gebhart/patrepeval huggingface dataset:
B Lymphocytes Treated In Vitro with Antigen Coupled to Cholera Toxin B Subunit Induce Antigen-Specific Foxp3+ Regulatory T Cells and Protect against Experimental Autoimmune Encephalomyelitis (2012)

The ability of activated B cells to protect against various experimental autoimmune or allergic diseases makes them attractive for use in cell-based therapies. We describe an efficient way to generate B cells with strong suppressive functions by incubating naive B cells with a relevant Ag conjugated to cholera toxin B subunit (CTB). This allows most B cells, irrespective of BCR, to take up and present Ag and induces their expression of latency-associated polypeptide (LAP)/TGF-β and after adoptive transfer also their production of IL-10. With OVA as model Ag, when naive T cells were cocultured in vitro with B cells pretreated with OVA conjugated to CTB (OVA/CTB) Ag-specific CD4(+) Foxp3 regulatory T (Treg) cells increased >50-fold. These cells effectively suppressed CD25(-)CD4(+) effector T (Teff) cells in secondary cultures. Adoptive transfer of OVA/CTB-treated B cells to mice subsequently immunized with OVA in CFA induced increase in Foxp3 Treg cells together with suppression and depletion of Teff cells. Likewise, adoptive transfer of B cells pulsed with myelin oligodendrocyte glycoprotein peptide(35-55) (MOGp) conjugated to CTB increased the number of Treg cells, suppressed MOGp-specific T cell proliferation and IL-17 and IFN-γ production, and prevented the development of experimental autoimmune encephalomyelitis. Similar effects were seen when B cells were given "therapeutically" to mice with early-stage experimental autoimmune encephalomyelitis. Our results suggest that B cells pulsed in vitro with relevant Ag/CTB conjugates may be used in cell therapy to induce Ag-specific suppression of autoimmune disease.
A Study of Ethanol Tolerance in Yeast (1989)

The ethanol tolerance of yeast and other microorganisms has remained a controversial area despite the many years of study. The complex inhibition mechanism of ethanol and the lack of a universally accepted definition and method to measure ethanol tolerance have been prime reasons for the controversy. A number of factors such as plasma membrane composition, media composition, mode of substrate feeding, osmotic pressure, temperature, intracellular ethanol accumulation, and byproduct formation have been shown to influence the ethanol tolerance of yeast. Media composition was found to have a profound effect upon the ability of a yeast strain to ferment concentrated substrates (high osmotic pressure) and to ferment at higher temperatures. Supplementation with peptone-yeast extract, magnesium, or potassium salts has a significant and positive effect upon overall fermentation rates. An intracellular accumulation of ethanol was observed during the early stages of fermentation. As fermentation proceeds, the intracellular and extracellular ethanol concentrations become similar. In addition, increases in osmotic pressure are associated with increased intracellular accumulation of ethanol. However, it was observed that nutrient limitation, not increased intracellular accumulation of ethanol, is responsible to some extent for the decreases in growth and fermentation activity of yeast cells at higher osmotic pressure and temperature.
Contributions of Conventional Plant Breeding to Food Production (1983)

Within a relatively short geological time frame, Neolithic man, or more probably woman, domesticated all the major cereal grains, legumes, and root crops that the world's people depend on for most of their calories and protein. Until very recently, crop improvement was in the hands of farmers. The cornerstones of modern plant breeding were laid by Darwin and Mendel in the late 19th century. As the knowledge of genetics, plant pathology, and entomology have grown during the 20th century, plant breeders have made enormous contributions to increased food production throughout the world. There have been major plant breeding break-throughs for maize and wheat, and promising research activities to raise yields in marginal production environments are ongoing. Since it is doubtful that significant production benefits will soon be forthcoming from the use of genetic engineering techniques with higher plants, especially polyploid species, most research funds for crop improvement should continue to be allocated for conventional plant breeding research.
Application of diversity indices and ecological indices to evaluate nematode community changes after soil fumigation (2004)

Soil nematode densities and family-level faunal compositions were investigated for five months after chloropicrin fumigation in soybean fields in Japan. Our objective was to examine whether diversity measurements and ecological indices can describe appropriately structural changes in nematode communities after chemical disturbance. The total nematode density in the fumigated plots drastically decreased just after chloropicrin treatment, but gradually recovered. After the chemical treatment, the dominant nematode taxon changed from Rhabditidae to Cephalobidae; the fungivorous nematode guild and guilds with cp value 3-5 (CP35, K-strategists) were hardly detected. In the non-fumigated control plots Rhabditidae still predominated, and the fungivorous guild and CP35 guilds increased. Among the diversity indices and the ecological indices examined, Shannon- Wiener's H', Maturity Index (MI), Maturity Index without opportunistic bacterivorous guilds (MI (2-5)), Enrichment Index (EI) and Structure Index (SI) described these structural changes in the nematode communities. The Channel Index failed to detect significant effect of fumigation on decomposition pathways because both the fungivorous nematode guild and Rhabditidae were reduced in the fumigated plots. Replacement of Rhabditidae with Cephalobidae in the plots required careful interpretation of MI and EI behaviors. Even under such a replacement, MI (2-5) and SI were still useful in evaluating appropriately the ecological status of nematode communities after chemical disturbances. Jpn. J. Nematol. 34 (2), 89-98 (2004).
Synthesis of Sulfotyrosine‐Containing Peptides by Incorporating Fluorosulfated Tyrosine Using an Fmoc‐Based Solid‐Phase Strategy (2015)

Abstract Tyrosine O‐sulfation is a common protein post‐translational modification that regulates many biological processes, including leukocyte adhesion and chemotaxis. Many peptides with therapeutic potential contain one or more sulfotyrosine residues. We report a one‐step synthesis for Fmoc‐fluorosulfated tyrosine. An efficient Fmoc‐based solid‐phase peptide synthetic strategy is then introduced for incorporating the fluorosulfated tyrosine residue into peptides of interest. Standard simultaneous peptide‐resin cleavage and removal of the acid‐labile side‐chain protecting groups affords the crude peptides containing fluorosulfated tyrosine. Basic ethylene glycol, serving both as solvent and reactant, transforms the fluorosulfated tyrosine peptides into sulfotyrosine peptides in high yield.
X-ray diffraction characterization of the structure of zein-Oleic acid films (1999)

Wide-angle (WAXS) and small-angle X-ray scattering (SAXS) studies of dry granular zein, zein fibers, zein–oleic acid resin, and zein–oleic acid films are reported. WAXS patterns showed two diffuse rings for these samples indicative of noncrystalline structures. Measured d-spacings of ∼ 4.6 Å and ∼ 10.5 Å were found for zein–oleic acid resins and films, consistent with the presence of α-helical segments. The granular zein and zein fibers had ∼ 4.6-Å and ∼ 9.5-Å spacings. Neither the films nor the fibers showed evidence of orientation of the molecular axes. SAXS studies of zein–oleic acid films indicated that the structure of the films was affected by preparation method. Biaxially drawn resin films showed periodicities of ∼ 170 Å along the film surface direction and ∼ 135 Å in the thickness direction, while the cast films had weaker intensity periodicities of ca. 80 Å for all beam directions; a weak, diffuse 45-Å spacing was also observed for both samples. The 170-Å periodicity was present in the resin before deformation and following uniaxial deformation. No SAXS periodicity was observed for the granular zein or zein fibers. Several structural models are presented for the resin films that are consistent with reports in the literature that zein, in solution, consist of prism-like particles consisting of four or more molecules. ? 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 1267-1281, 1999
Modeling, Fabrication, and Optimization of Niobium Cavities – Phase I: Quarterly Progress Report August 20, 2001 - November 20, 2001 (2001)

Multipacting is one of the major loss mechanisms in rf superconductivity cavities for accelerators. This loss mechanism limits the maximum amount of energy/power supported by the cavities. Optimal designs have been identified in others’ studies. In practice, these designs are not easily manufactured. Chemical etching processes used to polish the cavity walls result in a nonuniform surface etch. A nonuniform surface etch will leave some unclean areas with contaminants and micron size particles. These significantly affect mutipacting. Further, a nonuniform etch will leave areas with damaged grain structure, which is not good for superconducting properties. Typically, the depth of chemical polishing etch ranges between 10 to 150 microns.\nIt is the purpose of this study to examine the chemical etching process in the design of niobium cavities so to maximize the surface quality of the cavity walls while minimizing the multipacting losses. Single and multiple cavity cell geometries are to be investigated. Optimization techniques will be applied in search of the chemical etching processes, which will lead to cavity walls with near ideal properties.
Synchronized DMT for multipoint-to-point communications on HFC networks (2002)

This paper presents a method for synchronizing a large number of discrete-multitone-based modems for multipoint-to-point communications on hybrid fiber-coax (HFC) networks. Each newly-installed remote unit is first loop-timed to the central modem master clock. Ranging is then performed to determine the sample delay required to align at the central unit receiver the symbols transmitted by the remote with those transmitted by remote units already operating. Upon completing the synchronization procedure, the remote unit transmits a signal to train the central unit receiver so that the available upstream bandwidth can be used as efficiently as possible during steady-state operation.
BRAINnet: A STANDARDIZED GLOBAL HUMAN BRAIN PROJECT (2013)

Accepted August 20, 2012. Address correspondence to Stephen H. Koslow, BRAINnet, 71 Stevenson Street, Suite 400, San Francisco, CA 94105-0908, USA. Tel: 301-237-6690; E-mail: stephen.koslow@brainnet.net Technology and Innovation, Vol. 15, pp. 17–29, 2013 1949-8241/13 $90.00 + .00 Printed in the USA. All rights reserved. DOI: http://dx.doi.org/10.3727/194982413X13608676060457 Copyright  2013 Cognizant Comm. Corp. E-ISSN 1949-825X www.cognizantcommunication.com
Serum reference intervals and diagnostic ranges for free kappa and free lambda immunoglobulin light chains: relative sensitivity for detection of monoclonal light chains. (2002)

Reference and diagnostic intervals for serum FLCs have been developed for use with a new, automated immunoassay that makes the detection and quantification of monoclonal FLCs easier and more sensitive than with current methods. The serum FLC assay complements IFE and allows quantification of FLCs in light-chain-disease patients who have no detectable serum or urine M-spike.
Alzheimer's disease drug development pipeline: 2017 (2017)

The AD drug development pipeline has 105 agents divided among phase I, phase II, and phase III. The trials include a wide range of clinical trial populations, many mechanisms of action, and require a substantial number of clinical trial participants. Biomarkers are increasingly used in patient identification and as outcome measures, particularly in trials of DMTs.
Methylotrophic Bacteria: Biochemical Diversity and Genetics (1983)

Bacteria that are able to use methane as a sole carbon and energy source also carry out a broad range of biotransformations, some of which have industrial and environmental significance. Genetic studies on methylotrophs, including the use of recombinant DNA techniques, show promise for the isolation and cloning of genes coding for specific functions.
Reduction in Basic Fibroblast Growth Factor Mediated AngiogenesisIn Vivoby Linomide (1998)

Linomide (N-phenylmethyl-1,2-dihydro-4-hydroxyl-1-methyl-2-oxoquinoline-3-carbox-amide) is a novel immunomodulator with a potent anti-tumoral activity. This study was undertaken to test the effect of Linomide on basic fibroblast growth factor (bFGF) induced angiogenesis in vivo, which manifests itself in an increased number of blood vessels per unit of cell infiltrated area. Subcutaneously implanted polyvinyl alcohol sponges (PVS) in guinea pigs were used as a model system to quantitate angiogenesis in vivo. Oral treatment with Linomide was able to reduce significantly the bFGF induced blood vessel growth and proliferation within the implanted PVS, relative to untreated controls. In addition, Linomide significantly reduced the bFGF mediated augmentation of protein and collagen content in the implanted PVS, indicating an inhibition in the deposition of extracellular matrix (ECM). We conclude that the potent inhibition of bFGF induced angiogenesis by Linomide in vivo in addition to immunomodulatory effects may have potentially important clinical applications.
A phase II trial of paclitaxel in squamous cell carcinoma of the head and neck with correlative laboratory studies. (1995)

Head and neck cancer is a major cause of cancer-related deaths. In general, early stage head and neck cancers are effectively treated with either radiation or surgery. More advanced tumors often require combined-modality therapy with both radiation therapy and surgery. Recent investigations indicate that the addition of chemotherapy may be helpful. One of the newer chemotherapy agents that appears to have significant activity against head and neck cancer is paclitaxel (Taxol; Bristol-Myers Squibb Company, Princeton, NJ). Paclitaxel, originally derived from the western yew Taxus brevifolia, acts by increasing the stability of microtubules and preventing mitosis. Recent evidence indicates that the microtubule system is vital to the release of various cytokines and that modulation of cytokine release may play a major role in the drug's antitumor activity. We report a phase II trial of paclitaxel in patients with head and neck cancer, not only to evaluate its clinical effects, but also to study its effect on cytokine release. We assessed interleukin-1 beta (IL-1 beta) and tumor necrosis factor-alpha production by using a sensitive enzyme-linked immunosorbent assay to assess the serum of patients receiving paclitaxel and to detect cytokine release in vitro. The objective response rate was 36%, with 12% complete responses and 24% partial responses. No IL-1 beta or tumor necrosis factor-alpha was detected in patient serum at any time during the infusion of paclitaxel or after overnight incubation with patient monocytes. No proIL-1 beta was detected in in vitro cultures of paclitaxel-treated patient monocytes. When monocytes were stimulated with endotoxin, IL-1 beta production was greatest at 48 hours, suggesting that paclitaxel can prime cells to produce greater quantities of cytokines after a second stimulus.
Rapid Access of Antibodies to α5β1 Integrin Overexpressed on the Luminal Surface of Tumor Blood Vessels (2005)

Integrin alpha(5)beta(1) is overexpressed on endothelial cells of tumor vessels and is uniformly and rapidly accessible to antibodies in the bloodstream. Here, we determined whether antibodies rapidly gain access to integrin overexpressed on the abluminal (basolateral) surface of endothelial cells through vascular leakiness or whether the rapid accessibility results instead because the integrin is overexpressed on the luminal (apical) surface of endothelial cells due to loss of cell polarity. Using tumors in RIP-Tag2 transgenic mice as a model, we first compared the binding pattern of intravascular anti-alpha(5)beta(1) integrin antibody with the leakage pattern of nonspecific IgG. The distributions did not match: anti-alpha(5)beta(1) integrin antibody uniformly labeled the tumor vasculature, but IgG was located in patchy sites of leakage. We next injected an antibody to fibrinogen/fibrin, which resulted in patchy labeling of tumors that matched the leakage of IgG and the overall distribution of fibrin in tumors. Similarly, injected antibodies to the basement membrane protein fibronectin, a ligand of alpha(5)beta(1) integrin, or type IV collagen produced patchy sites of leakage instead of uniform labeling of vascular basement membrane. Differences in the kinetics of labeling, which for alpha(5)beta(1) integrin antibody was near maximal by 10 minutes but for the other antibodies gradually increased over 6 hours, indicated differences in accessibility of their respective targets. Isosurface rendering of confocal microscopic images was consistent with antibody binding to alpha(5)beta(1) integrin on the luminal surface of endothelial cells. Together, these findings indicate that the rapid accessibility of alpha(5)beta(1) integrin in RIP-Tag2 tumors results from overexpression of the integrin on the luminal surface of tumor vessels.
Human neural cell adhesion molecule L1 and rat homologue NILE are ligands for integrin alpha v beta 3. (1996)

Integrin alpha v beta 3 is distinct in its capacity to recognize the sequence Arg-Gly-Asp (RGD) in many extra-cellular matrix (ECM) components. Here, we demonstrate that in addition to the recognition of ECM components, alpha v beta 3 can interact with the neural cell adhesion molecule L1-CAM; a member of the immunoglobulin superfamily (IgSF). M21 melanoma cells displayed significant Ca(++)-dependent adhesion and spreading on immunopurified rat L1 (NILE). This adhesion was found to be dependent on the expression of the alpha v-integrin subunit and could be significantly inhibited by an antibody to the alpha v beta 3 heterodimer. M21 cells also displayed some alpha v beta 3-dependent adhesion and spreading on immunopurified human L1. Ligation between this ligand and alpha v beta 3 was also observed to promote significant haptotactic cell migration. To map the site of alpha v beta 3 ligation we used recombinant L1 fragments comprising the entire extracellular domain of human L1. Significant alpha v beta 3-dependent adhesion and spreading was evident on a L1 fragment containing Ig-like domains 4, 5, and 6. Importantly, mutation of an RGD sequence present in the sixth Ig-like domain of L1 abrogated M21 cell adhesion. We conclude that alpha v beta 3-dependent recognition of human L1 is dependent on ligation of this RGD site. Despite high levels of L1 expression the M21 melanoma cells did not display significant adhesion via a homophilic L1-L1 interaction. These data suggest that M21 melanoma cells recognize and adhere to L1 through a mechanism that is primarily heterophilic and integrin dependent. Finally, we present evidence that melanoma cells can shed and deposit L1 in occluding ECM. In this regard, alpha v beta 3 may recognize L1 in a cell-cell or cell-substrate interaction.
Quantitation of junctional and extrajunctional acetylcholine receptors by electron microscope autoradiography after (125)I-α-bungarotoxin binding at mouse neuromuscular junctions (1976)

The distribution and quantitation of 125I-alpha-bungarotoxin (alpha-BTX) binding sites and thus acetylcholine receptor (AChR) were determined in mouse sternomastoid muscle by electron microscope autoradiography. We found that a valid criterion for receptor saturation at the neuromuscular junction was the complete elimination of neurally evoked tetanic muscle contractions, since, when such a criterion was used for the endpoint of toxin incubation, alpha-BTX was bound to approximately 90% of total available endplate sites. When, without implying localization, the presynaptic axonal membrane was used as a convenient reference structure, the concentration of alpha-BTX relative to this membrane was determined to be 46,000 +/- 27% sites/mum2.
Effect of sodium bicarbonate ingestion on exhaustive resistance exercise performance (1993)

WEBSTER, M. J., M. N. WEBSTER, R. E. CRAWFORD, and L. B. GLADDEN. Effect of sodium bicarbonate ingestion on exhaustive resistance exercise performance. Med. Sci. Sports Exerc., Vol. 25, No. 8, pp. 960–965, 1993. Six weight trained males were studied prior to, during, and in recovery from exhaustive resistance exercise, 105 min after ingesting 300 mg·kg-1 of either a placebo or NaHCO3. The exercise test consisted of four sets of 12 repetitions with a fifth set to volitional fatigue on a Universal leg press machine at a resistance equaling approximately 70% of the subjects 1-repetition maximum. Arterialized venous blood was analyzed for lactate concentration, blood gas, and acid-base parameters. The ingestion of NaHCO3 produced a significant increase in resting pH (7.39 to 7.46), HCO3- (22.9 to 28.3 mEq·1-1), and oxygenated base excess (-1.3 to 4.4 mEq·1-1). With the completion of each exercise set, a progressive decline in the acid-base status of both groups was observed (pH set 1–5: NaHCO3, 7.40 to 7.31; placebo, 7.34 to 7.25; HCO3- set 1–5: NaHCO3, 25.3 to 17.9; placebo, 21.7 to 15.3 mEq·1-1; base excess set 1–5: NaHCO3, 3.7 to −7.1; placebo, −1.4 to −10.7 mEq·1-1); however, the NaHCO3 condition was significantly more alkaline than the placebo condition. Blood lactate concentration [La] progressively increased with the completion of each exercise set ([La] set 1–5: NaHCO3, 1.37 to 11.15; placebo, 1.31 to 9.81 mM); but were not significantly different between treatments. Repetitions performed in the final exercise set were not significantly different between groups (NaHCO3: 19.6 · 1.6, placebo: 18.2 · 1.1 repetitions). Whereas NaHCO3 has been shown to improve high-intensity running, cycling, and swimming performance, these findings indicate that NaHCO3 does not necessarily enhance exhaustive resistance exercise performance of the type typically used in strength training. However, additional experiments with a larger number of subjects and a more intense resistance exercise protocol appear to be warranted.