gebhart/patrepeval huggingface dataset:
Dietary fiber, inulin, and oligofructose: A review comparing their physiological effects (1993)

Dietary fiber is a general term. It covers a wide variety of substances that belong to the family of carbohydrates that resist hydrolysis by human alimentary enzymes but are fermented by colonic microflora. The main physiological effects of dietary fiber are primarily on gastric emptying and small intestinal transit time, resulting in an improved glucose tolerance and a decreased digestion of starch: second, on colonic transit time and large bowel functions due to fermentation by ceco-colonic microbial flora or bulking action. The so-called soluble dietary fibers are fermented to a large extent by a wide variety of anaerobic bacteria that result in an increase in bacterial biomass, an increase in fecal mass, a change in intracolonic pH, and production of short chain fatty acids and various gases as metabolic end products. The insoluble fibers are only marginally fermented: they serve almost exclusively as bulking agents that result in shorter transit time and increased fecal mass. The short chain fatty acids resulting from the colonic fermentation of dietary fiber are largely absorbed via the portal blood and reach both the liver and the peripheral tissues. They induce changes in glucose and fat metabolism leading to post-prandial hypoglycemia and long-term hypolipidemia. Inulin and oligofructose are fructans with a degree of polymerization of 2 to 60 and 2 to 20, respectively. Due to the structural conformation of their osidic bridge (beta 2-1), they both resist the hydrolysis by human alimentary enzymes. Moreover, when reaching the colon, both inulin and oligofructose are almost quantitatively fermented almost exclusively by colonic bifidobacteria and bacteroides. Such an extensive fermentation causes an increase in fecal bacterial biomass, a decrease in ceco-colonic pH, and produces a large amount of fermentation products among which the short chain fatty acids that exert systemic effects on lipid metabolism. Thus, both inulin and oligofructose have most of the characteristics of a dietary fiber and the proposal is made to classify them as such. Moreover, they are bifidogenic factors, because, due to still unknown reasons, they are primarily fermented by bifidobacteria. It is concluded from this review that "nondigestible fructo-oligosaccharides," even though they are not included in the carbohydrate fraction that is quantified as dietary fiber by classic analytical methods, have most of the physiological effects of a dietary fiber.(ABSTRACT TRUNCATED AT 400 WORDS)
DNA detection by strand displacement amplification and fluorescence polarization with signal enhancement using a DNA binding protein (1996)

Strand displacement amplification (9SDA) is an isothermal in vitro method of amplifying a DNA sequence prior to its detection. We have combined SDA with fluorescence polarization detection. A 5'-fluorescein-labelled oligodeoxynucleotide detector probe hybridizes to the amplification product that rises in concentration during SDA and the single- to double strand conversion is monitored through an increase in fluorescence polarization. Detection sensitivity can be enhanced by using a detector probe containing an EcoRI recognition sequence at its 5'-end that is not homologous to the target sequence. During SDA the probe is converted to a fully double-stranded form that specifically binds a genetically modified form of the endonuclease EcoRI which lacks cleavage activity but retains binding specificity. We have applied this SDA detection system to a target sequence specific for Mycobacterium tuberculosis.
Ultrasound Microbubbles for Molecular Diagnosis, Therapy, and Theranostics (2012)

Ultrasound imaging is clinically established for routine screening examinations of breast, abdomen, neck, and other soft tissues, as well as for therapy monitoring. Microbubbles as vascular contrast agents improve the detection and characterization of cancerous lesions, inflammatory processes, and cardiovascular pathologies. Taking advantage of the excellent sensitivity and specificity of ultrasound for microbubble detection, molecular imaging can be realized by binding antibodies, peptides, and other targeting moieties to microbubble surfaces. Molecular microbubbles directed against various targets such as vascular endothelial growth factor receptor-2, vascular cell adhesion molecule 1, intercellular adhesion molecule 1, selectins, and integrins were developed and were shown in preclinical studies to be able to selectively bind to tumor blood vessels and atherosclerotic plaques. Currently, the first microbubble formulations targeted to angiogenic vessels in prostate cancers are being evaluated clinically. However, microbubbles can be used for more than diagnosis: disintegrating microbubbles emit acoustic forces that are strong enough to induce thrombolysis, and they can also be used for facilitating drug and gene delivery across biologic barriers. This review on the use of microbubbles for ultrasound-based molecular imaging, therapy, and theranostics addresses innovative concepts and identifies areas in which clinical translation is foreseeable in the near future.
Improved Biodistribution and Radioimmunoimaging with Poly(ethylene glycol)-DOTA-Conjugated Anti-CEA Diabody (2005)

Diabodies are single chain antibody fragments (scFvs) that spontaneously form bivalent dimers of molecular size 50-55000. Radiolabeled diabodies are almost ideal tumor targeting agents due to their high avidity (bivalent) binding to tumor antigens and small size (50-55000) that leads to improved tumor-to-blood ratio compared to intact antibodies (150000). However, due to their high retention and metabolism in the kidney, radioiodine is the current radiolabel of choice for diabodies since radioiodine is rapidly excreted from the kidney once metabolized. We have previously shown that 111In-DOTA-diabody gives higher tumor uptake in nude mouse xenografts than 125I-diabody, but has extremely high kidney retention since its 111In-labeled metabolites are retained by and only slowly excreted from the kidney. When a diabody is conjugated to a bifunctional PEG-3400 derivative followed by reaction with cysteinyl-DOTA, the resulting product has an apparent molecular size of 75000 and a Stokes radius of 35 angstroms on size exclusion chromatography, compared to a Stokes radius of 25 angstroms for intact diabody. When radiolabeled, the conjugate gives high yields of 111In-labeled product, retains high immunoreactivity, and gives improved biodistributions (30-40%ID/g, 12-48 h) compared to 111In-DOTA-diabody (12-13%ID/g, 6-12 h). We show that the improved biodistribution is due to an increase in Stokes radius caused by the linear PEG-3400 since conjugation of diabody with multiple (PEG)12 linkers followed by reaction with cysteinyl-DOTA does not reduce kidney accumulation. We also show that 111In-cysteinyl-DOTA-PEG3400-diabody gives excellent tumor images in the nude mouse xenograft model and that 125I-PEG3400-diabody gives equivalent images to 125I-minibody (molecular size, 80000), but improved tumor-to-liver ratios, suggesting that this imaging agent can be used to image liver metastases.
TIM genes: a family of cell surface phosphatidylserine receptors that regulate innate and adaptive immunity (2010)

The TIM (T cell/transmembrane, immunoglobulin, and mucin) gene family plays a critical role in regulating immune responses, including allergy, asthma, transplant tolerance, autoimmunity, and the response to viral infections. The unique structure of TIM immunoglobulin variable region domains allows highly specific recognition of phosphatidylserine (PtdSer), exposed on the surface of apoptotic cells. TIM-1, TIM-3, and TIM-4 all recognize PtdSer but differ in expression, suggesting that they have distinct functions in regulating immune responses. TIM-1, an important susceptibility gene for asthma and allergy, is preferentially expressed on T-helper 2 (Th2) cells and functions as a potent costimulatory molecule for T-cell activation. TIM-3 is preferentially expressed on Th1 and Tc1 cells, and generates an inhibitory signal resulting in apoptosis of Th1 and Tc1 cells. TIM-3 is also expressed on some dendritic cells and can mediate phagocytosis of apoptotic cells and cross-presentation of antigen. In contrast, TIM-4 is exclusively expressed on antigen-presenting cells, where it mediates phagocytosis of apoptotic cells and plays an important role in maintaining tolerance. TIM molecules thus provide a functional repertoire for recognition of apoptotic cells, which determines whether apoptotic cell recognition leads to immune activation or tolerance, depending on the TIM molecule engaged and the cell type on which it is expressed.
Apoptosis or retinoblastoma: alternative fates of photoreceptors expressing the HPV-16 E7 gene in the presence or absence of p53. (1994)

A transgenic mouse model for retinoblastoma was produced previously by directing SV40 T antigen expression to retinal photoreceptor cells using the promoter of the interstitial retinol-binding protein (IRBP) gene. This gene becomes active prior to the terminal differentiation of photoreceptors. Because T antigen-transforming activity is attributable, at least in part, to the inactivation of the retinoblastoma (pRb) and p53 tumor suppressor proteins, we addressed the role of p53 in the development of retinoblastoma in mice. Transgenic mice expressing HPV-16 E7 under the control of the IRBP promoter were generated to inactivate pRb in photoreceptors while leaving p53 intact. Rather than developing retinoblastomas, the retinas of these mice degenerate due to photoreceptor cell death at a time in development when photoreceptors are normally undergoing terminal differentiation. The dying cells exhibit the histological and ultrastructural features of apoptosis and contain fragmented DNA. p53 is required for the induction of apoptosis in this model, because mice expressing E7 in a p53 nullizygous background develop retinal tumors instead of undergoing retinal degeneration.
Magnesium metabolism. A review with special reference to the relationship between intracellular content and serum levels (1988)

Magnesium (Mg++) is a ubiquitous element in nature, playing a role in photosynthesis and many metabolic functions in humans. All enzymatic reactions that involve adenosine triphosphate have an absolute requirement for Mg++. Levels of Mg++ are controlled by the kidneys and gastrointestinal tract and appear closely linked to calcium, potassium, and sodium metabolism. The clinical manifestations and causes of abnormal Mg++ status are protean. Testing for altered Mg++ homeostasis is problematic. Serum levels, which are those generally measured, reflect only a small part of the total body content of Mg++. The intracellular content can be low, despite normal serum levels in a person with clinical Mg++ deficiency. Future directions in research related to intracellular content of Mg++ are discussed. Treatment of altered Mg++ status depends on the clinical setting and may include the addition of a potassium/Mg++-sparing drug to an existing diuretic regimen. Guidelines for therapy are given.
Ultrafast parallel laser processing of materials for high throughput manufacturing (2009)

Laser patterning is a key industrial process in the manufacturing of organic light emitting diode (OLED) displays, solid-state lighting foils and solar cells. Ultrafast lasers are of particular interest for this application as they may enable selective ablative removal of OLED layers with minimal energy density requirements on the target. Since sufficient laser output from commercial laser sources is currently exceeding single beam process requirements, parallel processing with multiple beams could provide a novel route for up-scaling processing speed and reduce manufacturing costs. In this paper, we propose the use of a reflective liquid crystal on silicon spatial light modulator, driven by fast computer-generated holograms, for splitting a parent laser beam into a number of beamlets and to digitally manipulate their position and laser intensity on the target. With successful blocking of the non-diffracted zero order beam and subsequent delivery of the SLM diffracted beams using a galvanometer scanner and flat-field f-theta lens, we demonstrate high throughput precision patterning of silicon and thin film electrodes (ITO anode and metal cathode) on flexible and glass substrates. It is additionally shown that, by carefully adjusting the number of beams per line, one can selectively remove different amount of materials simultaneously in adjacent locations all within a single scanning step. Microscopic examination with optical microscopy and white light interferomety revealed the extent of resolution, process quality and assisted quantification of the process speed gain. The benefits and current limitations of this technique are discussed in detail.
Band parameters for nitrogen-containing semiconductors (2003)

We present a comprehensive and up-to-date compilation of band parameters for all of the nitrogen-containing III–V semiconductors that have been investigated to date. The two main classes are: (1) “conventional” nitrides (wurtzite and zinc-blende GaN, InN, and AlN, along with their alloys) and (2) “dilute” nitrides (zinc-blende ternaries and quaternaries in which a relatively small fraction of N is added to a host III–V material, e.g., GaAsN and GaInAsN). As in our more general review of III–V semiconductor band parameters [I. Vurgaftman et al., J. Appl. Phys. 89, 5815 (2001)], complete and consistent parameter sets are recommended on the basis of a thorough and critical review of the existing literature. We tabulate the direct and indirect energy gaps, spin-orbit and crystal-field splittings, alloy bowing parameters, electron and hole effective masses, deformation potentials, elastic constants, piezoelectric and spontaneous polarization coefficients, as well as heterostructure band offsets. Temperature and alloy-composition dependences are also recommended wherever they are available. The “band anticrossing” model is employed to parameterize the fundamental band gap and conduction band properties of the dilute nitride materials.
Synthesis and NKT Cell Stimulating Properties of Fluorophore- and Biotin-Appended 6‘ ‘-Amino-6‘ ‘-deoxy-galactosylceramides (2002)

Alpha-galactosylceramides are potent stimulators of human T cells. Stimulation occurs through binding of the glycolipids by CD1d, presentation to T cells, and formation of a CD1d-glycolipid-T cell receptor complex. To facilitate the elucidation of the structural features of glycolipids necessary for T cell stimulation, alpha-galactosylceramides have been prepared with small molecules appended at the C6 position of the sugar. The appended molecules do not significantly influence the abilities of the glycolipids to stimulate T cells. [reaction: see text]
A history of the Apple human interface group (1998)

article Free Access Share on A history of the Apple human interface group Author: S. Joy Mountford View Profile Authors Info & Claims ACM SIGCHI BulletinVolume 30Issue 2April 1998 pp 144–146https://doi.org/10.1145/279044.279175Published:01 April 1998Publication History 0citation453DownloadsMetricsTotal Citations0Total Downloads453Last 12 Months232Last 6 weeks63 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Efficient Delivery of Streptavidin to Mammalian Cells:  Clathrin-Mediated Endocytosis Regulated by a Synthetic Ligand (2002)

The efficient delivery of macromolecules to living cells presents a formidable challenge to the development of effective macromolecular therapeutics and cellular probes. We describe herein a novel synthetic ligand termed "Streptaphage" that enables efficient cellular uptake of the bacterial protein streptavidin by promoting noncovalent interactions with cholesterol and sphingolipid-rich lipid raft subdomains of cellular plasma membranes. The Streptaphage ligand comprises an N-alkyl derivative of 3 beta-cholesterylamine linked to the carboxylate of biotin through an 11-atom tether. Molecular recognition between streptavidin and this membrane-bound ligand promotes clathrin-mediated endocytosis, which renders streptavidin partially intracellular within 10 min and completely internalized within 4 h of protein addition. Analysis of protein uptake in Jurkat lymphocytes by epifluorescence microscopy and flow cytometry revealed intracellular fluorescence enhancements of over 300-fold (10 microM ligand) with >99% efficiency and low toxicity. Other mammalian cell lines including THP-1 macrophages, MCF-7 breast cancer cells, and CHO cells were similarly affected. Structurally related ligands bearing a shorter linker or substituting the protonated steroidal amine with an isosteric amide were ineffective molecular transporters. Confocal fluorescence microscopy revealed that Streptaphage-induced uptake of streptavidin functionally mimics the initial cellular penetration steps of Cholera toxin, which undergoes clathrin-mediated endocytosis upon binding to the lipid raft-associated natural product ganglioside GM1. The synthetic ligand described herein represents a designed cell surface receptor capable of targeting streptavidin conjugates into diverse mammalian cells by hijacking the molecular machinery used to organize cellular membranes. This technology has potential applications in DNA delivery, tumor therapy, and stimulation of immune responses.
Procalcitonin guidance for reduction of antibiotic use in low‐risk outpatients with community‐acquired pneumonia (2011)

Under PCT guidance, antibiotic use was reduced and duration of antibiotic treatment was shortened in low-risk outpatients with CAP, without apparent harm.
Inhibition of polyunsaturated fatty acid accumulation in plants expressing a fatty acid epoxygenase (2000)

Earlier, we described the isolation of a Crepis palaestina cDNA (Cpal2) which encoded a Δ12-epoxygenase that could catalyse the synthesis of 12,13-epoxy-cis-9-octadecenoic acid (18:1E) from linoleic acid (18:2). When the Cpal2 gene was expressed under the control of a seed-specific promoter in Arabidopsis plants were able to accumulate small amounts 18:1E and 12,13-epoxy-cis-9,15-octadec-2-enoic acid in their seed lipids. In this report we give results obtained from a detailed analysis of transgenic Arabidopsis plants containing the Cpal2 gene. The seeds from these plants accumulate varying levels of 18:1E, but show a marked increase in 18:1 and equivalent decrease in 18:2 and 18:3. We further observed that the co-expression of a C. palaestina Δ12-desaturase in Arabidopsis appears to return the relative proportions of the C18 seed fatty acids to normal levels and results in a 2-fold increase in total epoxy fatty acids.
An HPF compiler for the IBM SP2 (1995)

We describe pHPF, an research prototype HPF compiler for the IBM SP series parallel machines. The compiler accepts as input Fortran 90 and Fortran 77 programs, augmented with HPF directives; sequential loops are automatically parallelized. The compiler supports symbolic analysis of expressions. This allows parameters such as the number of processors to be unknown at compile-time without significantly affecting performance. Communication schedules and computation guards are generated in a parameterized form at compile-time. Several novel optimizations and improved versions of well-known optimizations have been implemented in pHPF to exploit parallelism and reduce communication costs. These optimizations include elimination of redundant communication using data-availability analysis; using collective communication; new techniques for mapping scalar variables; coarse-grain wavefronting; and communication reduction in multi-dimensional shift communications. We present experimental results for some well-known benchmark routines. The results show the effectiveness of the compiler in generating efficient code for HPF programs.
Intracranially Administered Anti-Αβ Antibodies Reduce β-Amyloid Deposition by Mechanisms Both Independent of and Associated with Microglial Activation (2003)

Active immunization against the -amyloid peptide () with vaccines or passive immunization with systemic monoclonal anti-A antibodies reduces amyloid deposition and improves cognition in APP transgenic mice. In this report, intracranial administration of anti- antibodies into frontal cortex and hippocampus of Tg2576 transgenic APP mice is described. The antibody injection resulted initially in a broad distribution of staining for the antibody, which diminished over 7 d. Although no loss of immunostaining for deposited A was apparent at 4 hr, a dramatic reduction in the load was discernible at 24 hr and was maintained at 3 and 7 d. A reduction in the thioflavine-S-positive compact plaque load was delayed until 3 d, at which time microglial activation also became apparent. At 1 week after the injection, microglial activation returned to control levels, whereas and thioflavine-S staining remained reduced. The results from this study suggest a two-phase mechanism of anti- antibody action. The first phase occurs between 4 and 24 hr, clears primarily diffuse deposits, and is not associated with observable microglial activation. The second phase occurs between 1 and 3 d, is responsible for clearance of compact amyloid deposits, and is associated with microglial activation. The results are discussed in the context of other studies identifying coincident microglial activation and amyloid removal in APP transgenic animals.
Effect of CD26/dipeptidyl peptidase IV on Jurkat sensitivity to G2/M arrest induced by topoisomerase II inhibitors (2003)

CD26/dipeptidyl peptidase IV (DPPIV) is a surface antigen with multiple functions, including a role in T-cell activation and the development of certain human cancers. We previously demonstrated that CD26/DPPIV enhanced sensitivity of Jurkat cells to doxorubicin. We now show that expression of CD26/DPPIV enhanced sensitivity of CD26 Jurkat transfectants to G(2)-M arrest mediated by the antineoplastic agent etoposide. The increased sensitivity to etoposide-induced G(2)-M arrest was associated with disruption of cell cycle-related events, including hyperphosphorylation of p34(cdc2) kinase, change in cdc25C expression and phosphorylation, and alteration in cyclin B1 expression. CD26/DPPIV-associated enhancement of doxorubicin and etoposide-induced G(2)-M arrest was also observed in serum-free media, suggesting an effect of CD26 on cell-derived processes rather than serum-derived factors. Importantly, our work elucidated a potential mechanism for the enhanced susceptibility of CD26-expressing Jurkat cells to the topoisomerase II inhibitors by demonstrating that CD26/DPPIV surface expression was associated with increased topoisomerase II alpha levels and enhanced enzyme activity. Besides being the first to show a functional association between the multifaceted molecule CD26 and the key cellular protein topoisomerase II alpha, our studies provide additional evidence of a potential role for CD26 in the treatment of selected malignancies.