gebhart/patrepeval huggingface dataset:
Breakpoint clustering in t(4;11)(q21;q23) acute leukemia (1991)

Chromosome 11 band q23 is commonly involved in nonrandom chromosomal translocations in hematopoietic malignancies, especially in infant acute leukemias. By using pulsed-field gel electrophoresis (PFGE) with restriction endonuclease digests of DNA from both a leukemia cell line (RS4;11) bearing the t(4;11)(q21;q23) and from human/hamster hybrid cells, we have been able to construct a detailed restriction map of the chromosome 11q23 region and have localized the t(4;11) chromosome 11 breakpoint to a region located approximately 200 to 230 kb telomeric to the CD3 gamma region and approximately 580 kb centromeric to the PBGD gene. PFGE analyses of DNA from clinical leukemia specimens and cell lines indicated a tight clustering of breakpoints in all eight t(4;11) acute leukemias studied. These data strongly suggest that discrete genetic loci are interrupted on both chromosomes 4 and 11 in a manner likely to be critically involved in the pathogenesis of t(4;11) acute leukemias. To our knowledge, these results represent the first evidence of breakpoint clustering in t(4;11) acute leukemias. In contrast to t(4;11), other 11q23 abnormalities studied to date have frequently shown evidence for alternative breakpoint sites in 11q23.
Videotape Program Production at CBS Studio Center (1978)

The one-inch helical videotape recorder has been utilized by CBS to configure a film-style (one VTR per camera) videotape production system at CBS Studio Center in Hollywood. Operating experience with these machines is discussed, with emphasis on observations of video, audio, and transport performance. In addition, this paper describes a unique system for synchronization of one-inch VTRs in post production that has allowed CBS to offer an alternative to traditional multi-camera videotape production methods.
Measurement of Prostate-Specific Antigen in Serum as a Screening Test for Prostate Cancer (1991)

The combination of measurement of the serum PSA concentration and rectal examination, with ultrasonography performed in patients with abnormal findings, provides a better method of detecting prostate cancer than rectal examination alone.
Cationic Lipid/Polynucleotide Condensates for in Vitro and in Vivo Polynucleotide Delivery - the Cytofectins (1993)

Cationic liposomes have been used extensively during the last 5 years to facilitate delivery of DNA, MRNA, antisense molecules and proteins into living cells. Since their initial description in 1987 several reagents have become commercially available. Other cationic lipid reagents not yet commercially available, have been described showing advantages relative to the commercial products. Their widespread utility has been further established from in vivo studies showing delivery to catheterized blood vessels, lung epithelial cells, brain tissue and xenopus embryos. Finally, the compounds have been introduced into man in a gene therapy clinical trial recently initiated by Nabel etal. Because there is now a rapidly growing list of compounds that act by a similar mechanism we are referring to this class of polynucleotide delivery reagents as the “Cytofectins”.
Characterization of long non-coding RNA transcriptome in high-energy diet induced nonalcoholic steatohepatitis minipigs (2016)

Today, obesity and nonalcoholic steatohepatitis are a worldwide epidemic, although how these syndromes are regulated with respect to lncRNAs remains largely unknown. Our previous studies have revealed important pathological features and molecular characteristics of nonalcoholic steatohepatitis in the minipig model, and in this study, we analyze the features of lncRNAs and their potential target genes. Minipig samples only from liver were analyzed using next-generation deep sequencing. In total, we obtained 585 million raw reads approximately 70.4 Gb of high quality data. After a strict five-step filtering process, 1,179 lncRNAs were identified, including 89 differentially expressed lncRNAs (P < 0.05) in the experiment group relative to the control group. The cis and trans analysis identified target genes that were enriched for specific GO terms (P < 0.01), including immune processes, chemokine activity, cytokine activity, and G-protein coupled receptor binding, which are closely related to nonalcoholic steatohepatitis. The predicted protein-coding targets of the differentially expressed lncRNAs were further analyzed, such as PPAR, FADS2, DGAT2, ACAA2, CYP2E1, ADH4, and Fos. This study reveals a wealth of candidate lncRNAs involved in NASH and their regulated pathways, which should facilitate further research into the molecular mechanisms of this disorder.
High-speed wavelength-swept semiconductor laser with a polygon-scanner-based wavelength filter (2003)

Ultrahigh-speed tuning of an extended-cavity semiconductor laser is demonstrated. The laser resonator comprises a unidirectional fiber-optic ring, a semiconductor optical amplifier as the gain medium, and a novel scanning filter based on a polygonal scanner. Variable tuning rates up to 1150 nm/ms (15.7-kHz repetition frequency) are demonstrated over a 70-nm wavelength span centered at 1.32 microm. This tuning rate is more than an order of magnitude faster than previously demonstrated and is facilitated in part by self-frequency shifting in the semiconductor optical amplifier. The instantaneous linewidth of the source is <0.1 nm for 9-mW cw output power and a low spontaneous-emission background of -80 dB.
Phase aware proximity correction for advanced masks (2000)

In this paper we describe the use of sparse aerial image simulation coupled with process simulation, using the variable threshold resist (VTR) model, to do optical and process proximity correction (OPC) on phase shift masks (PSM). We will describe the OPC of PSM, including attenuated PSM, clear field PSM, and double exposure PSM. We will explain the method used to perform such OPC and show examples of critical dimension control improvements generated from such a technique. Simulations, PSM assignment and model based OPC corrections are performed with Calibre Workbench, Calibre DRC, Calibre PSMgate and Calibre OPCpro tools from Mentor Graphics. In conclusion we will show that PSM techniques need to be corrected by a phase aware proximity correction tool in order to achieve both pattern fidelity as well as small feature size on the wafer in a production environment.
Cloning of the zebrafishkrox-20gene (krx-20) and its expression during hindbrain development (1993)

To begin to examine the function of genes that control early development in the hindbrain, we have screened an embryonic zebrafish cDNA library with a murine krox-20 gene probe that contained the conserved zinc finger regions. We have isolated two overlapping cDNAs, zf187 and zf201 which are homologues of the murine krox-20 gene. The N-terminal of the longest cDNA (zf201) contains two acidic regions identical to those of the murine krox-20. This indicates that the functional organisation of these proteins is probably conserved. Northern Blot analysis identified a single transcript of 2.0 kb. Wholemount in situ hybridisation established that expression of the zebrafish gene (krx-20) first appears at 100% epiboly as a single anterior domain of the prospective neuroepithelium, followed very soon after by a second more posterior domain. The alternating pattern of expression of this gene in rhombomeres(r) r3 and r5 is apparent by 12 hr post-fertilisation, that is prior to the morphological appearance of the rhombomeres. Around 14 hr neural crest migration begins from the dorsal surface of r5, moving caudally into r6 and then ventrally towards the pharyngeal arches. Crest migration is not apparent at or after 16 hr. No neural crest migration was observed from r3. Expression of krx-20 is down regulated firstly in r3 around 26 hr and later in r5 around 30 hr.
Molecular cloning of a cyclic GMP-stimulated cyclic nucleotide phosphodiesterase cDNA. Identification and distribution of isozyme variants. (1991)

We have cloned a 4.2-kilobase pair (kb) cDNA that encodes the cyclic GMP-stimulated phosphodiesterase (cGS PDE) from a bovine adrenal cortex library. The 921-residue polypeptide deduced from the cDNA nucleotide sequence is nearly identical with the complete amino acid sequence of the cGS PDE purified from a soluble bovine heart extract. Moreover, PPD-S49 cells transfected with the cGS PDE cDNA express a soluble cAMP hydrolytic activity that is enhanced by cGMP. Total RNA isolated from several bovine tissues were screened for cGS PDE transcript by Northern blot analysis. The cGS PDE cDNA appears to hybridize to a single 4.5-4.6-kb mRNA species. Although the cGS PDE mRNA is most abundant in the adrenal cortex, it is also concentrated in the adrenal medulla and heart and in anatomically distinct regions of the brain and kidney. A mRNA species encoding a putative variant cGS PDE isoform was detected by RNase protection. Total RNA isolated from adrenal cortex, adrenal medulla, liver, kidney, trachea, lung, spleen, and T-lymphocytes completely protected a 452-base riboprobe encoding 100 residues of the adrenal cortex cGS PDE amino terminus. In contrast, RNAs isolated from brain (cerebral cortex, hippocampus, and basal ganglia) protected only 268 bases of this riboprobe. The RNase protection pattern of this same probe using heart RNA showed major bands at both 268 and 452 bases, suggesting that two different cGS PDE mRNA species are expressed. These results indicate that the cGS PDE is widely expressed in a variety of tissues. Moreover, these studies suggest that at least one different cGS PDE isoform having a structurally distinct amino-terminal domain is expressed in brain and heart.
The Metabolism of Sphingomyelin (1966)

A sphingomyelin-cleaving enzyme has been found in rat liver tissue. The enzyme, originally present in subcellular particulate fractions, could be released in a soluble form by treatment with appropriate detergents and was partially purified by conventional procedures. The most highly purified enzyme preparations catalyzed the hydrolysis of sphingomyelin, whereas lecithin and phosphatidylethanolamine were unaffected. The products of the reaction were identified as phosphorylcholine and ceramide. Lecithin was a competitive inhibitor of the reaction.
CD63 antigen. A novel lysosomal membrane glycoprotein, cloned by a screening procedure for intracellular antigens in eukaryotic cells. (1991)

To clone the CD63 antigen, originally described as a blood platelet activation marker, we adapted the expression cloning procedure of Seed and Aruffo (Seed, B., and Aruffo, A. (1987) Proc. Natl. Acad. Sci. U.S. A. 84, 3365-3369) to allow cloning of intracellular antigens. A megakaryocyte expression cDNA library was transiently transfected into MOP-8 mouse fibroblasts cultured on polyvinylidene difluoride membranes. Individual cells expressing intracellular CD63 were identified by autoradiography. cDNA was extracted from positive spots and reintroduced into Escherichia coli. After two screening rounds, a CD63 cDNA clone was isolated as assessed by immunofluorescence and Western blot analysis. The single long open reading frame of 238 amino acids contained four putative transmembrane regions and three N-glycosylation sites. The CD63 gene was expressed in a wide variety of cells. Surprisingly, CD63 was identical to ME491, an antigen reported as a melanoma-associated antigen (Hotta, H., Ross, A. H., Huebner, K., Isobe, M., Wendeborn, S., Chao, M. V., Ricciardi, R. P., Tsujimoto, Y., Croce, C. M., and Koprowski, H. (1988) Cancer Res. 48, 2955-2962). By immunoelectron microscopy, co-localization with the lysosomal glycoproteins lamp-1 and -2 identified CD63 as a novel lysosomal membrane glycoprotein. CD63 was not related to the lysosomal glycoprotein family but contained the putative lysosomal targeting signal Gly-Tyr in its short cytoplasmic tail.
Synthesis and characterization of a Pseudomonas aeruginosa alginate-toxin A conjugate vaccine (1991)

Alginate from Pseudomonas aeruginosa 3064 was depolymerized by controlled heating in dilute acid. The resulting depolymerized alginate (Mr less than 60,000) was covalently coupled to toxin A with adipic acid dihydrazide as a spacer molecule and carbodiimide as a linker. The resulting conjugate was composed of toxin A and depolymerized alginate at a ratio of 4:1 and possessed an Mr of 260,000. The conjugate was nontoxic and nonpyrogenic. While native alginate (Mr greater than 640,000) given in a range of doses was poorly immunogenic in mice and rabbits, the conjugate induced high levels of antibody which bound to native alginate. Rabbits, but not mice, also produced an antitoxin immunoglobulin antibody response. Alginate derived from three other strains of P. aeruginosa competed with the homologous 3064 alginate for binding to anticonjugate antibody. This indicates that the conjugate elicits an antibody response able to recognize heterologous alginates. The serum from rabbits immunized with the conjugate was effective at promoting the uptake and killing of mucoid strains of P. aeruginosa by human polymorphonuclear leukocytes. In contrast, immunization with native alginate did not engender an opsonic antibody response. Rabbit anticonjugate antibody also neutralized the cytotoxic potential of toxin A.
Likely HIV Cofactor Found (1996)

Researchers learned some 12 years ago that the AIDS virus, HIV, needs to latch onto a cell protein called CD4 to enter and infect cells. But they've known for a decade that CD4 by itself is not sufficient to get the virus into cells. Also required is some unknown “cofactor.” That cofactor eluded their efforts to discover it, however, until perhaps now. Work reported in this issue indicates that the cofactor is a protein called fusin, a discovery that may help solve several mysteries about AIDS. Among them: how HIV destroys cells and why it appears not to harm some infected people. It may also be possible to limit HIV infectivity by designing new drugs that work by binding to fusin.
Spatially resolved cathodoluminescence spectra of InGaN quantum wells (1997)

Spatially resolved cathodoluminescence (CL) spectrum mapping revealed a strong exciton localization in InGaN single-quantum-wells (SQWs). Transmission electron micrographs exhibited a well-organized SQW structure having abrupt InGaN/GaN heterointerfaces. However, comparison between atomic force microscopy images for GaN-capped and uncapped SQWs indicated areas of InN-rich material, which are about 20 nm in lateral size. The CL images taken at the higher and lower energy side of the spatially integrated CL peak consisted of emissions from complementary real spaces, and the area was smaller than 60 nm in lateral size.
Nanotube film based on single-wall carbon nanotubes for strain sensing (2004)

Carbon nanotubes change their electronic properties when subjected to strains. In this study, the strain sensing characteristic of carbon nanotubes is used to develop a carbon nanotube film sensor that can be used for strain sensing on the macro scale. The carbon nanotube film is isotropic due to randomly oriented bundles of single-wall carbon nanotubes (SWCNTs). Using experimental results it is shown that there is a nearly linear change in voltage across the film when it is subjected to tensile and compressive stresses. The change in voltage is measured by a movable four-point probe in contact with the film. Multidirectional and multiple location strains can be measured by the isotropic carbon nanotube film.
Chromosomal Translocations in Lymphoid Malignancies Reveal Novel Proto-Oncogenes (1992)

Chromosomal translocation within B and T cell malignancies has proven a rich source for proto-oncogenes. The obligate DNA breaks within immunoglobulin (Ig) and T cell receptor (TCR) loci are frequently the sites of recurrent translocations. Burkitt's lymphoma established the paradigm by introducing the myc oncogene from chromosome segment 8q24 into the Ig heavy chain gene locus at 14q32. Molecular cloning of an aberrant Ig rearrangement in follicular lymphoma revealed Bcl-2. Bcl-2 constitutes the first member of a new category of oncogenes: regulators of programmed cell death. Bcl-2 blocks apoptosis and maintains long-term immune responsiveness including B-cell memory. The PRAD1 gene of parathyroid adenomas appears to be the elusive Bcl-1 gene of t(11;14)(q13;q32) bearing lymphomas. It proves to be a novel G1 cyclin. Acute lymphoblastic leukemias (ALL) pre-B phenotype produce a E2A/PBX fusion protein that possesses the leucine zipper of E2A with the homeodomain of PBX. Two molecular forms of the BCR/ABL fusion protein are produced by the Philadelphia chromosome. A deregulated p210 tyrosine kinase is found in chronic myelogenous leukemia, while a p190 form predominates in Ph+ ALL. In contrast, T-cell ALLs introduce a potpourri of genes into their T cell receptor loci. However, a common theme is emerging. These oncogenes (Ttg1, Ttg2, SCL, LylI, H0X11) all belong to classic families of transcription factors, possessing LIM domains, helix-loop-helix motifs, or homeodomains. Provocatively, these transcription factors are normally intended for lineages other than T cells. These genes have widened the horizons of both oncogenesis and normal development.
Neuroprotective Effects of Phenylbutyrate in the N171-82Q Transgenic Mouse Model of Huntington's Disease (2004)

Huntington's disease (HD) is caused by an expansion of exonic CAG triplet repeats in the gene encoding the huntingtin protein (Htt), however, the means by which neurodegeneration occurs remains obscure. There is evidence that mutant Htt interacts with transcription factors leading to reduced histone acetylation. We report that administration of the histone deacetylase inhibitor phenylbutyrate after onset of symptoms in a transgenic mouse model of HD significantly extends survival and attenuates both gross brain and neuronal atrophy. Administration of phenylbutyrate increased brain histone acetylation and decreased histone methylation levels as assessed by both immunocytochemistry and Western blots. Phenylbutyrate increased mRNA for components of the ubiquitin-proteosomal pathway and down-regulated caspases implicated in apoptotic cell death, and active caspase 3 immunoreactivity in the striatum. These results show that administration of phenylbutyrate, at doses that are well tolerated in man, exerts significant neuroprotective effects in a transgenic mouse model of HD, and therefore represents a very promising therapeutic approach for HD.
Appreciating Traditional Forms of Healing Conflict in Africa and the World (2010)

Traditional African methods of healing and ways of coping with conflict have much in common, even when it comes to acceptance in the western world. Most westerners approach both concepts with great skepticism. Many western-educated Africans have also retreated from traditional concepts of conflict resolution in favor of solutions offered by formal court systems, binding arbitration, official sanctions, and western-style mediation. Some critics go so far as to suggest that traditional African conflict resolution systems are barbaric and have no place in the modern world. This essay examines the effectiveness of these underappreciated traditional norms within the context of different worldviews and the framework of an optimal psychology. Emphasis will be placed on the ways in which traditional strategies can be better understood and appreciated within this culturally congruent framework, which places the highest importance on values for truth, justice, peace, harmony, order, balance, reciprocity, and sustainability. The key components of five strategies will be discussed: Gacaca in Rwanda; michu and luba basa in Ethiopia; mato oput in Uganda; the Akobo Peace Conference in Sudan; and one of the world’s most successful traditional peace conferences following Somaliland’s declaration of independence from Somalia in 1991. These examples of successful traditional conflict resolution processes are provided by Professor David H. Shinn, who served for thirty-seven years in the United States Foreign Service and was stationed at embassies in Kenya, Tanzania, Mauritania, Cameroon, and Sudan and as ambassador to Burkina Faso and Ethiopia (Shinn, 2005). The aim of this piece is to illuminate the notable commonalities among people acknowledging African descent on the continent and throughout the diaspora in their pursuit of justice, providing an Afrogenic analysis of cosmopolitanism based on optimal theory. The normal binary of traditional methods versus those imported from the west for providing more effective strategies to resolve conflict will be expanded to include consideration of the role of a cultural worldview (Myers, 2008). Within this consideration is awareness that trust in traditional strategies, cultural strengths, and effectiveness can be obstructed by the larger colonial and neocolonial historical context of psychological oppression and the reality of control, subjugation, and dehumanization constructed and imposed on those acknowledging African descent. Other factors to be considered include the nature of the violence perpetrated and whether it is personal or impersonal. The ways in which traditional means to mitigate or resolve conflict, analyzed in light of the theory of optimal psychology, will add to the sympathy and empathy of cosmopolitanism, which is the hallmark for universal understanding described by Appiah (2006) as the legacy of Black Studies, the third-level criteria of insight derived from classical African civilization.
Oat Products and Lipid Lowering (1992)

<h3>Objectives.</h3> —To test the a priori hypothesis that consumption of oats will lower the blood total cholesterol level and to assess modifiers and confounders of this association. <h3>Data Sources.</h3> —A computerized literature (MEDLINE) search and the Quaker Oats Co identified published and unpublished trials as of March 1991. Raw data were requested for all trials. <h3>Study Selection.</h3> —Trials were included in summary effect size estimates if they were randomized and controlled, if a formal assessment of diet and body weight changes occurred, and, if raw data were not received, if there was enough information in the published report to perform calculations. <h3>Data Synthesis.</h3> —Twenty trials were identified. Using the methods of DerSimonian and Laird, a summary effect size for change in blood total cholesterol level of -0.13 mmol/L (-5.9 mg/dL) (95% confidence interval [Cl], -0.19 to -0.017 mmol/L [-8.4 to -3.3 mg/dL]) was calculated for the 10 trials meeting the inclusion criteria. The summary effect size for trials using wheat control groups was -0.11 mmol/L (-4.4 mg/dL) (95% Cl, -0.21 to -0.01 mmol/L [-8.3 to -0.38 mg/dL]). Calculation of Keys scores demonstrated that substituting carbohydrates for dietary fats and cholesterol did not account for the majority of blood cholesterol reduction. Larger reductions were seen in trials in which subjects had initially higher blood cholesterol levels (≥5.9 mmol/L [≥229 mg/dL]), particularly when a dose of 3 g or more of soluble fiber was employed. <h3>Conclusion.</h3> —This analysis supports the hypothesis that incorporating oat products into the diet causes a modest reduction in blood cholesterol level. (<i>JAMA</i>. 1992;267:3317-3325)
A Double-Adaptive File Compression Algorithm (1983)

We describe a one-pass compression scheme which presumes no statistical properties of the data being compressed. The model structure adaptively selects a subset of first-order Markov contexts, based on an estimate of the candidate context's popularity. The probability distributions for the unselected (lumped) first-order contexts are made the same, reducing cost over a full first-order Markov model. Symbol repetitions are handled in special secondorder Markov contexts. The statistics for each symbol are adaptively determined by an extension of earlier work.