gebhart/patrepeval huggingface dataset:
Importance of P-Cadherin, β-Catenin, and Wnt5a/Frizzled for Progression of Melanocytic Tumors and Prognosis in Cutaneous Melanoma (2005)

Alterations in the expression and subcellular localization of cell adhesion markers are important in the development and progression of melanocytic tumors, and strong cytoplasmic P-cadherin expression and loss of nuclear beta-catenin staining were associated with aggressive melanoma behavior and reduced patient survival.
High concentration of beta-defensin-2 in oral squamous cell carcinoma. (2002)

We have previously reported the presence of human beta-defensin-2 (HBD-2), a peptide with antimicrobial and cytotoxic properties, in oral squamous cell carcinomas. The aim of the present study was to measure the concentration of HBD-2 in abnormal tissues such as oral squamous cell carcinomas. HBD-2 was extracted from tissue samples in the presence of retinoic acid and subjected to reversed-phase HPLC. The fraction representing peak 17 (P17) was obtained by elution using a linear gradient of acetonitrile. Amino acid sequencing and homology studies were subsequently performed, and the molecular weight of P17 was calculated to be 432702 daltons. This molecular weight was consistent with HBD-2. The concentration of HBD-2 in the oral squamous cell carcinoma samples was 3.85+/-1.87 microg/mg which was much higher than in normal oral epithelium (0.04+/-0.02 microg/mg).
Negative photoresists for optical lithography (1997)

Negative photoresists are materials that become insoluble in developing solutions when exposed to optical radiation. They were the first systems used to pattern semiconductor devices, and still comprise the largest segment of the photoresist industry because they are widely used to define the circuitry in printed wiring boards. However, the current use of negative resists in the semiconductor industry has been limited by past difficulties in achieving high-resolution patterns. Recent advances in the chemistry of negative-resist systems, however, have provided materials with wide processing latitude and high resolution that are used to manufacture IBM's advanced CMOS devices and to achieve high-aspect-ratio patterns for micromachining applications. This paper provides an overview of the history and chemistry of negative-resist systems and their development in IBM.
Cognitive Based Neural Prosthetics (2006)

Intense activity in neural prosthetic research has recently demonstrated the possibility of robotic interfaces that respond directly to the nervous system. The question remains of how the flow of information between the patient and the prosthetic device should be designed to provide a safe, effective system that maximizes the patient’s access to the outside world. Much recent work by other investigators has focused on using decoded neural signals as low-level commands to directly control the trajectory of screen cursors or robotic end-effectors. Here we review results that show that high-level, or cognitive, signals can be decoded from planned arm movements. These results, coupled with fundamental limitations in signal recording technology, motivate an approach in which cognitive neural signals play a larger role in the neural interface. This proposed paradigm predicates that neural signals should be used to instruct external devices, rather than control their detailed movement. This approach will reduce the effort required of the patient and will take advantage of established and on-going robotics research in intelligent systems and human-robot interfaces.
A GIS procedure for automatically calculating the USLE LS factor on topographically complex landscape units (1996)

ABSTRACT: A computer algorithm to calculate the USLE and RUSLE LS-factors over a two-dimensional landscape is presented. When compared to a manual method, both methods yield broadly similar results in terms of relative erosion risk mapping. However, there appear to be important differences in absolute values. Although both methods yield similar slope values, the use of the manual method leads to an underestimation of the erosion risk because the effect of flow convergence is not accounted for. The computer procedure has the obvious advantage that it can easily be linked to GIS software. If data on land use and soils are available, specific K, C and P-values can be assigned to each land unit so that predicted soil losses can then be calculated using a simple overlay procedure. The algorithm leaves the user the choice to consider land units as being hydrologically isolated or continuous. A comparison with soil data showed a reasonably good agreement between the predicted erosion risk and the intensity of soil truncation observed in the test area.
Religion and Society in Arab Sind. By Derryl N. Maclean. Monographs and Theoretical Studies in Sociology and Anthropology in Honour of Nels Anderson, No. 25. The Netherlands: E. J. Brill, 1989. x 191 pp. (1993)

Religion and Society in Arab Sind. By Derryl N. Maclean. Monographs and Theoretical Studies in Sociology and Anthropology in Honour of Nels Anderson, No. 25. The Netherlands: E. J. Brill, 1989. x 191 pp. - Volume 52 Issue 1
[Influence of endothelial cells on the proliferation of scar-derived fibroblast in hypertropic scar tissue]. (2002)

The endothelial cells may secrete some active products, which may enhance the proliferation of the scar-derived fibroblasts and stimulate the fibroblasts into the S-stage of cell generation cycle.
Apolipoprotein A-I Promotes the Formation of Phosphatidylcholine Core Aldehydes That Are Hydrolyzed by Paraoxonase (PON-1) during High Density Lipoprotein Oxidation with a Peroxynitrite Donor (2001)

High density lipoprotein (HDL) is rich in polyunsaturated phospholipids that are sensitive to oxidation. However, the effect of apolipoprotein A-I and paraoxonase-1 (PON-1) on phosphatidylcholine oxidation products has not been identified. We subjected native HDL, trypsinized HDL, and HDL lipid suspensions to oxidation by the peroxynitrite donor, 3-morpholinosydnonimine. HDL had a basal level of phosphatidylcholine mono- and di-hydroperoxides that increased to a greater extent in HDL, compared with either trypsinized HDL or HDL lipid alone. Phosphatidylcholine core aldehydes, which were present in small amounts, increased 10-fold during oxidation of native HDL, compared with trypsinized HDL (p = 0.004), and 4-fold compared with HDL lipid suspensions (p = 0.0021). In addition, the content of lysophosphatidylcholine increased 300% during oxidation of native HDL, but only 80 and 25%, respectively, during oxidation of trypsinized HDL and HDL lipid suspensions. Phosphatidylcholine isoprostanes accumulated in comparable amounts during the oxidation of all three preparations. Incubation of apolipoprotein A-I with 1-palmitoyl-2-linoleoyl glycerophosphocholine proteoliposomes in the presence of 3-morpholinosydnonimine or apoAI with phosphatidylcholine hydroperoxides resulted in a significant increase in phosphatidylcholine core aldehydes with no formation of lysophosphatidylcholine. We propose that apolipoprotein A-I catalyzes a one-electron oxidation of alkoxyl radicals. Purified PON-1 hydrolyzed phosphatidylcholine core aldehydes to lysophosphatidylcholine. We conclude that, upon HDL oxidation with peroxynitrite, apolipoprotein AI increases the formation of phosphatidylcholine core aldehydes that are subsequently hydrolyzed by PON1.
Resistance to Antiviral Drugs: The End of Innocence (1989)

Until recently, the problem of resistance to antiviral drugs has been more potential than real. Although individual reports of resistant viruses have appeared, such isolates have been rare and usually of low virulence. The articles by Erlich et al.1 and Erice et al.2 in this issue of the Journal, as well as reports published elsewhere,3 , 4 indicate that the situation has changed dramatically. Progressive disease due to acyclovir-resistant herpes simplex virus and to ganciclovir-resistant cytomegalovirus in patients with the acquired immunodeficiency syndrome (AIDS) or who are otherwise immunocompromised is now a reality with important ramifications.Resistance of herpes simplex virus . . .
Pandemic H1N1 Influenza A Viruses Are Resistant to the Antiviral Activities of Innate Immune Proteins of the Collectin and Pentraxin Superfamilies (2010)

Acquired immune responses elicited to recent strains of seasonal H1N1 influenza viruses provide limited protection against emerging A(H1N1) pandemic viruses. Accordingly, pre-existing or rapidly induced innate immune defenses are of critical importance in limiting early infection. Respiratory secretions contain proteins of the innate immune system, including members of the collectin and pentraxin superfamilies. These mediate potent antiviral activity and act as an initial barrier to influenza infection. In this study, we have examined the sensitivity of H1N1 viruses, including pandemic virus strains, for their sensitivity to collectins (surfactant protein [SP]-D and mannose-binding lectin [MBL]) and to the pentraxin PTX3. Human SP-D and MBL inhibited virus-induced hemagglutinating activity, blocked the enzymatic activity of the viral neuraminidase, and neutralized the ability of H1N1 viruses to infect human respiratory epithelial cells in a manner that correlated with the degree of glycosylation in the globular head of the hemagglutinin. Recent seasonal H1N1 viruses expressed three to four N-glycosylation sequons on the head of hemagglutinin and were very sensitive to inhibition by SP-D or MBL, whereas A(H1N1) pandemic viruses expressed a single N-glycosylation sequon and were resistant to either collectin. Of interest, both seasonal and pandemic H1N1 viruses were resistant to PTX3. Thus, unlike recent seasonal H1N1 strains of influenza virus, A(H1N1) pandemic viruses are resistant to the antiviral activities of innate immune proteins of the collectin superfamily.
Aging-Associated Vascular Phenotype in Mutant Mice With Low Levels of BubR1 (2007)

These findings demonstrate that BubR1 insufficiency in mice results in phenotypic changes reminiscent of vascular aging in humans and suggest a role for BubR1 in suppressing the vascular aging process.
Kissing-Loop Model of HIV-1 Genome Dimerization:  HIV-1 RNAs Can Assume Alternative Dimeric Forms, and All Sequences Upstream or Downstream of Hairpin 248−271 Are Dispensable for Dimer Formation (1996)

The genome of all retroviruses consists of two identical RNAs noncovalently linked near their 5' end. Dimerization of genomic RNA is thought to modulate several steps in the retroviral life cycle, such as recombination, translation, and encapsidation. The kissing-loop model of HIV-1 genome dimerization [Laughrea, M., & Jetté, L. (1994) Biochemistry 33, 13464-13474; Skripkin et al. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 4945-4949] posits that the 248-270 region of the HIV-1 genome, by forming a hairpin and initiating dimerization through a loop-loop interaction, is the full or at least the core dimerization domain of HIV-1 RNA. Here, we show by nested deletion analysis that the 3' boundary of the HIV-1 dimerization domain is immediately downstream of hairpin 248-270 and that the isolated region 248-271 dimerizes at least as readily as longer RNAs. Among various HIV-1Lai RNA transcripts containing hairpin 248-270, all form two types of dimer, as is implicit in the kissing-loop model. The high-stability dimer resists semidenaturing conditions and the low-stability dimer cannot, which is consistent with the model. At physiological temperatures, low-stability dimers are usually formed, as if dimerization without nucleocapsid proteins corresponded to loop-loop interaction without switching from intra- to interstrand hydrogen bonding. Our results show that the 3' DLS (a sequence immediately 3' from the 5' splice junction and originally thought to be the dimerization domain of the HIV-1 genome) and adjacent nucleotides are not necessary for efficient dimerization of HIV-1Lai RNA at low and high ionic strength. Upstream of hairpin 248-270 exists another "DLS-like" sequence that we name 5' DLS: like the isolated 3' DLS, the isolated 5' DLS forms an apparently nonphysiological structure that can become substantially dimeric at high ionic strength.
A Novel Class of Retinoid Antagonists and Their Mechanism of Action (1996)

Retinoids regulate a broad range of biological processes through two subfamilies of nuclear retinoid receptors, the retinoic acid receptors (RARs) and the retinoid X receptors (RXRs). Recently, we reported a novel type of retinoic acid antagonist (SR11335) and showed that this compound can inhibit retinoic acid (RA)-induced activation of a human immunodeficiency virus type 1 (HIV-1) promoter construct that contains a special RA response element (RARE). We have now further characterized the antagonism mediated by SR11335 and of newly synthesized structurally related compounds. Two compounds, SR11330 and SR11334, which are poor transactivators, also showed antagonist activities, inhibiting all-trans-RA (tRA) and 9-cis-RA. The retinoids inhibited transcriptional activation of RAR/RXR heterodimers effectively, while inhibition of RXR homodimers was less efficient. Inhibition was observed on several RAREs, including the TREpal, betaRARE, apoAI-RARE, and CRBPI-RARE. In addition, the antagonists inhibited tRA-induced differentiation of HL-60 cells. The antagonist did not interfere with DNA binding of the receptors. In limited proteolytic digestion assays, SR11335 induced resistance of the receptors to proteolysis, but the pattern of the degradation was not altered from that induced by tRA, suggesting that these antagonists induce their biological effects by competing with agonists for binding to RARs, thereby preventing the induction of conformational changes of the receptors necessary for transcriptional activation.
Internet packet filter management and rectangle geometry (2001)

We consider rule sets for internet packet routing and filtering, where each rule consists of a range of source addresses, a range of destination addresses, a priority, and an action. A given packet should be handled by the action from the maximum priority rule that matches its source and destination. We describe new data structures for quickly finding the rule matching an incoming packet, in near-linear space, and a new algorithm for determining whether a rule set contains any conflicts, in time O(n3/2).
Speckle Reduction in Projection Systems (2009)

A speckle pattern is a quasi-random interference pattern which typically emerges when lasers are used as illumination sources in projection applications and which severely degrades the image quality. Since in most projection applications high speckle disturbance is not tolerable, speckle reduction is a major issue. This work gives an introduction into the theoretical description of speckle and investigates different practical methods for speckle reduction in laser projection systems.
Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coli. (1993)

The rpoS gene of Escherichia coli encodes a putative RNA polymerase sigma factor that is considered to be the central regulator of gene expression in stationary phase. The gene product (sigma 38) was overproduced using the cloned rpoS gene and purified to homogeneity. Reconstituted RNA polymerase holoenzyme (E sigma 38) was found to recognize in vitro a number of typical sigma 70-type promoters, including the lacUV5 and trp promoters. Some, however, were recognized exclusively or preferentially by E sigma 70, whereas at least one, fic, was favored by E sigma 38. Thus E. coli promoters can be classified into three groups: the first group is recognized by E sigma 70 and E sigma 38, but the second and third groups are recognized substantially by either E sigma 70 or E sigma 38 alone. In contrast to other minor sigma factors, sigma 38 shares a set of amino acid sequences common among the principal sigma factors of eubacteria and is therefore a member of the RpoD-related protein family. The intracellular level of sigma 38 was demonstrated to increase in vivo upon entry into stationary phase. These results together indicate that sigma 38 is a second principal sigma factor in stationary-phase E. coli.
Desorption from interstellar grains (1985)

Different desorption mechanisms from interstellar grains are considered to resolve the conflict between the observed presence of gaseous species in molecular clouds and their expected depletion onto grains. The physics of desorption is discussed with particular reference to the process of grain heating and the specific heat of the dust material. Impulsive heating by X-rays and cosmic rays is addressed. Spot heating of the grains by cosmic rays and how this can lead to desorption of mantles from very large grains is considered. It is concluded that CO depletion on grains will be small in regions with A(V) less than five from the cloud surface and n(H) less than 10,000, in agreement with observations and in contrast to expectations from pure thermal equilibrium. Even in very dense and obscured regions and in the absence of internal ultraviolet sources, the classical evaporation of CO or N2 and O2-rich mantles by cosmic rays is important.
<title>Update on focal-plane image processing research</title> (1991)

An update on research activities at Columbia University in the area of focal-plane image processing is presented. Two thrust areas have been pursued: image reorganization for image compression and image half-toning. The image reorganization processor is an integration of a 256 X 256 frame-transfer CCD imager with CCD-based circuitry for pixel data reorganization to enable difference encoding for hierarchical image compression. The reorganization circuitry occupies 2 of the total chip area and is performed using three parallel-serial-parallel (SP3) registers, a pixel resequencing block, and a sampling block for differential output. The chip has achieved a CTE of 0.99994 in this new SP3 architecture, at an output rate of 83 X 103 pixels/sec. (0.9996 at 2 X 106 pixels/sec) and an overall output amplifier sensitivity of 3.2 (mu) V/electron. The half-toning chip design has been described previously, and consists of a 256 X 256 frame transfer imager, a pipeline register, and comparator circuit. Functional testing of these elements is reported at this time.
ChemInform Abstract: Experimental and Theoretical Host—Guest Photochemistry; Control of Reactivity with Host Variation and Theoretical Treatment with a Stress Shaped Reaction Cavity; Mechanistic and Exploratory Organic Photochemistry. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Diffusion dependent cell behavior in microenvironments (2005)

Understanding the interaction between soluble factors and cells in the cellular microenvironment is critical to understanding a wide range of diseases. Microchannel culture systems provide a tool for separating diffusion and convection based transport making possible controlled studies of the effects of soluble factors in the cellular microenvironment. In this paper we compare the proliferation kinetics of cells in traditional culture flasks to those in microfluidic channels, and explore the relationship between microchannel geometry and cell proliferation. PDMS (polydimethylsiloxane) microfluidic channels were fabricated using micromolding methods. Fall armyworm ovarian cells (Sf9) were homogeneously seeded in a series of different sized microchannels and cultured under a no flow condition. The proliferation rates of Sf9 cells in all of the microchannels were slower than in the flask culture over the first 24 h of culture. The proliferation rates in the microchannels then continuously decreased reaching 5% of that in the flasks over the next 48 h and maintained this level for 5 days. This growth inhibition was reversible and influenced only by the cell seeding density and the channel height but not the channel length or width. One possible explanation for the observed dimension-dependent cell proliferation is the accumulation of different functional molecules in the diffusion dominant microchannel environment. This study provides insights into the potential effects of the diffusion of soluble factors and related effects on cell behavior in microenvironments relevant to the emerging use of microchannel culture systems.
The signal for Golgi retention of bovine beta 1,4-galactosyltransferase is in the transmembrane domain. (1992)

The expression and localization of bovine beta 1,4-galactosyltransferase (Gal T) has been studied in mammalian cells transfected with Gal T cDNA constructs, and the role of the amino-terminal domains of Gal T in Golgi localization examined. Here we demonstrate that the transmembrane (signal/anchor) domain of bovine Gal T contains a positive Golgi retention signal. Bovine Gal T was characterized in transfected cells with anti-bovine Gal T antibodies, affinity-purified from a rabbit antiserum using a bacterial recombinant fusion protein. These affinity-purified antibodies recognized native bovine Gal T and showed minimum cross-reactivity with Gal T from non-bovine sources. Bovine Gal T cDNA was expressed, as active enzyme, transiently in COS-1 cells and stably in murine L cells, and the product was shown to be localized to the Golgi complex by immunofluorescence using the polypeptide-specific antibodies. A low level of surface bovine Gal T was also detected in the transfected L cells by flow cytometry. The removal of 18 of the 24 amino acids from the cytoplasmic domain of bovine Gal T did not alter the Golgi localization of the product transiently expressed in COS-1 cells or stably expressed in L cells. Both the full-length bovine Gal T and the cytoplasmic domain deletion mutant were N-glycosylated in the transfected L cells, indicating both proteins have the correct N(in)/C(out) membrane orientation. Deletion of both the cytoplasmic and signal/anchor domains of bovine Gal T and incorporation of a cleavable signal sequence resulted in a truncated soluble bovine Gal T that was rapidly secreted (within 1 h) from transfected COS-1 cells. Replacement of the signal/anchor domain of bovine Gal T with the signal/anchor domain of the human transferrin receptor resulted in the transport of the hybrid molecule to the cell surface of transfected COS-1 cells. Furthermore, a hybrid construct containing the signal/anchor domain of Gal T with ovalbumin was efficiently retained in the Golgi complex, whereas ovalbumin anchored to the membrane by the transferrin receptor signal/anchor was expressed at the cell surface of transfected COS-1 cells. Overall, these studies show that the hydrophobic, signal/anchor domain of Gal T is both necessary and sufficient for Golgi localization.
Liver extracellular matrix in health and disease (2003)

Liver fibrosis is the hallmark of every chronic liver disease. It is also the major factor of morbidity and mortality due to the development of cirrhosis and its complications including hepatocellular carcinoma. But even at the beginning of the process of liver fibrosis and due to the strategic position of the extracellular matrix at the interface between blood flow and epithelial compartment, any quantitative or qualitative modification of extracellular matrix will rapidly affect structure and function of the liver. The development of several animal models of liver fibrosis as well as isolation and cultivation of hepatic stellate cells, the major fibrogenic cell type in the liver, led to the gathering of recent knowledge on the mechanism of liver fibrosis. Activation of hepatic stellate cells is a key event in this process and many details on this finely tuned mechanism are now available. In addition to these experimental data, experience from chronic hepatitis C now allows the development of new concepts and perspectives such as liver fibrosis regression and antifibrotic therapies.