gebhart/patrepeval huggingface dataset:
Cell Shape and Patterning Considerations for Magnetic Random Access Memory (MRAM) Fabrication (2018)

Industrial and academic development laboratories worldwide are working to perfect the circuit designs, fabrication methods and integration schemes required for successful commercial production of Magnetic Random Access Memory (MRAM) devices, a new kind of nonvolatile memory technology that some forecast to be a “universal” memory replacement for DRAM,SRAM and flash.Among the more important issues for MRAM cell design and fabrication are the basic configuration of the magnetic memory element (pseudospin-valve or magnetic tunneling junction, for example), the material set used to fabricate the magnetic memory element, the shape of the magnetic memory element and the patterning techniques used to fabricate the cell. Two important attributes of the MRAM cell may be unfamiliar to those with experience in other IC fabrication processes. These are the special considerations that must be taken when designing the physical shape of the magnetic memory storage element and the specific fabrication techniques that need to be applied to pattern the many layers of alloys (NiFe, for example) and metals (ruthenium, cobalt) found in the MRAM stack. Ion milling has been the historically- important method of record for fabricating low-density MRAM products for applications with limited production volumes. Now that large IDMs like IBM and Infineon, Motorola, Philips, STMicroelectronics and NEC are approaching MRAM processing in earnest, the perceived manufacturing limitations of ion milling have motivated development teams to consider other methods, including wet etch, plasma etch and damascene for patterning MRAM stacks. We review here the theory of MRAM operation, discuss the interaction between the physical shape of the MRAM cell and its ability to store binary information, present the various options for patterning MRAM stacks as championed by the major IDMs with public MRAM programs, and summarize some of our own work on plasma etching MRAM devices.
Enhancement of Migration by Protein Kinase Cα and Inhibition of Proliferation and Cell Cycle Progression by Protein Kinase Cδ in Capillary Endothelial Cells (1997)

Activation of protein kinase C (PKC) induces angiogenesis, migration, and proliferation of endothelial cells (EC), but can also prevent growth factor-induced EC proliferation. To determine whether these disparate effects are mediated by substrates of individual PKC isoenzymes, PKCalpha and PKCdelta were overexpressed in rat microvascular EC. Basal and stimulated migration were enhanced in PKCalpha EC compared with either PKCdelta or control EC. Serum-induced growth of PKCdelta EC was decreased, while that of PKCalpha cells was similar to control EC. Phorbol ester markedly inhibited PKCdelta EC growth but enhanced growth of PKCalpha and control EC. To determine possible causes for this altered proliferation, the effect of PKCdelta on adhesion, mitogen-activated protein kinase activity, and cell cycle progression was measured. Adherence of PKCdelta EC to vitronectin was significantly enhanced. Serum-induced extracellular signal-regulated kinase-2 activity was increased equally in both PKCalpha and PKCdelta EC above that of control, while extracellular signal-regulated kinase-1 activity was similar in all EC. Cell cycle analysis suggested that PKCdelta EC entered S phase inappropriately and were delayed in passage through S phase. Thus, PKCalpha may mediate some proangiogenic effects of PKC activation; conversely, PKCdelta may direct antiangiogenic aspects of overall PKC activation, including slowing of the cell cycle progression.
The Complicity of Northern States in Slavery (2010)

When discussing the origins of the American Civil War, there is often still a short-hand at work, namely: The North = Good Guys; The South = Bad Guys. The truth is far more complicated.
A High-Rate Buried-Data Channel for Audio CD (1995)

Subtractive buried data is a new proposal for conveying a high-data data channel (with up to 350 kbit/s or more) compatibly within the data stream of an audio CD without significant impairment of existing CD performance. This proposal uses pseudorandomized data as noise-shaped subtractive dither for the conventional audio. The new data channel may be used for high-quality data-reduced related audio channels, or even for data-compressed video or computer data, while retaining compatibility with existing audio CD players
An element within the 5′ untranslated region of human Hsp70 mRNA which acts as a general enhancer of mRNA translation (2001)

The untranslated regions of mRNAs encoding heat-shock proteins have been reported to contain elements important to the post-transcriptional regulation of these key components of the stress response. In this report we describe an element from the 5'UTR of human Hsp70 mRNA that increases the efficiency of mRNA translation. Cloning of this region upstream of the coding sequence of two different reporter genes (firefly luciferase and chloramphenicol acetyltransferase) increases expression of the reporter under normal cell culture conditions by up to an order of magnitude. This effect was observed in three different promoter contexts (HSP, SV40 and CMV) and in six cell lines. The increase in protein production is not accompanied by any alteration in mRNA levels, suggesting that the element facilitates translation. 5' or 3' truncated sequences are ineffective in enhancing reporter expression, suggesting that the activity arises from the secondary structure of the element, rather than from some smaller defined motif. Computer analysis of this region revealed that it is able to form stable secondary structures (DeltaG approximately -292.6 kJ x mol(-1)). The Hsp70 element does not seem to act as an internal ribosome entry site. Incorporation of the sequence into plasmids used for DNA vaccination produces increased antibody responses, confirming that the sequence is functional in primary cells. These data suggest that the 5'UTR of human Hsp70 mRNA plays an important role in determining Hsp70 expression levels, and that it contains an element of general utility in enhancing recombinant protein expression systems.
Prevalence and Distribution of Carcinoma in Patients with Solitary and Multiple Thyroid Nodules on Sonography (2006)

In a patient with one or more thyroid nodules larger than 10 mm in diameter, the likelihood of thyroid cancer per patient is independent of the number of nodules, whereas the likelihood per nodule decreases as the number of nodules increases. For exclusion of cancer in a thyroid with multiple nodules larger than 10 mm, up to four nodules should be considered for FNA. Sonographic characteristics can be used to prioritize nodules for FNA based on their individual risk of cancer.
Neuroendocrine regulation of cytokine production during experimental influenza viral infection: effects of restraint stress-induced elevation in endogenous corticosterone (1996)

A murine model of influenza viral infection was used to examine the neuroendocrine regulation of cytokine production. Restraint stress (RST) was used to activate the hypothalamic-pituitary-adrenal axis and elevate corticosterone (CORT) levels in influenza A/Puerto Rico/8/34 (PR8) virus-infected C57BL/6 mice. The type II glucocorticoid receptor antagonist RU486 was used to specifically examine the modulation of PR8 virus-specific cytokine responses by CORT. RST suppressed the PR8 virus- specific production of Th1-type (IL-2 and IFN-gamma) and Th2-type IL-10) cytokines by cells from the regional lymph nodes and spleens. In addition, IL-6 production by splenocytes was inhibited by RST; however, IL-6 production by cells from the regional lymph nodes was enhanced. Treatment of mice with RU486 prevented the effects of RST, suggesting that the RST-induced alterations in cytokine responses were mediated by CORT. Furthermore, CORT was shown to inhibit the PR8 virus-specific production of both Thl-type and Th2-type cytokines in vitro at doses corresponding to the physiologic range of free plasma CORT following hypothalamic-pituitary-adrenal axis activation.
Hematopoietic stem cells do not repair the infarcted mouse heart (2004)

Mobilization or i.v. injection of BM cells do not have a measurable effect on cardiac regeneration.
Real-time hidden surface removal in a flight simulator (2002)

The authors investigate four different concepts which are candidates to resolve the hidden surface removal problem without the use of priorities. All four are based on determining a linear depth order consistent with the partial order of primitives in a span. A span is a small subimage of the image being generated. The first approach examines parallel sorting of all the depth values of all primitives in a span. The second approach, for each pixel in a span, builds a list of all the primitives in that span, totally ordered by depth. These lists represent the partial order of the primitives, and are later enumerated to give a total order. The third approach performs up to k pairwise comparisons in parallel between primitives to determine if a depth relationship exists. If one exists, the pair is stored in a partial order graph which is later enumerated to create a total order. The fourth approach involves the use of a pipeline of length k, which, at any given time, contains up to k primitives which are closest. If there are more than k primitives in a span, more than one iteration is needed. The fourth approach appears to be the most promising, even though there are situations in which it generates an incorrect ordering.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mechanisms of regulation of PFKFB expression in pancreatic and gastric cancer cells (2014)

Enzymes 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 and -4 (PFKFB-3 and PFKFB-4) play a significant role in the regulation of glycolysis in cancer cells as well as its proliferation and survival. The expression of these mRNAs is increased in malignant tumors and strongly induced in different cancer cell lines by hypoxia inducible factor (HIF) through active HIF binding sites in promoter region of PFKFB-4 and PFKFB-3 genes. Moreover, the expression and hypoxia responsibility of PFKFB-4 and PFKFB-3 was also shown for pancreatic (Panc1, PSN-1, and MIA PaCa-2) as well as gastric (MKN45 and NUGC3) cancer cells. At the same time, their basal expression level and hypoxia responsiveness vary in the different cells studied: the highest level of PFKFB-4 protein expression was found in NUGC3 gastric cancer cell line and lowest in Panc1 cells, with a stronger response to hypoxia in the pancreatic cancer cell line. Overexpression of different PFKFB in pancreatic and gastric cancer cells under hypoxic condition is correlated with enhanced expression of vascular endothelial growth factor (VEGF) and Glut1 mRNA as well as with increased level of HIF-1α protein. Increased expression of different PFKFB genes was also demonstrated in gastric, lung, breast, and colon cancers as compared to corresponding non-malignant tissue counterparts from the same patients, being more robust in the breast and lung tumors. Moreover, induction of PFKFB-4 mRNA expression in the breast and lung cancers is stronger than PFKFB-3 mRNA. The levels of both PFKFB-4 and PFKFB-3 proteins in non-malignant gastric and colon tissues were more pronounced than in the non-malignant breast and lung tissues. It is interesting to note that Panc1 and PSN-1 cells transfected with dominant/negative PFKFB-3 (dnPFKFB-3) showed a lower level of endogenous PFKFB-3, PFKFB-4, and VEGF mRNA expressions as well as a decreased proliferation rate of these cells. Moreover, a similar effect had dnPFKFB-4. In conclusion, there is strong evidence that PFKFB-4 and PFKFB-3 isoenzymes are induced under hypoxia in pancreatic and other cancer cell lines, are overexpressed in gastric, colon, lung, and breast malignant tumors and undergo changes in their metabolism that contribute to the proliferation and survival of cancer cells. Thus, targeting these PFKFB may therefore present new therapeutic opportunities.
The FSHD Atrophic Myotube Phenotype Is Caused by DUX4 Expression (2011)

These results constitute a proof of concept for the development of therapeutic approaches for FSHD targeting DUX4 expression.
Translational efficiency of the Escherichia coli adenylate cyclase gene: mutating the UUG initiation codon to GUG or AUG results in increased gene expression. (1985)

Roy et al. [Roy, A., Haziza, C. & Danchin, A. (1983) EMBO J. 2, 791-797] established that translation of Escherichia coli adenylate cyclase initiates at a UUG codon, and they suggested this might decrease the efficiency of translation. We investigated the effect of varying the initiation codon on the expression of the adenylate cyclase (cya) gene. Using oligonucleotide-directed mutagenesis, we changed the UUG initiation codon to GUG and the more common initiator AUG and assayed for cya gene expression in a number of ways. First, the GUG initiation codon, in place of UUG, doubled cya expression when cya was expressed from the dual cya P1/P2 promoters. The corresponding AUG codon construct was nonviable. Second, when the cya gene was placed under the transcriptional control of the thermoinducible phage lambda PL promoter, the relative amounts of cya gene product were 1:2:6 for the UUG, GUG, and AUG initiation codons, respectively. Finally, the cya P2 promoter, Shine-Dalgarno sequence, and the DNA corresponding to the first 86 codons of cya were fused to DNA encoding the E. coli galactokinase gene beginning at the second codon. The relative amounts of the fusion polypeptides, which had galactokinase activity, were 1:2:3 for the UUG, GUG, and AUG initiation codons, respectively. These results demonstrate that the cya UUG initiation codon limits cya expression at the level of translation.
Quantitation of phenylalanine and its trans‐cinnamic, benzoic and hippuric acid metabolites in biological fluids in a single GC‐MS analysis (2007)

We describe a sensitive, simple and convenient stable isotope dilution assay developed to study endogenous metabolism of administered stable isotope-labeled phenylalanine (Phe) in phenylketonuric (PKU) mice treated experimentally with phenylalanine ammonia lyase (PAL). Mouse urine and plasma containing endogenous and administered labeled Phe together with internal standard Phe bearing a different pattern of labeling are converted by in situ diazotization to 2-chloro-3-phenylpropionic acid (CPP). A single solvent extraction is then used to isolate the isotopomers of CPP along with the trans-cinnamic acid (TCA) produced from Phe by PAL, as well as the TCA metabolites benzoic and hippuric acids. This procedure eliminates the need for a separate ion-exchange isolation step for Phe on a second sample aliquot and separate GC-MS analysis. Extracted CPP and the Phe metabolites are then measured by conversion to the pentafluorobenzyl esters and a single analysis by electron capture negative ion GC-MS. The estimated lower limit of quantitation is 0.1 microM.
<title>Depth-image-based rendering (DIBR), compression, and transmission for a new approach on 3D-TV</title> (2004)

This paper presents details of a system that allows for an evolutionary introduction of depth perception into the existing 2D digital TV framework. The work is part of the European Information Society Technologies (IST) project "Advanced Three-Dimensional Television System Technologies" (ATTEST), an activity, where industries, research centers and universities have joined forces to design a backwards-compatible, flexible and modular broadcast 3D-TV system. At the very heart of the described new concept is the generation and distribution of a novel data representation format, which consists of monoscopic color video and associated per-pixel depth information. From these data, one or more "virtual" views of a real-world scene can be synthesized in real-time at the receiver side (i.e. a 3D-TV set-top box) by means of so-called depth-image-based rendering (DIBR) techniques. This publication will provide: (1) a detailed description of the fundamentals of this new approach on 3D-TV; (2) a comparison with the classical approach of "stereoscopic" video; (3) a short introduction to DIBR techniques in general; (4) the development of a specific DIBR algorithm that can be used for the efficient generation of high-quality "virtual" stereoscopic views; (5) a number of implementation details that are specific to the current state of the development; (6) research on the backwards-compatible compression and transmission of 3D imagery using state-of-the-art MPEG (Moving Pictures Expert Group) tools.
Nanocrystal‐Based Luminescent Composites for Nanoimprinting Lithography (2007)

CdSe@ZnS nanocrystals are incorporated in acrylic acid or amine-functionalized PMMA copolymers (see image) to obtain fluorescent nanocomposites characterized by homogeneous NC dispersion and a significant increase in emission efficiency, without modifying the excellent processability of the thermoplastic polymer. Such properties permit the fabrication of highly luminescent nanostructures at the micro- and nanoscale, extending the patterning resolution limit by means of nanoimprinting lithography.
Auditing to keep online storage services honest (2007)

A growing number of online service providers offer to store customers &amp;apos; photos, email, le system backups, and other digital assets. Currently, customers cannot make informed decisions about the risk of losing data stored with any particular service provider, reducing their in-centive to rely on these services. We argue that third-party auditing is important in creating an online service-oriented economy, because it allows customers to eval-uate risks, and it increases the efciency of insurance-based risk mitigation. We describe approaches and sys-tem hooks that support both internal and external audit-ing of online storage services, describe motivations for service providers and auditors to adopt these approaches, and list challenges that need to be resolved for such au-diting to become a reality.
Genetics of amyotrophic lateral sclerosis (1996)

Amyotrophic lateral sclerosis (ALS) is a paralytic disorder caused by degeneration of motor neurons in the brain and spinal cord. Identification of mutations in the gene for Cu,Zn superoxide dismutase (SOD1) in a subset of ALS families made it possible to develop a transgenic mouse model of ALS and to investigate its pathogenesis. These investigations suggest that mutant SOD1 acts through a toxic gain of function which may involve generation of free radicals. Conformational change in the mutant SOD1 protein, especially the distortion of the 'rim' of the electrostatic guidance channel may be central to this toxic gain of function and to the pathogenesis of ALS.
Genes of the RecE and RecF Pathways of Conjugational Recombination in Escherichia coli (1984)

Conjugational recombination in wild-type Escherichia coli K-12 depends on the products of a large number of genes. In the wild type, three of these genes have been identified: recA (Clark and Margulies 1965), recB (Howard-Flanders and Theriot 1966), and recC (Emmerson and Howard-Flanders 1967). Mutations in either recB or recC do not result in complete recombination deficiency, and suppression by sbcA (Barbour et al. 1970) and sbcB (Kushner et al. 1971) mutations have led to the discovery of other recombination genes. Against the recB recC sbcB multiple-mutant background, mutations in the following genes were detected by reduction in conjugational recombination frequencies: recA (Horii and Clark 1973), recF (Horii and Clark 1973), recJ (Lovett and Clark 1984), recN (Lloyd et al. 1983), and ruv (Lloyd et al. 1984; S. Lovett and A.J. Clark, unpubl.). Against the recB recC sbcA multiple-mutant background, mutations in the following genes were similarly detected: recA (Gillen...
An Ecologically Motivated Analysis of Plant-Herbivore Interactions in Native Tobacco (2001)

You can't always get what you want, but if you try some time, you just might find, you get what you need…

Mick Jagger

Mick Jagger is not a biologist, but his lyrics echo a major ecological paradigm: that tradeoffs (e.g. “costs”) constrain organisms at all functional scales, from those
Anchorage dependence of mitogen-induced G1 to S transition in primary T lymphocytes. (1999)

Anchorage dependence defines the cellular requirement for integrin-mediated adhesion to substrate to initiate DNA replication in response to growth factors. In this study we investigated whether normal T cells, which spend extended periods in a nonadherent state, show similar requirements for cell cycle progression in response to TCR stimulation. Resting primary T lymphocytes were induced to enter the cell cycle by TCR triggering, and leukocyte integrins were either engaged using purified ICAM-1 or inhibited with function-blocking mAbs. Our data indicate that leukocyte integrins complement TCR-driven mitogenic signals not as a result of their direct clustering but, rather, via integrin-dependent organization of the actin cytoskeleton. Leukocyte integrin-dependent reorganization of the actin cytoskeleton cooperates with the TCR to effect mitogen-activated protein kinase activation, but also represents a required late (4-8 h poststimulation) component in the mitogenic response of normal T cells. Prolonged leukocyte integrin-dependent spreading, in the context of intercellular contact, is a requisite for the production of the mitogenic cytokine IL-2, which, in turn, is involved in the induction of D3 cyclin and is primarily responsible for the decrease in the cyclin-dependent kinase inhibitor p27kip, resulting in retinoblastoma protein inactivation and S phase entry. Thus, T lymphocytes represent a peculiar case of anchorage dependence, in which signals conveyed by integrins act sequentially with the activating stimulus to effect a sustained production of the essential mitogenic cytokine.
Geological impacts on Mangaweka Deviation, State Highway 1, North Island (1998)

The Mangaweka Deviation on State Highway 1 between Mangaweka and Utiku in the central North Island was reconstructed over an 8 year period in the 1970s. Three engineering geological lessons related to slope stability are apparent from a review of the investigations, construction, and operation of this section of highway. These are the performance of cut slopes in colluvium, the hazard presented by natural slopes above the highway, and the influence of lithology on the degree of surface degradation (slabbing and slaking) in 'papa ' bedrock.
The “cancer immunogram” (2016)

Visualizing the state of cancer–immune system interactions may spur personalized therapy
NOTES ON FLORA OF TEXAS USA WITH ADDITIONS RANGE EXTENSIONS AND ONE CORRECTION (1989)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.