gebhart/patrepeval huggingface dataset:
TA1, a highly conserved oncofetal complementary DNA from rat hepatoma, encodes an integral membrane protein associated with liver development, carcinogenesis, and cell activation. (1995)

Hepatocellular carcinoma is characterized by changes in gene expression associated with cell growth and differentiation. Cell surface antigenic changes have also been described based on differential antibody reactivity between normal and neoplastic liver. We obtained a novel tumor-associated cDNA designated TA1 on the basis of its differential expression between hepatoma cells and normal liver. Sequence analysis predicted a 723-base pair open reading frame with the deduced amino acid sequence encoding an integral membrane protein containing multiple hydrophobic transmembrane domains. Database searches revealed TA1 as the likely rat homologue of E16, a recently cloned human cDNA associated with lymphocyte activation. Although noncoding sequences diverged significantly, the 95% conservation of the predicted proteins between species strongly suggests an important, although as yet undefined, function in normal cells. TA1 transcripts were detected in normal adult rat tissues including testes, brain, ovary, spleen, mammary gland, and uterus with the highest steady-state expression in placenta. Although no expression was detected in normal liver, all rat hepatomas examined expressed an abundant 3.2-kilobase transcript. TA1 expression was closely associated with progression in this tumor model and suggests this molecule, originally linked to cell activation, also plays a role in the malignant phenotype.
Arginine-rich cationic proteins of human eosinophil granules: comparison of the constituents of eosinophilic and neutrophilic leukocytes. (1977)

Several arginine-rich cationic proteins previously isolated from granules of leukemic myeloid cells have been found to reside primarily in human eosinophil leukocytes. The major component has a molecular weight of 21,000 and it contains approximately 2.6 moles of zinc per mole of protein. Velocity centrifugation of cytoplasm from leukocytes of patients with marked eosinophilia showed that this group of proteins is packaged in the crystalloid-containing large eosinophil granules. Approximately 30% of the protein content of eosinophil granules belonged to this group of cationic proteins. Bactericidal or esterolytic activities of the cationic proteins were not detected, nor did they inhibit guinea pig anaphylatoxin or histamine-induced contraction. The basic protein previously demonstrated in guinea pig eosinophils may be analogous to the group of basic proteins of human eosinophils but great differences are found for molecular weight and amino acid composition.
The neurotrophic factor, n‐hexacosanol, reduces the neuronal damage induced by the neurotoxin, kainic acid (1991)

The long-chain fatty alcohol, n-hexacosanol, has been shown to possess neurotrophic properties in vitro on rat CNS cultures (Borg et al., 1987) and to promote the survival of septal cholinergic neurons after experimental axotomy (Borg et al., 1990). Long-chain alcohols have also been shown to be synthesized and metabolised by rat brain during development (Bishop and Hayra, 1981; Natarajan et al., 1984). The present study was undertaken in order to find out if a nonproteic neurotrophic factor like n-hexacosanol may be able to reduce the neuronal damages induced by the excitatory amino acid, kainic acid. When administered chronically by intraperitineal injection, hexacosanol (1 mg/kg) protected the pyramidal neurons of the hippocampus from the neurotoxic degeneration induced by an intracerebroventricular infusion of kainic acid in rats; the extent of the damage was limited to a small part of the CA3 region. Morphometric analysis showed that 72% of the neurons that would have died following kainic acid injection were spared by hexacosanol. Moreover the increased locomotor activity induced by the neurotoxin was also inhibited by hexacosanol and the behavioral effect was statistically correlated to the extent of neuronal loss. The present study suggests a possible role for nonproteic neurotrophic compounds against neurotoxic damages on central neurons. Moreover the peripheral administration of hexacosanol may lead to a significant breakthrough in the treatment of exicotoxin-related human diseases.
Changes of AI Receptive Fields With Sound Density (2002)

Primates engage in auditory behaviors under a broad range of signal-to-noise conditions. In this study, optimal linear receptive fields were measured in alert primate primary auditory cortex (A1) in response to stimuli that vary in spectrotemporal density. As density increased, A1 excitatory receptive fields systematically changed. Receptive field sensitivity, expressed as the expected change in firing rate after a tone pip onset, decreased by an order of magnitude. Spectral selectivity more than doubled. Inhibitory subfields, which were rarely recorded at low sound densities, emerged at higher sound densities. The ratio of excitatory to inhibitory population strength changed from 14.4:1 to 1.4:1. At low sound densities, the sound associated with the evocation of an action potential from an A1 neuron was broad in spectrum and time. At high sound densities, a spike-evoking sound was more likely to be a spectral or temporal edge and was narrower in time and frequency range. Receptive fields were used to predict responses to a novel high-noise-density stimulus. The predictions were highly correlated with the actual responses to the 2-s complex sound excerpt. The structure of prediction failures revealed that neurons with prominent inhibitory fields had relatively poor linear predictions. Further, the finding that stochastic variance is limiting in prediction even after averaging 150 repetitions means that high-fidelity representations of simple sounds in A1 must be distributed over at least hundreds of neurons. Auditory context alters A1 responses across multiple parameter spaces; this presents a challenge for reconstructing neural codes.
The extra domain A of fibronectin stimulates murine mast cells via Toll-like receptor 4 (2007)

The activation of mast cells by extra domain A of fibronectin (FN-EDA), an endogenous ligand of TLR4, and its contribution to the pathogenesis of rheumatoid arthritis (RA) in vivo were examined. FN-EDA, but no other domain of the fibronectin fragment, III(11) (FN-III(11)) and III(12) (FN-III(12)), stimulated bone marrow-derived murine mast cells (BMMCs) dose-dependently to secret cytokines (TNF-alpha, IL-6, and IL-1beta), similar to the pattern produced by LPS. FN-EDA-induced cytokine production was mediated by TLR4, as cytokine production by FN-EDA was absent in TLR4-deficient (TLR4-/-) BMMCs. We examined the roles of TLR4-mediated mast cell activation by this form of fibronectin fragment in the pathogenesis of RA in vivo. The injection of FN-EDA, but not FN-III(11)and FN-III(12), to joints resulted in joint swelling of mice in vivo. Genetically mast cell-deficient WBB6F(1)-W/W(v) mice exhibited significantly less swelling and cytokine production compared with mast cell-sufficient +/+ mice, suggesting that swelling and inflammatory cytokine production were partially dependent on tissue mast cells. Reduced swelling and cytokine production were recovered by the reconstitution of tissue mast cells by the injection of BMMCs from wild-type mice but not from TLR4-/- mice. Altogether, these results suggest that the TLR4-mediated activation of mast cells by endogenous ligand FN-EDA might contribute to the pathogenesis of RA through proinflammatory cytokine production.
Multiple environments of fluorinated anesthetics in intact tissues observed with 19F NMR spectroscopy (1983)

The incorporation of two fluorine-containing general anesthetic agents, halothane and methoxyflurane, into erythrocytes (from three different species), rabbit muscle and rabbit nerve, was followed with 19F NMR spectroscopy. Two major findings emerged from these studies: (1) multiple environments indicative of domain structure in the membrane can be observed depending on the anesthetic and the tissue type; and (2) the 19F chemical shifts of a given anesthetic were characteristic for the tissue examined. Halothane showed a single resonance in erythrocytes and multiple resonances in muscle and nerve, while methoxyflurane showed multiple resonances in both muscle and erythrocytes. The range of the 19F chemical shifts for the multiple peaks was as great as 6 ppm.
Uniform Price Auctions and Optimal Power Flow (2010)

This technical note describes and illustrates how standard uniform price auctions can be extended to the context of electricity markets cleared by an optimal power flow.
KOC is a novel molecular indicator of malignancy (2003)

The detection of malignant cells in fine-needle aspirates (FNA's) using marker genes is hampered by the fact that these markers are only expressed by certain malignancies or lack sensitivity and/or specificity. Here we report the results of a prospective pilot study examining the expression of KOC (KH-domain containing protein over expressed in cancer), a novel onco-foetal gene, in 76 patients who underwent fine-needle aspiration for further diagnosis of abdominal lesions, aszites, cysts or cerebrospinal fluid. Aspirates were examined by cytology and by a KOC RT-PCR assay. KOC expression was a highly sensitive and specific indicator of malignancy. The KOC assay could be useful to facilitate screening for malignant disease and to improve the diagnostic accuracy of FNAs.
A higher dimensional theory of electrical contact resistance (2009)

The electrical contact resistance is computed for a local constriction of finite length and finite transverse dimension in a conducting current channel. Conformal mapping is used for a rectangular current channel, and an electrostatic code is used for a cylindrical current channel. The connecting bridge, which models a local electrical contact, is assumed to be made of the same conducting material as the main current channel. Very simple analytic scaling laws for the contact resistance are constructed for a wide range of geometrical aspect ratios between the main current channel and its connecting bridge, which may assume a rectangular shape (for Cartesian channel), and a cylindrical or funnel shape (for cylindrical channel). These scaling laws have been confirmed by spot checks with numerical code results. They are generalizations of the classical theory of Holm and Timsit on the contact resistance of the “a-spot,” defined as a small circular area of zero thickness through which current can flow. Potential applications and extensions of the theory are indicated.
A General, Selective Synthesis of Thiol Esters (1975)

Use of diethyl phosphorochloridate and Tl(I) thiolates constitutes a general, selective synthesis of thiol esters. Primary, secondary, and tertiary alkane- and arenethiols of various carboxylic acids, including those containing hydroxy groups have been prepared under mild conditions.
Honey Bee Toxicology (2014)

Insecticides are chemicals used to kill insects, so it is unsurprising that many insecticides have the potential to harm honey bees (Apis mellifera). However, bees are exposed to a great variety of other potentially toxic chemicals, including flavonoids and alkaloids that are produced by plants; mycotoxins produced by fungi; antimicrobials and acaricides that are introduced by beekeepers; and fungicides, herbicides, and other environmental contaminants. Although often regarded as uniquely sensitive to toxic compounds, honey bees are adapted to tolerate and even thrive in the presence of toxic compounds that occur naturally in their environment. The harm caused by exposure to a particular concentration of a toxic compound may depend on the level of simultaneous exposure to other compounds, pathogen levels, nutritional status, and a host of other factors. This review takes a holistic view of bee toxicology by taking into account the spectrum of xenobiotics to which bees are exposed.
Multiple integrins mediate cell attachment to cytotactin/tenascin. (1993)

To identify potential cell surface receptors for chicken cytotactin (CT), we have characterized the ability of recombinant fusion proteins spanning the proximal fibronectin (FN) type III repeats of the molecule to support attachment of glioma and carcinoma cell lines. The third FN type III repeat, which contains the RGD tripeptide, supported cell attachment and cell spreading; however, mutation of RGD to RAD did not result in significant loss of either activity. In addition, the same repeat of mouse CT, which contains a natural mutant, RVD, also supported cell attachment and spreading, although at a lower level; both activities were increased by mutation of the RVD sequence to RGD. Studies utilizing RGD-containing peptides and well-characterized antibodies to integrins indicated that cell attachment to the third FN type III repeat was mediated by at least two different integrin receptors of the alpha v subtype. Additional cellular receptors may also be involved in cell attachment to CT. For example, an antibody to the beta 1 subfamily of integrins partially inhibited binding of cells to intact CT but did not inhibit cell binding to the third FN type III repeat. These findings suggest that the RGD site in CT is able to mediate cell attachment to integrins and thus is not a cryptic adhesion site. They also open the possibility that the functions of CT in processes such as counteradhesion, cell migration, cell proliferation, and cell differentiation may be mediated in part by interaction with multiple integrins.
Lasers in additive manufacturing (2016)

Additive manufacturing is a topic of considerable ongoing interest, with forecasts predicting it to have major impact on industry in the future. This paper focusses on the current status and potential future development of the technology, with particular reference to the role of lasers within it. It begins by making clear the types and roles of lasers in the different categories of additive manufacturing. This is followed by concise reviews of the economic benefits and disadvantages of the technology, current state of the market and use of additive manufacturing in different industries. Details of these fields are referenced rather than expanded in detail. The paper continues, focusing on current indicators to the future of additive manufacturing. Barriers to its development, trends and opportunities in major industrial sectors, and wider opportunities for its development are covered. Evidence indicates that additive manufacturing may not become the dominant manufacturing technology in all industries, but represents an excellent opportunity for lasers to increase their influence in manufacturing as a whole.
Pincher-generated Nogo-A endosomes mediate growth cone collapse and retrograde signaling (2010)

Nogo-A is one of the most potent myelin-associated inhibitors for axonal growth, regeneration, and plasticity in the adult central nervous system. The Nogo-A-specific fragment NogoDelta20 induces growth cone collapse, and inhibits neurite outgrowth and cell spreading by activating RhoA. Here, we show that NogoDelta20 is internalized into neuronal cells by a Pincher- and rac-dependent, but clathrin- and dynamin-independent, mechanism. Pincher-mediated macroendocytosis results in the formation of NogoDelta20-containing signalosomes that direct RhoA activation and growth cone collapse. In compartmentalized chamber cultures, NogoDelta20 is endocytosed into neurites and retrogradely transported to the cell bodies of dorsal root ganglion neurons, triggering RhoA activation en route and decreasing phosphorylated cAMP response element binding levels in cell bodies. Thus, Pincher-dependent macroendocytosis leads to the formation of Nogo-A signaling endosomes, which act both within growth cones and after retrograde transport in the cell body to negatively regulate the neuronal growth program.
The Impact of Genomics on the Study of Natural Variation in Arabidopsis (2003)

The genomic revolution is having a tremendous impact on the study of natural variation. It is making it possible finally to discover the molecular basis of complex traits, a fundamental question in evolutionary biology, and a question of immense practical importance in many other fields. The
High‐efficiency nano‐ and micro‐HPLC – High‐resolution Orbitrap‐MS platform for top‐down proteomics (2010)

In terms of resolution, mass accuracy, and sensitivity, the Orbitrap represents one of the most potent mass analyzers available today. We here elucidate the potential of interfacing Orbitrap-MS to ion-pair RP HPLC for intact protein analysis. Using gradients of ACN and monolithic columns of 1.0 and 0.10 mm id, peak capacities between 120 and 130 were achievable within 20-25 min separation time. Compared with silica-based stationary phases, protein recovery and carryover from monolithic columns were found clearly superior. Intact proteins were detectable in a mass range covering 5.7-150 kDa with LODs in the low femtomol range. Compared with UV detection, MS detection with a scanning speed of 1.6 s per spectrum on average led to a 26% increase in chromatographic peak widths, whereas chromatographic patterns were mostly preserved in extracted ion chromatograms at an acquisition rate of 0.5 s per spectrum. Isotopic resolution of multiply charged ions was demonstrated for proteins up to 42 kDa. A micro-HPLC-Orbitrap-MS setup employing a 1.0 mm id column was utilized to characterize a 150 kDa recombinant monoclonal antibody. The applicability of nano-HPLC-Orbitrap-MS to the analysis of highly complex protein mixtures is demonstrated for the 70% ethanol extractable subproteome of wheat grains.
VISUAL PANEL: From an ordinary paper to a wireless and mobile input device (2000)

This paper presents a vision-based gesture interface system, VISUAL PANEL, which employs an arbitrary quadrangle-shaped panel (e.g., an ordinary paper) and a tip pointer (e.g., fingertip) as an intuitive input device. The system can accurately and reliably track the panel and the tip pointer. The panel tracking continuously determines the projective mapping between the panel at the current position and the display, which in turn maps the tip position to the corresponding position on the display. By detecting the clicking and dragging actions, the system can fulfill many tasks such as controlling a remote large display, and simulating a physical keyboard. Users can naturally use their fingers or other tip pointers to issue commands and type texts. The system, which runs at around 22Hz on PIII 800MHz PC, is scalable and extensible. Further potential applications include multiple-persons interactions. Keywords: Vision-based user interface,
Layered 3D (2011)

We develop tomographic techniques for image synthesis on displays composed of compact volumes of light-attenuating material. Such volumetric attenuators recreate a 4D light field or high-contrast 2D image when illuminated by a uniform backlight. Since arbitrary oblique views may be inconsistent with any single attenuator, iterative tomographic reconstruction minimizes the difference between the emitted and target light fields, subject to physical constraints on attenuation. As multi-layer generalizations of conventional parallax barriers, such displays are shown, both by theory and experiment, to exceed the performance of existing dual-layer architectures. For 3D display, spatial resolution, depth of field, and brightness are increased, compared to parallax barriers. For a plane at a fixed depth, our optimization also allows optimal construction of high dynamic range displays, confirming existing heuristics and providing the first extension to multiple, disjoint layers. We conclude by demonstrating the benefits and limitations of attenuation-based light field displays using an inexpensive fabrication method: separating multiple printed transparencies with acrylic sheets.
Identification of a cell line that expresses a cell surface and a soluble form of the gp330/receptor-associated protein (RAP) Heymann nephritis antigenic complex. (1993)

gp330 is a large glycoprotein located in clathrin-coated pits at the surface of the glomerular and proximal tubule epithelia in the rat kidney. It was originally identified as the target of autoimmune antibodies in Heymann nephritis (HN) and has since been shown to be a member of the low density lipoprotein receptor gene family and to form a stable association with receptor-associated protein (RAP), which together constitute the HN antigen complex (HNAC). Progress in defining the normal functions of gp330 as well as the molecular mechanisms of HN has been hampered by the lack of an available kidney cell line that expresses this protein. We here report the identification of a rat yolk sac carcinoma cell line (L2) that synthesizes HNAC and expresses it in coated pits at the cell surface. gp330 and RAP from L2 cells are immunologically identical to their kidney counterparts, and peptide maps of gp330 yielded identical peptide fragments. Characterization of the cell line revealed that there are 3.3 x 10(4) gp330 molecules per L2 cell and that the cells produce a soluble form of gp330 that is released into the medium. Heparin ligand blot analysis demonstrated that RAP but not gp330 binds heparin. By heparin affinity chromatography, gp330 and RAP copurify, indicating that the glycosaminoglycan binding site within RAP is accessible when the subunit is complexed with gp330. These results indicate that the L2 cell line provides a valid and useful model for studies on the function of HNAC and the pathogenesis of HN.
A method for obtaining digital signatures and public-key cryptosystems (1978)

An encryption method is presented with the novel property that publicly revealing an encryption key does not thereby reveal the corresponding decryption key. This has two important consequences: (1) Couriers or other secure means are not needed to transmit keys, since a message can be enciphered using an encryption key publicly revealed by the intented recipient. Only he can decipher the message, since only he knows the corresponding decryption key. (2) A message can be “signed” using a privately held decryption key. Anyone can verify this signature using the corresponding publicly revealed encryption key. Signatures cannot be forged, and a signer cannot later deny the validity of his signature. This has obvious applications in “electronic mail” and “electronic funds transfer” systems. A message is encrypted by representing it as a number M, raising M to a publicly specified power e, and then taking the remainder when the result is divided by the publicly specified product, n , of two large secret primer numbers p and q. Decryption is similar; only a different, secret, power d is used, where e * d ≡ 1(mod (p - 1) * (q - 1)). The security of the system rests in part on the difficulty of factoring the published divisor, n .
Real-Time Ultrasound for Diagnosis of Symptomatic Venous Thrombosis and for Screening of Patients at Risk: Correlation with Ascending Conventional Venography (1989)

This is a prospective study of 108 patients in two distinct groups undergoing real-time ultrasonography (US) and ascending conventional venography within the same day. The two patient groups consisted of the following: Those patients evaluated because of suspicion of deep venous thrombosis of lower limbs (69 patients) and those at high risk for venous thrombosis (19 patients with a recent hip fracture, 20 with a suspected pulmonary embolism). In the diagnosis group 48 patients had venographic evidence of thrombosis. The predictive value of abnormal findings from real-time US was 97%, and that of a negative study was 75%. Thus, real-time US may have a role as a diagnostic procedure, to be followed by x-ray venography in patients with negative US results. By contrast, real-time US is far less sensitive as a screening test in patients without clinical evidence of thrombosis. Only 3 of 9 patients with thrombosis were detected, with a 50% sensitivity for proximal vein thrombosis. Therefore, the use of real-time US for screening high-risk patients must be limited to very high risk patients in whom other tests are ineffective (as in hip surgery).