terminal and the C-terminal ITIMs are both necessary to recruit SHP-1. The two KIR ITIMs, therefore, are neither mandatory for inhibition nor redundant. Rather than simply amplifying inhibitory signals, they differentially contribute to the recruitment of distinct phosphatases that may cooperate to inhibit cell activation.
Characterization of the Effects of Antiangiogenic Agents on Tumor Pathophysiology (2001)

A variety of strategies have been proposed to control tumor growth and metastasis by inhibiting tumor angiogenesis. To optimally combine such antiangiogenic approaches with conventional therapy, improved methods are needed to characterize the underlying pathophysiologic changes. The objective of the current work was to demonstrate the utility of a combination of recently developed immunohistochemical and image analysis techniques in quantitating changes in tumor vasculature and hypoxia. Murine MCa-35 mammary carcinomas were frozen after administration of two COX-2 inhibitors: meloxicam and celecoxib (Celebrex). Total blood vessels were visualized using anti-CD31 staining, perfused vessels by intravenous injection of DiOC7, and tumor hypoxia by EF5 uptake. Although both agents produced similar reductions in tumor volume compared with untreated tumors, varied effects on tumor vasculature and hypoxia were noted. Meloxicam reduced total vessel numbers significantly, whereas celecoxib had no effect. Both drugs substantially increased perfused vessel densities. Although mean hypoxic marker uptake was unchanged from matched controls, intratumor EF5 heterogeneities were significantly different between drugs. The results suggest that COX-2 inhibitors can have varying effects on tumor pathophysiology. Successful use of these drugs to enhance radiation response will likely require optimization of drug choice, dose schedule, and direct physiologic monitoring.
Histone H1 Depletion Impairs Embryonic Stem Cell Differentiation (2012)

Pluripotent embryonic stem cells (ESCs) are known to possess a relatively open chromatin structure; yet, despite efforts to characterize the chromatin signatures of ESCs, the role of chromatin compaction in stem cell fate and function remains elusive. Linker histone H1 is important for higher-order chromatin folding and is essential for mammalian embryogenesis. To investigate the role of H1 and chromatin compaction in stem cell pluripotency and differentiation, we examine the differentiation of embryonic stem cells that are depleted of multiple H1 subtypes. H1c/H1d/H1e triple null ESCs are more resistant to spontaneous differentiation in adherent monolayer culture upon removal of leukemia inhibitory factor. Similarly, the majority of the triple-H1 null embryoid bodies (EBs) lack morphological structures representing the three germ layers and retain gene expression signatures characteristic of undifferentiated ESCs. Furthermore, upon neural differentiation of EBs, triple-H1 null cell cultures are deficient in neurite outgrowth and lack efficient activation of neural markers. Finally, we discover that triple-H1 null embryos and EBs fail to fully repress the expression of the pluripotency genes in comparison with wild-type controls and that H1 depletion impairs DNA methylation and changes of histone marks at promoter regions necessary for efficiently silencing pluripotency gene Oct4 during stem cell differentiation and embryogenesis. In summary, we demonstrate that H1 plays a critical role in pluripotent stem cell differentiation, and our results suggest that H1 and chromatin compaction may mediate pluripotent stem cell differentiation through epigenetic repression of the pluripotency genes.
Nonpeptidic Tetrafluorophenoxymethyl Ketone Cruzain Inhibitors as Promising New Leads for Chagas Disease Chemotherapy (2010)

A century after discovering that the Trypanosoma cruzi parasite is the etiological agent of Chagas disease, treatment is still plagued by limited efficacy, toxicity, and the emergence of drug resistance. The development of inhibitors of the major T. cruzi cysteine protease, cruzain, has been demonstrated to be a promising drug discovery avenue for this neglected disease. Here we establish that a nonpeptidic tetrafluorophenoxymethyl ketone cruzain inhibitor substantially ameliorates symptoms of acute Chagas disease in a mouse model with no apparent toxicity. A high-resolution crystal structure confirmed the mode of inhibition and revealed key binding interactions of this novel inhibitor class. Subsequent structure-guided optimization then resulted in inhibitor analogues with improvements in potency despite minimal or no additions in molecular weight. Evaluation of the analogues in cell culture showed enhanced activity. These results suggest that nonpeptidic tetrafluorophenoxymethyl ketone cruzain inhibitors have the potential to fulfill the urgent need for improved Chagas disease chemotherapy.
Campbell-like integration of heterologous plasmid DNA into the chromosome of Lactococcus lactis subsp. lactis (1989)

Integrable vectors were constructed based on the plasmid pHV60, which is essentially a pBR322 replicon carrying a chloramphenicol resistance marker, by inserting 1.3-kilobase chromosomal fragments of Lactococcus lactis subsp. lactis MG1363 into this plasmid. Three constructs as well as pHV60 were electroporated to strain MG1363. Transformants were obtained with all constructs, and also with pHV60 (albeit with low frequency). By using Southern hybridizations, it appeared that pHV60 showed homology with the chromosome of MG1363, and that it most probably uses this homology to integrate in a Campbell-like manner. The presence of chromosomal sequences in pHV60 stimulated insertion elsewhere in the chromosome by a factor of 5 to 100. In all cases the integrated plasmids were amplified, at a selective pressure of 5 micrograms of chloramphenicol per ml, to a level of approximately 15 copies per chromosome. Although the amplification was gradually lost under nonselective conditions, one copy remained stably integrated in the chromosome. The results show that a Campbell-like integration strategy can be used to improve the accessibility of the lactococcal chromosome for genetic analysis and is potentially useful in stabilizing unstable genes in lactococci.
Effect of Different Mouthrinses on Morning Breath (2001)

The results of this study demonstrate that morning halitosis can be successfully reduced via daily use of mouthrinses. CHX-Alc and CHX-CPC-Zn mouthrinses result in a significant reduction of the microbial load of tongue and saliva.
The Credit Rating Industry (1995)

Investors and regulators have been increasing their reliance on the opinions of the credit rating agencies. This article shows that although the ratings provide accurate rank-orderings of default risk, the meaning of specific letter grades varies over time and across agencies. Noting that current regulations do not explicitly adjust for agency differences, the authors argue that a reassessment of the use of ratings and the adequacy of public oversight is overdue.
Comparison Between Bone Marrow Mesenchymal Stromal Cells (BM-MSC) and Lung Mesenchymal Stromal Cells (Lung-MSC) For Epithelial Regeneration (2013)

Abstract Developing a therapeutic strategy for lung regeneration still remains complex. Stem cell-based therapeutical approaches have been suggested as a potential tool; among them, human mesenchymal stromal cells (MSC) possess some promising features to this aim. MSC are stem cells residing in many tissue, i.e. bone marrow (BM), adipose tissue, cord blood, lung, etc., and they are capable of differentiating into different cell types of mesodermal origin, such as fat, bone and cartilage. To assess MSC epithelial differentiation potential, through a partially known process called Mesenchymal to Epithelial Transition (MET), MSC were collected from bone (BM) aspirates and lung biopsies after informed consent. MSC were characterized by immunophenotyping and clonogenicity assay. MSC mesodermal differentiation potential was assessed by testing their ability to differentiate into adipocytes, osteoblasts and chondrocytes. MSCs at different culture passages were induced to acquire the epithelial phenotype by culturing in presence of retinoic acid. The epithelial differentiation was checked by quantitative RT-PCR, immunofluorescence and a functional assay based on the Trans Epithelial Electrical Resistance Measurement (TEER). In presence of retinoic acid, MSC from BM and, mostly, lung upregulated a panel of general epithelial genes (cytokeratin 18, occludin, tight junction protein and claudin) and downregulated some specific mesenchymal markers (smooth muscle actin, snail2, vimentin, THY1), as detected by quantitative RT-PCR. Immunofluorescence confirmed the presence of E-cadherin4, occludin and cytokeratin 18 in a small number of cells (about 0,2 %). Trans Epithelial Electrical Resistance (TEER) measurement confirmed that MSC can acquire in vitro partial epithelial polarization after retinoic acid treatment. These data show that MSC can be induced to differentate into cells resembling some morphological, phenotypical and functional properties of epithelial cells. BM-MSC are less prone to acquire an epithelial phenotype as compared to hLung-MSC. Additional in vivo studies on mouse model with lung damage are in progress. Disclosures: No relevant conflicts of interest to declare.
Molybdenum accumulation in chlD mutants of Escherichia coli (1989)

The content of molybdenum in wild-type and chlD cells was measured under a variety of growth conditions to determine if cells with a defective chlD gene were able to accumulate molybdenum. The chlD cells accumulated less molybdenum than wild-type cells did but concentrated molybdenum to a level at least 20-fold higher than the concentration in the culture medium. Molybdenum was present within spheroplasts of chlD cells and was not dialyzable. The chlD cells accumulated as much molybdenum as wild-type cells did when grown in medium containing 0.1 mM molybdate; thus, the capability of incorporation of molybdenum into cellular component(s) was equivalent to that of the wild type under these conditions.
Three-Dimensional Analysis of Retinal Layer Texture: Identification of Fluid-Filled Regions in SD-OCT of the Macula (2010)

Optical coherence tomography (OCT) is becoming one of the most important modalities for the noninvasive assessment of retinal eye diseases. As the number of acquired OCT volumes increases, automating the OCT image analysis is becoming increasingly relevant. In this paper, a method for automated characterization of the normal macular appearance in spectral domain OCT (SD-OCT) volumes is reported together with a general approach for local retinal abnormality detection. Ten intraretinal layers are first automatically segmented and the 3-D image dataset flattened to remove motion-based artifacts. From the flattened OCT data, 23 features are extracted in each layer locally to characterize texture and thickness properties across the macula. The normal ranges of layer-specific feature variations have been derived from 13 SD-OCT volumes depicting normal retinas. Abnormalities are then detected by classifying the local differences between the normal appearance and the retinal measures in question. This approach was applied to determine footprints of fluid-filled regions--SEADs (Symptomatic Exudate-Associated Derangements)--in 78 SD-OCT volumes from 23 repeatedly imaged patients with choroidal neovascularization (CNV), intra-, and sub-retinal fluid and pigment epithelial detachment. The automated SEAD footprint detection method was validated against an independent standard obtained using an interactive 3-D SEAD segmentation approach. An area under the receiver-operating characteristic curve of 0.961 +/- 0.012 was obtained for the classification of vertical, cross-layer, macular columns. A study performed on 12 pairs of OCT volumes obtained from the same eye on the same day shows that the repeatability of the automated method is comparable to that of the human experts. This work demonstrates that useful 3-D textural information can be extracted from SD-OCT scans and--together with an anatomical atlas of normal retinas--can be used for clinically important applications.
Development of a Low-cost, Portable Hardware Platform to Support Hands-on Learning in the Teaching of Control and Systems Theory (2014)

This paper describes the development of a hardware platform designed to support the teaching of a variety of systems engineering concepts to students at all stages of the curriculum. From concept, the hardware was designed to be low-cost, portable and robust allowing sufficient numbers of hardware units to be acquired. This enabled each student on the course to be loaned their own piece of equipment, either to work with in class or for use as a ‘take home lab’. This provided the students with a more flexible, experimental based learning experience than traditional classroom based teaching. The hardware platform consisted of a miniature three degrees-of freedom helicopter that is interfaced to a personal computer (PC) via a National Instruments myDAQ data acquisition module. This was housed in a small, foam-lined carrying case for portability. Details of the course and assessment, based around the hardware platform, are presented, along with feedback received from the students. This feedback was from the first run of a new MSc course in the spring semester of 2013, and indicated that the new hardware was received positively with the students appreciating the hands-on nature of the teaching it provided.
Adaptation of islets of Langerhans to pregnancy: increased islet cell proliferation and insulin secretion correlates with the onset of placental lactogen secretion. (1992)

To elucidate the temporal profile of adaptive changes of the islets of Langerhans to the increased insulin demands of pregnancy, we have studied islet cell proliferation and insulin secretion during gestation in the rat. 5-Bromo-2'-deoxyuridine incorporation into dividing islet cells was significantly (P less than 0.05) increased over age-matched controls by day 10, rose continuously to a peak at day 14, and then returned to control levels by day 18. By day 20, cell division was significantly inhibited (P less than 0.05). The pattern of changes in insulin secretory profiles observed with perfused pancreata of pregnant animals was similar to that obtained for islet cell proliferation. Both the threshold of glucose-stimulated insulin secretion and the amount of above threshold insulin secretion began to diverge from controls by day 10. By day 12, the glucose-stimulation threshold was significantly decreased from 5.7 mM glucose to 3.3 mM (P less than 0.05), remained at this low level through day 15, and returned toward normal by day 20. Concomitant with the increased sensitivity of B cells to glucose, the above threshold insulin secretion was significantly increased by day 12 (P less than 0.05), peaked at day 15, and returned to control levels by day 20. This insulin secretory data demonstrates that the increased sensitivity of B cells to glucose is an important component of the adaptation of islets during pregnancy to the increased demand for insulin at physiological concentrations of plasma glucose. To correlate the above changes in islet cell proliferation and insulin secretion with levels of placental lactogen (PL), serum lactogenic hormone activity was measured by Nb2 lymphoma cell replication assays. This analysis revealed the expected biphasic pattern: a midpregnancy peak at day 12, followed by a nadir at day 14, and then continuously elevated levels until term. The bioassay data agreed with the known secretory profiles of rat (r) PL-I (midpregnancy) and rPL-II (late pregnancy). Our results provide the first systematic evaluation of changes in islet function during pregnancy in the rat. In addition, they provide evidence that rPL-I may be the critical hormonal signal which triggers the primary adaptive changes in islet function characteristic of pregnancy. The return to normal values of insulin secretion and inhibition of cell division observed at day 20 in the presence of high concentrations of rPL-II suggests that other inhibitory influences become dominant in the later stages of rat pregnancy.(ABSTRACT TRUNCATED AT 400 WORDS)
Phase II Trial of Vorinostat in Recurrent Glioblastoma Multiforme: A North Central Cancer Treatment Group Study (2009)

Vorinostat monotherapy is well tolerated in patients with recurrent GBM and has modest single-agent activity. Histone acetylation analysis and RNA expression profiling indicate that vorinostat in this dose and schedule affects target pathways in GBM. Additional testing of vorinostat in combination regimens is warranted.
Helicobacter pylori - Specific CD4 + CD25 high Regulatory T Cells Suppress Memory T-Cell Responses to H . pylori in Infected Individuals (2003)

Helicobacter pylori colonizes the gastric and duodenal mucosa. The infection normally persists for life and causes peptic ulcers and gastric cancer in a subset of infected individuals. We hypothesized that the inability to clear the infection may be a consequence of H. pylori-specific regulatory T cells that actively suppress T-cell responses. Therefore, we characterized the T-cell responses to H. pylori in H. pylori-infected individuals without any subjective symptoms and in uninfected control subjects and investigated the role of regulatory CD4+ CD25(high) T cells during infection. The stimulation of CD4+ peripheral blood T cells with monocyte-derived dendritic cells pulsed with a membrane preparation of H. pylori resulted in proliferation and gamma interferon production in both infected and uninfected individuals. Sorted memory cells from infected individuals responded less than cells from uninfected subjects, and the unresponsiveness could be abolished by depletion of CD4+ CD25(high) regulatory T cells or the addition of interleukin 2. Furthermore, CD4+ CD25(high) T cells suppressed H. pylori-induced responses in cocultures with CD25(low/-) cells. Tetanus toxoid induced comparable responses in memory cells from infected and uninfected individuals in both the presence and the absence of regulatory T cells, suggesting that the suppression was H. pylori specific. In conclusion, we have shown that H. pylori-infected individuals have impaired memory CD4+ T-cell responses to H. pylori that are linked to the presence of H. pylori-specific regulatory T cells that actively suppress the responses.
Quantitative Studies and Taste Reconstitution Experiments of the Sour and Lingering Mouthful Orosensation in a Debittered Extract of Traditional Japanese Dried and Fermented Skipjack Tuna (Hongarebushi) (2013)

Hongarebushi, Japanese dried skipjack tuna and a high quality ingredient of Japanese dashi, was investigated for its taste active composition. The recent investigation focused on a debittered fish fraction, which revealed a strong umami and salt impact accompanied with a pleasant and pronounced sourness. Whereas the umami and salt tastes could be correlated to monosodium glutamate (MSG), ribonucleotides, and mineral salts, the pleasant sourness was not exclusively induced by organic acids. The essential compound imparting the sour orosensation, persistence, and mouthfulness of the debittered skipjack tuna extract was investigated, and omission experiments emphasized the impact of N-acetylglutamic acid (NAG) on the overall taste sensation of the debittered fish extract. This metabolite, which is known to be present as a minor constituent in animal- and plant-derived foods, was quantified in this study for the first time in seafood, soybean products, dried shiitake mushrooms, and dried fish in notable amounts. Furthermore, it was described for the first time as an essential taste contributor to the nonvolatile profile of a foodstuff, in this case of a debittered extract of hongarebushi.