gebhart/patrepeval huggingface dataset:
Membrane fusion: studies with a calcium-sensitive dye, arsenazo III, in liposomes. (1977)

Fusion between vesicles, cells, or organelles may be defined as confluence of two membrane-bound compartments without access of their solutes to external milieu. To study fusion by this criterion, we have trapped the metallochromic calcium-sensitive dye, arsenazo III (AIII), partially calcium-saturated (AIII-Ca) in one population of liposomes (phoshatidylcholine 90:dicetylphosphate 10), and ethylene glycol-bis(beta-aminoethyl ether)-N,N'-tetraacetate (EGTA) in a second. In such mixtures, interaction of EGTA with AIII-Ca was measured by a large color shift from blue leads to red (decreased absorbance at 660 nm). Fusion of liposomes (but also lysis and diffusion across the membranes) was proportional to these decrements. The exogenous "fusogens," lysolecithin and retinol, were added to liposomes for 5-24 hr at 37 degrees; after rechromatography, measurements were made of total dye, fraction of dye converted from AIII-Ca to AIII, and total lipid. After correction for lysis and diffusion, lysolecithin (200 microng/ml) induced 23% fusion (volume of AIII liposomes confluent with EGTA liposomes) and retinol (300 microng/ml) induced 15%. With one molar percent cortisol (a membrane stabilizer) in the liposome membranes, fusion induced by fusogens was reduced 2-fold. Neither multi-nor unilamellar liposomes fused with each other in the absence of exogenous fusogens, despite wide variations in molar lipid ratios. Results suggest that liposome-liposome fusion is a slow process requiring exogenous fusogens, which may depend upon contributions of other membrane constituents to mimic closely the fusion of natural membranes.
Milestones in the Biochemistry of Silicon: From Basic Research to Biotechnological Applications (1999)

6.7 Gigatonnes of silicon are processed each year by marine organisms. Since it was known that silicon is an essential element for many biological systems, significant advances in the biochemistry of this element have been achieved from the classical viewpoint of silicon being a purely inorganic element. This article describes the proteins, genes, and molecular mechanisms of silicon metabolism in diatoms and sponges. These studies may help to reveal the role of silicon for optimal development and growth in many plants and animals as well as initiate the development of new technological methods for the shape-controlled production of new patterned silicone-based materials.
Latent transforming growth factor-beta from human platelets. A high molecular weight complex containing precursor sequences. (1988)

Human platelets, when induced to degranulate by thrombin, secrete transforming growth factor-beta (TGF-beta) in a biologically latent form. In this form, TGF-beta cannot bind to its cellular receptor, nor can it be immunoprecipitated by polyclonal antisera to TGF-beta, suggesting that the receptor-binding site and other TGF-beta epitopes may be masked. Western blot analysis of the platelet secretate indicates that the latent form of TGF-beta is a 220-235 kDa complex, in which mature TGF-beta (25 kDa) is noncovalently associated with sequences from the remainder of the precursor (74 kDa), and a third unidentified entity (approximately 135 kDa). The third component is immunologically unrelated to other growth factor binding proteins. The complex is glycosylated, and gel filtration analysis suggests it may exist in solution as higher molecular weight aggregates. Further chromatographic analysis indicates that in its latent form, the platelet TGF-beta cannot bind to alpha 2-macroglobulin (alpha 2M), but that if the platelet latent TGF-beta is activated by transient acidification, the released active TGF-beta will bind to alpha 2M. We have previously identified the latent form of TGF-beta found in serum as an alpha 2M.TGF-beta complex (O'Connor-McCourt, M. D., and Wakefield, L. M. (1987) J. Biol. Chem. 262, 14090-14099). We now propose that the latent TGF-beta secreted by platelets may be a cellular delivery complex, whereas the latent form found in serum may represent a clearance complex. Thus alpha 2M may scavenge excess TGF-beta that is released when the platelet latent form is activated, possibly by the clotting process. Finally, we have shown that the latent form of TGF-beta secreted by a variety of cell types in culture is similar, if not identical to that secreted by platelets.
Contribution of the rib cage to breathing in tetraplegia. (1985)

In tetraplegia there is often paradoxical inward motion of the rib cage during inspiration. The volume of this negative contribution is difficult to estimate but can be obtained by optical mapping. The partitioning of ventilation between the rib cage and abdomen in six normal subjects, 10 stable tetraplegic patients, and one tetraplegic patient at intervals during rehabilitation has been studied by this technique. In normal subjects the tidal volume and the vital capacity were the sum of positive contributions from the rib cage and abdomen. In stable tetraplegic subjects with similar neurological levels, the rib cage contribution varied widely but the total chest wall displacement could not be predicted from the vital capacity. In the patient studied sequentially rib cage paradox reversed with time after injury, and this was associated with an absolute increase in vital capacity and an improvement in the action of the diaphragm.
Location-Specific Biological Functionalization on Nanotubes:  Attachment of Proteins at the Ends of Nanotubes Using Au Nanocrystal Masks (2003)

We developed a novel method to immobilize proteins at a specific location on nanotubes. In this report, avidin was immobilized only at the ends of peptide nanotubes using Au nanocrystals as protective masks on the sidewalls of nanotubes. While the Au nanocrystal-masked nanotubes adsorbed avidin on their entire surfaces, the chemical etching of the Au nanocrystal masks removed avidin molecules from the sidewalls, but avidin at the nanotube ends remained bound. The chemical etching process did not denature avidin and the nanotube ends could recognize and immobilize onto the complimentary biotin SAMs.
Neurologic Improvement in a Type 3 Gaucher Disease Patient Treated with Imiglucerase/Miglustat Combination (2007)

Combined imiglucerase and miglustat therapy may be beneficial for some neuronopathic forms of GD.
Khayyam: a tunable spatial heterodyne spectrometer for observing diffuse emission line targets (2012)

We describe first results from a new instrument-telescope configuration that combines all of the capabilities necessary to obtain high resolving power visible band spectra of diffuse targets from small aperture telescopes where significant observing time can be obtained. This instrument –Khayyam- is a tunable all-reflective spatial heterodyne spectrometer (SHS) that is mounted to a fixed focal plane shared by the 0.6m Coude auxiliary telescope and the 3m Shane telescope on Mt. Hamilton. Khayyam has an up to 78 arcmin input field of view, resolving power up to 176000, and a tunable bandpass from 350-700 nm. It is being field tested for initial use to study spatially extended solar system targets where high resolving power is necessary to separate multimodal signals, crowded molecular bands, and to sample low velocities (&lt;10 km/s) and rapid temporal cadence is necessary to track physical evolution. Two of the best comet targets during next year is comet C/2011 L4 (PanSTARRS), and C/2011 F1 (LINEAR). Our goal is to sequentially measure isotopic ratios of <sup>14</sup>N:<sup>15</sup>N and <sup>12</sup>C:<sup>13</sup>C in CN, along with the production rate and the production rate ratios of varies daughter species, particularly C<sub>2</sub>, C<sub>3</sub>, NH<sub>2</sub>, OI, and CN, as a function of heliocentric distance and time.
Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation (2011)

Ten-eleven translocation 1-3 (Tet1-3) proteins have recently been discovered in mammalian cells to be members of a family of DNA hydroxylases that possess enzymatic activity toward the methyl mark on the 5-position of cytosine (5-methylcytosine [5mC]), a well-characterized epigenetic modification that has essential roles in regulating gene expression and maintaining cellular identity. Tet proteins can convert 5mC into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) through three consecutive oxidation reactions. These modified bases may represent new epigenetic states in genomic DNA or intermediates in the process of DNA demethylation. Emerging biochemical, genetic, and functional evidence suggests that Tet proteins are crucial for diverse biological processes, including zygotic epigenetic reprogramming, pluripotent stem cell differentiation, hematopoiesis, and development of leukemia. Insights into how Tet proteins contribute to dynamic changes in DNA methylation and gene expression will greatly enhance our understanding of epigenetic regulation of normal development and human diseases.
The action of a bacterial agarase on agarose, porphyran and alkali -treated porphyran (1969)

1. A purified extracellular agarase from a Cytophaga species was used to hydrolyse agarose, porphyran and alkali-treated porphyran. 2. The hydrolysate from agarose was separated by gel filtration into the series of neoagarosaccharides, the predominant member of which was the tetrasaccharide. 3. Enzyme action on alkali-treated porphyran gave neoagarosaccharides and other oligosaccharides containing 6-O-methyl-d-galactose units. From the composition of these oligosaccharides it is deduced that action of the enzyme on a d-galactosidic linkage is four to five times faster than on the 6-O-methyl-d-galactosidic linkage. 4. Enzyme action on native porphyran gives a similar series of oligosaccharides but in smaller yield, much of the polysaccharide being either not degraded or only degraded to a series of large, highly sulphated oligosaccharides. 5. For porphyran, it is concluded that 6-O-methyl ether groups are distributed randomly on half the d-galactose units, but that the 6-sulphate groups on l-galactose units tend to occur in blocks.
Quantize-map-forward (QMF) relaying (2013)

We present the design and experimental evaluation of a wireless system that exploits relaying in the context of WiFi. We opt for WiFi given its popularity and wide spread use for a number of applications, such as smart homes. Our testbed consists of three nodes, a source, a relay and a destination, that operate using the physical layer procedures of IEEE802.11. We deploy three main competing strategies that have been proposed for relaying, Decode-and-Forward (DF), Amplify-and-Forward (AF) and Quantize-Map-Forward (QMF). QMF is the most recently introduced of the three, and although it was shown in theory to approximately achieve the capacity of arbitrary wireless networks, its performance in practice had not been evaluated. We present in this work experimental results---to the best of our knowledge, the first ones---that compare QMF, AF and DF in a realistic indoor setting. We find that QMF is a competitive scheme to the other two, offering in some cases up to 12% throughput benefits and up to 60% improvement in frame error-rates over the next best scheme.
The Paradox of Rising Incomes and Increasing Hardship (1991)

Official statistics show that the real incomes of the poorest households, and of those living on social security, have risen in recent years. If so, their hardships should be easing. In fact they appear to be continuing or even worsening. This article looks at six possible solutions to this paradox. There is insufficient evidence to prove or disprove any, but some are more plausible and better supported by evidence than others. The solution may itself be paradoxical. Hardships like lacking heat, shelter or even food may be the result of incomes that are low compared with other incomes, rather than to the cost of fuel, rent etc.
Design of an RF transceiver (1998)

As cellular technology matures, there is an ever increasing demand for greater integration of functions within the handset. Constantly the market demands smaller radio subsystems, incorporating fewer ICs, with lower power consumption and improved RF performance. Many silicon vendors offer radio chipsets with varying levels of integration. This paper describes the BRIGHT RF ICs which are highly integrated radio transceivers designed for the GSM digital cellular system. The BRIGHT devices are the result ofa 4 year collaboration between The Technology Partnership and Hitachi which has brought together ITP's GSM system expertise and Hitachi's world class linear IC technology. This paper will concentrate on the recent dual-band device (BRIGHT2/HD155121F) which is based on the earlier single band 900MHz and 1800MHz devices. System considerations which led to the BRIGHT architecture are discussed and measured results are presented.
Lithium amplifies agonist-dependent phosphatidylinositol responses in brain and salivary glands (1982)

1. The effect of Li+ on the agonist-dependent metabolism of [3H]inositol has been studied in rat brain, rat parotid and the insect salivary gland. 2. When brain or parotid slices were incubated in the presence of [3H]inositol, Li+ was found to amplify the ability of agonists such as carbachol, phenylephrine, histamine, 5-hydroxytryptamine and Substance P to elevate the amount of label appearing in the inositol phosphates. 3. A different approach was used with the insect salivary gland, which was prelabelled with [3H]inositol. After washing out the label, the subsequent release of [3H]inositol induced by 5-hydroxytryptamine was greatly decreased by Li+. During Li+ treatment there was a large accumulation of [3H]inositol 1-phosphate. 4. This ability of Li+ to greatly amplify the agonist-dependent accumulation of myo-inositol 1-phosphate offers a novel technique for identifying those receptors that function by hydrolysing phosphatidylinositol. 5. The therapeutic action of Li+ may be explained by this inhibition of myo-inositol 1-phosphatase, which lowers the level of myo-inositol and could lead to a decrease in the concentration of phosphatidylinositol, especially in those neurons that are being stimulated excessively. This alteration in phosphatidylinositol metabolism may serve to reset the sensitivity of those multifunctional receptors that generate second messengers such as Ca2+, cyclic GMP and the prostaglandins.
Allele specificity of structural requirement for peptides bound to HLA-DRB1*0405 and -DRB1*0406 complexes: implication for the HLA-associated susceptibility to methimazole-induced insulin autoimmune syndrome. (1994)

Self-peptides bound to HLA-DR4 (DRA-DRB1*0405 complex) were eluted from the purified DR4 complex, fractionated on reverse-phase HPLC, and subjected to NH2-terminal sequencing. Seven independent sequences were obtained, and all putative peptides synthesized bound to DRB1*0405 as well as DRB1*0406 complex, which differ only at DR beta residues 37, 57, 74, and 86. Binding assay using analogue peptides of a DR4 binder GSTVFDNLPNPE revealed that FxxLxN is an important anchor motif necessary for binding (where x is any amino acid), which was common to DRB1*0405 and 0406. Determination of the binding affinity of 60 synthetic AAFAALANAA-based analogue peptides showed that substituting F to W or C; L to F, W, or Y; and N to Q or S on AAFAALANAA changed the affinity substantially between DRB1*0405 and DRB1*0406. It is noteworthy that all patients with methimazole-induced insulin autoimmune syndrome are positive for DRB1*0406 and negative for DRB1*0405. Interestingly, the quantitative structural motif identified in this study predicted that 8TSICSLYQLE17 of human insulin alpha chain may bind specifically to DRB1*0406 using its 10IxxLxQ15 motif. Indeed, DRB1*0406 complex bound 8TSICSLYQLE17 with a high affinity, and in striking contrast, DRB1*0405 complex did not. Furthermore, a short-term T cell line specific to human insulin established from a DRB1*0406-bearing individual did show reactivity with a peptide fragment containing the 10IxxLxQ15 motif. Although this fragment probably exists at a very low level under normal physiological conditions due to the disulfide bond between flanking cysteine residues (6Cys-11Cys), a reducing compound such as methimazole may cleave the disulfide bond in vivo and allow DR alpha-DRB1*0406 complex on antigen-presenting cells to bind much of the linear fragment of insulin alpha chain, which may lead to the activation of self-insulin-specific T-helper cells.
Tuberculosis Surveillance by Analyzing Google Trends (2011)

Tuberculosis (TB) is a major global health concern, causing nearly ten million new cases and over one million deaths every year. The early detection of possible epidemic is the first and important defense line against tuberculosis. However, traditional surveillance approaches, e.g. US Centers for Disease Control and Prevention (CDC), publish the TB morbidity surveillance results on a quarterly basis, with months of reporting lag. Moreover, in some developing countries, where most infections occur, there may not be enough medical resources to build traditional surveillance systems. To improve early detection of tuberculosis outbreaks, we developed a syndromic approach to estimate the actual number of TB cases using Google Search Volume. Specifically, the search volume of nineteen TB-related terms, obtained from January 2004 to April 2009, were examined for surveillance purpose. Contemporary TB surveillance data were extracted from the CDCs reports to build and evaluate the syndromic system. We estimate the actual TB occurrences using a non-stationary dynamic system. Respective models are built to monitor both national-level and state-level TB activities. The surveillance results of the syndromic system can be updated every day, which is twelve weeks ahead of CDCs reports.
Measuring Field Supplied Proppant Conductivity – Issues Discovered in an Operator's Multi-Year Testing Program in the Bakken Shale (2014)

Abstract The Bakken shale oil boom in North Dakota resulted in a two-year period of significant equipment, personnel and materials shortage in 2010 and 2011, following which a period of more rational supply and demand has been seen in the stimulation industry. Throughout the four year period Liberty Resources was designing and pumping multi-stage fracture treatments averaging ~4 Million pounds of ceramic proppant per well. A total of 88 wells were stimulated with 2565 separate fracture stages, placing over 283 Million pounds of proppant. At its height of activity the company managed two 24-hour frac fleets. Key to the well design was the use of a high conductivity ceramic proppant in order to preserve longer term productivity from the wells which have closure stress approaching 10,000 psi. Ceramic proppants were initially categorized into one of three groups based on manufacturer supplied conductivity test data: Highest performing proppants; these materials were given a preferred status for supply. Materials having conductivity that was close to Category A proppants; frac service companies were allowed to substitute these materials when no Category A proppant was available. Ceramic proppant that had test data significantly below Category A proppants; and were never to be utilized even if it meant postponing the fracture stimulation of the well. Samples of each proppant type supplied to the field on each well site were sent for post-treatment testing at an independent testing laboratory to verify if the actual product delivered replicated the manufacturer supplied data that had been used in the design and the initial categorization of the proppant. Standard sieve, crush testing and a 50-hour long-term conductivity test were run on all samples. This paper presents the results of these test data over the past four years. Significant results include: As a standard across the industry it appears that while sieve data are in specification, manufacturer crush and conductivity technical data is only representative of the best materials being delivered to the well site. In a number of cases field proppant quality was significantly below that of the manufacturer's technical literature. After further investigation this resulted in some products being re-categorized lower than their initial Category A or B designations. Proppant pumped with severely reduced conductivity resulted in a measureable decrease in well productivity. As material supply options improved the company used the field testing data to select a preferred proppant with test data that consistently met the highest level of performance.
Pruritus: an overview of current concepts (2011)

Pruritus is an integral part of the patient's symptoms in numerous dermatological and systemic diseases in humans and animals. Comparable to chronic pain, pruritus can have a dramatic impact on the quality of life of the patient. In recent years, pruritus has been defined as an autonomous, pain-independent sensation, and itch-specific neurons, mediators, spinal neurons and cortical areas have been identified. These observations have not only improved our understanding of the neurobiology of itch but will also lead to improved diagnosis and to the development of new and more efficient therapeutic options. This article reviews the role of itch fibres and their response to various mediators of pruritus including histamine, vasoactive intestinal peptide (VIP), calcitonin gene-related peptide (CGRP), and substance P (SP), and opioids. Substances that may be involved in the induction or modulation of itch may be termed pruritogenic mediators and examples discussed include proteases, lipid mediators, neuropeptides, opioids and various cytokines. There is no single, generally accepted clinical classification of chronic pruritus. In the past pruritus has been classified on the basis of the neuroanatomical origin and on the potential underlying disease. Therapeutic options for the management of pruritus are discussed including topical and systemic therapies, assuming that trigger factors have been eliminated where possible. Topical agents may include capsaicin, the calcineurin inhibitors tacrolimus and pimecrolimus, and cannabinoid agonists such as N-palmitoyl ethanolamine. Systemic therapies may include antihistamines, anticonvulsants, opiate receptor antagonist or agonists, antidepressants, ciclosporin, and UV light.
RNA-directed DNA methylation induces transcriptional activation in plants (2009)

A class-C floral homeotic gene of Petunia, pMADS3, is specifically expressed in the stamen and carpels of developing flowers. We had previously reported the ect-pMADS3 phenomenon in which introduction of a part of the pMADS3 genomic sequence, including intron 2, induces ectopic expression of endogenous pMADS3. Unlike transcriptional or posttranscriptional gene silencing triggered by the introduction of homologous sequences, this observation is unique in that the gene expression is up-regulated. In this study, we demonstrated that the ect-pMADS3 phenomenon is due to transcriptional activation based on RNA-directed DNA methylation (RdDM) occurring in a particular CG in a putative cis-element in pMADS3 intron 2. The CG methylation was maintained over generations, along with pMADS3 ectopic expression, even in the absence of RNA triggers. These results demonstrate a previously undescribed transcriptional regulatory mechanism that could lead to the generation of a transcriptionally active epiallele, thereby contributing to plant evolution. Our results also reveal a putative negative cis-element for organ-specific transcriptional regulation of class-C floral homeotic genes, which could be difficult to identify by other approaches.