gebhart/patrepeval huggingface dataset:
Nuclear Localization of Peptidylarginine Deiminase V and Histone Deimination in Granulocytes (2002)

Peptidylarginine deiminase (PAD) deiminates arginine residues in proteins to citrulline residues Ca(2+) dependently. There are four types of PADs, I, II, III, and V, in humans. We studied the subcellular distribution of PAD V in HL-60 granulocytes and peripheral blood granulocytes. Expression of green fluorescent protein-tagged PADs in HeLa cells revealed that PAD V is localized in the nucleus, whereas PAD I, II, and III are localized in the cytoplasm. PAD V deletion mutants indicated that the sequence residues 45-74 have a nuclear localization signal (NLS). A sequence feature of this NLS is a three-lysine residue cluster preceded by a proline residue and is not found in the three other PADs. Substitution of the lysine cluster by an alanine cluster abrogated the nuclear import activity. These results suggested that the NLS is a classical monopartite NLS. HL-60 granulocytes, neutrophils, and eosinophils stained with antibody specific for PAD V exhibited distinct positive signals in the nucleus. Subcellular fractionation of HL-60 granulocytes also showed the nuclear localization of the enzyme. When neutrophils were stimulated with calcium ionophore, protein deimination occurred in the nucleus. The major deiminated proteins were identified as histones H2A, H3, and H4. The implication of PAD V in histone modifications is discussed.
Genetic Influences Determining Progenitor Cell Mobilization and Leukocytosis Induced by Granulocyte Colony-Stimulating Factor (1997)

The mechanisms involved in the mobilization of progenitor cells into the blood by granulocyte colony-stimulating factor (G-CSF) and other cytokines are poorly understood. To identify important influences on this complex process, in vivo murine models were used. Granulocyte-macrophage colony-stimulating factor (GM-CSF) transgenic, Max41 transgenic, W/Wv, Mpl-null, GM-CSF receptor (beta chain)-null mice, wild-type littermate controls, and six inbred strains of mice were injected with 200 microg/kg/d G-CSF for 5 days. Three parameters of response were monitored: white blood cell count (WCC), peripheral blood progenitor cell (PBPC) numbers, and spleen weight. In all genotypes studied, G-CSF induced increases in these three parameters. However, PBPC mobilization in W/Wv and Mpl-null mice was only 30% and 9%, respectively, of that observed in wild-type mice. In contrast, perturbations of GM-CSF signalling had no demonstrable effect on in vivo responses to G-CSF. Broad variability was evident between inbred strains for each parameter of the response to G-CSF. A 10-fold range in response was observed for circulating progenitor cell numbers, similar to that observed for normal human subjects receiving G-CSF. The interstrain differences were in the distribution of mature and progenitor cells between peripheral blood, bone marrow, and spleen rather than in the total numbers of these cells in the body. Results of an F2 intercross of low-responding C57BL/6 and intermediate-responding SJL mice indicated that regulation of progenitor cell mobilization is a complex genetic trait, that there is a correlation between this trait and WCC response (r2 = .5), and that this approach may serve as a useful model for the identification of genes involved in the mobilization process.
The quantitative determination of phenylalanine hydroxylase in rat tissues. Its developmental formation in liver (1972)

A sensitive method was developed for determining the phenylalanine hydroxylase activity of crude tissue preparations in the presence of optimum concentrations of the 6,7-dimethyl-5,6,7,8-tetrahydropterin cofactor (with ascorbate or dithiothreitol to maintain its reduced state) and substrate. Tissue distribution studies showed that, in addition to the liver, the kidney also contains significant phenylalanine hydroxylase activity, one-sixth (in rats) or half (in mice) as much per g as does the liver. The liver and the kidney enzyme have similar kinetic properties; both were located in the soluble phase and were inhibited by the nucleo-mitochondrial fraction. Phenylalanine hydroxylase, like most rat liver enzymes concerned with amino acid catabolism, develops late. On the 20th day of gestation, the liver (and the kidney) is devoid of phenylalanine hydroxylase and at birth contains 20% of the adult activity. During the second postnatal week of development, when the phenylalanine hydroxylase activity was about 40% of the adult value, an injection of cortisol doubled this value. Cortisol had no significant effect on phenylalanine hydroxylase in adult liver or on phenylalanine hydroxylase in kidney at any age.
Text Image Compression Using Soft Pattern Matching (1997)

We present a method for both lossless and lossy compression of bi-level images that consist mostly of printed or typed text. The key feature of the method is soft pattern matching, a way of making use of the information in previously encountered characters without risking the introduction of character substitution errors. We can obtain lossless compression which is about 20% better than that of the JBIG standard by direct application of this method. By allowing some loss based partly on the pattern matching using a technique called selective pixel reversal, we can obtain compression ratios about 2–4 times the compression ratios of JBIG and 3–8 times those of G3 facsimile with no visible loss of quality. If used in facsimile machines, these compression improvements would translate directly into communication cost reductions of the same factors, or into the capability of transmitting images at higher resolution with no increase in the number of bits sent.
Completely Erasable Phase Change Optical Disk (1992)

A phase change optical disk using a new quaternary system of Ag-In-Sb-Te as the active layer will be reported. With this disk, “complete erasure” of the recorded signal has been achieved. A carrier-to-noise ratio of 47 dB and an erase ratio of -47 dB were obtained in the two-pass writing-erasing mode with a linear velocity of 7 m/s and a writing power of 11 mW. In the one-pass overwriting mode, a carrier-to-noise ratio greater than 40 dB was obtained and this recorded signal was also completely erased. The peak power and the bias power for the overwriting were 10 mW and 5 mW, respectively. The facts that the widths of the written marks are narrow and that no large crystalline grains are observed in the periphery of the written marks are considered to be the major causes for the high erasability. We also found that the existence of fine crystalline particles in the initialized active layer can be considered to be of great advantage to high sensitivity.
A Re-engineering Methodology for Componentization of Legacy System (2003)

This paper intents to suggest the re-engineering methodology to transform and integrate the legacy systems to new system in modern environment. While existing reverse engineering and re-engineering approaches have focused on analyzing and maintaining the source code of program. our methodology can provide the procedures and techniques for evolving into new system by recovering the reverse engineering informations and transforming them into component informations. Our methodology for componentization of legacy system is consisted of plan step, reverse engineering step, componentization step, and delivery step, and we describes activities and detail procedures about each step.
DNSSEC and IPv6 A6 aware server/resolver message size requirements (2001)

This document mandates support for EDNS0 (Extension Mechanisms for DNS) in DNS entities claiming to support either DNS Security Extensions or A6 records. This requirement is necessary because these new features increase the size of DNS messages. If EDNS0 is not supported fall back to TCP will happen, having a detrimental impact on query latency and DNS server load. This document updates RFC 2535 and RFC 2874, by adding new requirements.
Salt Tolerance of Glycinebetaine-Deficient and -Containing Maize Lines (1995)

Pairs of homozygous near-isogenic glycinebetaine-containing (Bet1/Bet1) and -deficient (bet1/bet1) F8 lines of Zea mays L. (maize) were tested for differences in salt (150 mM NaCl or 127.25 mM NaCl plus 22.5 mM CaCl2) tolerance. The Bet1/Bet1 lines exhibited less shoot growth inhibition (as measured by dry matter accumulation, leaf area expansion rate and/or, plant height extension rate) under salinized conditions in comparison to their nearisogenic bet1/bet1 sister lines. These growth differences were associated with maintenance of a significantly higher leaf relative water content, a higher rate of carbon assimilation, and a greater turgor in Bet1/Bet1 lines than in bet1/bet1 lines under salinized conditions. These results strongly suggest that a single gene conferring glycinebetaine accumulation (and/or a tightly linked locus) plays a key role in osmotic adjustment in maize.
Insertional inactivation of the major autolysin gene of Streptococcus pneumoniae (1988)

The lytA gene encoding the major pneumococcal autolysin (N-acetylmuramoyl-L-alanine amidase) was inactivated by inserting the 2-kilobase MspI fragment of pE194 containing the staphylococcal ermC gene. Stable autolysis-deficient (Lyt-) mutants and their isogenic Lyt+ parents were used in experiments designed to test possible physiological functions of the amidase. No autolysis could be induced in the mutants grown at 37 degrees C by deoxycholate, by incubation in stationary phase, or by treatment with penicillin. On the other hand, the Lyt- mutants exhibited normal growth rates and yields and normal adaptive responses during shifts from one growth temperature or nutritional condition to another. There was no evidence for impeded cell separation (chain formation). Colonies of Lyt- insertional mutants produced normal hemolytic zones on blood agar; they showed normal (high) levels of competence for genetic transformation. Lyt- mutants were also able to produce type 3 and 6 capsular polysaccharides, and such strains showed the same degree of virulence in mice as did the isogenic Lyt+ parent. The physiological function(s) of the amidase remains a puzzle.
Tuning the upconversion photoluminescence lifetimes of NaYF4:Yb3+, Er3+ through lanthanide Gd3+ doping (2018)

The multiplexing capacity of conventional fluorescence materials are significantly limited by spectral overlap and background interference, mainly due to their short-lived fluorescence lifetimes. Here, we adopt a novel Gd<sup>3+</sup> doping strategy in NaYF<sub>4</sub> host materials, realized tuning of upconversion photoluminescence (UCPL) lifetimes at selective emissions. Time-correlated single-photon counting (TCSPC), was applied to measure the photoluminescence lifetimes accurately. We demonstrated the large dynamic range of lifetimes of upconversion nanoparticles with good upconversion quantum yields, mainly owing to the dominance of high efficient energy transfer upconversion mechanism. The exceptional tunable properties of upconversion materials allow great potential for them to be utilized in biotechnology and life sciences.
An Envelope-Tracking CMOS-SOS Power Amplifier with 50% Overall PAE and 29.3 dBm Output Power for LTE Applications (2012)

This paper presents a CMOS envelope tracking power amplifier for LTE band-13 (782 MHz) applications. The envelope amplifier is implemented in 0.18 μm bulk CMOS process while the RF power amplifier is designed in 0.35 μm CMOS Silicon-on-Sapphire (SOS) technology. To overcome low breakdown voltage limit of MOSFETs, a stacked FET structure is used. The complete envelope tracking system achieves an overall PAE of 50% for 16 QAM, 10 MHz LTE signal with 6.6 dB peak-to-average ratio (PAPR), while delivering 29.3 dBm output power. A memory-less digital pre-distortion (DPD) is employed to linearize the overall system, which pushes ACLR down to -46.5 dBc.
Pseudomonas fluorescens Encodes the Crohn's Disease-Associated I2 Sequence and T-Cell Superantigen (2002)

Commensal bacteria have emerged as an important disease factor in human Crohn's disease (CD) and murine inflammatory bowel disease (IBD) models. We recently isolated I2, a novel gene segment of microbial origin that is associated with human CD and that encodes a T-cell superantigen. To identify the I2 microorganism, BLAST analysis was used to identify a microbial homologue, PA2885, a novel open reading frame (ORF) in the Pseudomonas aeruginosa genome. PCR and Southern analysis identified Pseudomonas fluorescens as the originating species of I2, with homologues detectable in 3 of 13 other Pseudomonas species. Genomic cloning disclosed a locus containing the full-length I2 gene (pfiT) and three other orthologous genes, including a homologue of the pbrA/pvdS iron response gene. CD4(+) T-cell responses to recombinant proteins were potent for I2 and pfiT, but modest for PA2885. pfiT has several features of a virulence factor: association with an iron-response locus, restricted species distribution, and T-cell superantigen bioactivity. These findings suggest roles for pfiT and P. fluorescens in the pathogenesis of Crohn's disease.
Intervening sequences in evolution and development (1990)

Michael G. Rossman: Introductory comments on the function of domains in protein structure S.K. Holland, & C.C.F. Blake: Proteins, exons, and molecular evolution W. Ford Doolittle: Understanding introns: origins and functions Edwin M. Stone, & Robert J. Schwartz: Intron-dependent evolution of progenotic enzymes Joseph P. Stein, Maxwell J. Scott, & Bert W. O'Malley: Intervening sequences in molecular evolution Philip S. Perlman, Craig Peebles, & Charles Daniels: Types of introns and splicing mechanisms Christopher W.J. Smith, David Knaack, & Bernardo Nadal-Ginard: Alternative mRNA splicing in the generation of protein diversity and the control of gene expression.
Production of b-cells from human embryonic stem cells (2008)

The making of functional pancreatic islets in renewable numbers has been a goal of stem cell biologists since early 2000. Since that time, many studies have reported successful creation of glucose-responsive pancreatic b-cells. Not until the more recent systematic application of developmental principles to stem cell biology systems were breakthroughs achieved on directed specification of the required early developmental intermediates. The most important first step is the formation of the definitive endoderm (DE) lineage which is compulsory for production of the epithelium of the pancreas and the other important endoderm-derived organs such as the liver, intestine and lung. The formation of DE from embryonic stem cells made possible additional experimentation aimed at directing the endoderm to further specified foregut and pancreatic endoderm lineages. With these discoveries came the first production of immature pancreatic endocrine cells. Most recently, the production in vivo of glucose-responsive insulin-producing cells with the capacity to correct Steptozotocin-induced hyperglycaemia in mice has been achieved. The work leading up to this achievement, in relation to the other principle human stem cell studies conducted in this area, will be briefly described. The necessary steps and ideal characteristics of embryonic stem cell-based differentiation to pancreatic b-cells capable of glucose stimulated insulin secretion will be underscored.
Association between Mammographic Breast Density and Breast Cancer Tumor Characteristics (2005)

These results suggest that breast density is related to tumor size, lymph node status, and lymphatic or vascular invasion in screen-detected cancers. Additional studies are needed to address whether these associations are due to density masking the detection of some tumors, a biological relationship, or both.
Flotation Separation of SiC from Wastes in the Silicon Wafer Slicing Process (2006)

シリコン単結晶からのシリコンウエハーのスライシング工程では，SiC粒子をラッピングオイルに混合した潤滑油を用いてワイヤソーによってシリコンが切断されている．シリコン単結晶をスライシングした後，SiCと削られたSiの混合物を含む研削廃液が発生する．SiCおよびSiの粒子径は，それぞれ約10 µmおよび約1 µmであり，これらの重量比は9 : 1程度である．研削廃液中の粒子は，油をフィルタープレスで除去した後に焼成処理すると，SiCとSiO2を含む混合物になる．廃棄物の減容化や環境上の観点から，有価物であるSiCをSiO2から分離・再生することが望ましい．上述の目的に対しては，浮選法が適用できる．陽イオン性界面活性剤であるドデシルトリメチルアンモニウムクロライドおよびトリメチルオクチルアンモニウムクロライドを界面活性剤として用いた．SiCおよびSiO2粒子上への界面活性剤の吸着量が測定された．ドデシルトリメチルアンモニウムクロライド存在下でpH，ガス流速，浮選時間を変化させて，SiCとSiO2の浮選挙動を調べた．あわせて，粗選工程，精選工程および清掃選工程を含む一連の浮選プロセスを適用してSiCの純度と収率について検討を行った．一連の浮選プロセスで得られるSiCの純度および収率は，それぞれ99.7%および96.7%であった．
Initiating and Cancer-Propagating Cells in TEL-AML1 -Associated Childhood Leukemia (2008)

Understanding cancer pathogenesis requires knowledge of not only the specific contributory genetic mutations but also the cellular framework in which they arise and function. Here we explore the clonal evolution of a form of childhood precursor-B cell acute lymphoblastic leukemia that is characterized by a chromosomal translocation generating a TEL-AML1 fusion gene. We identify a cell compartment in leukemic children that can propagate leukemia when transplanted in mice. By studying a monochorionic twin pair, one preleukemic and one with frank leukemia, we establish the lineal relationship between these "cancer-propagating" cells and the preleukemic cell in which the TEL-AML1 fusion first arises or has functional impact. Analysis of TEL-AML1-transduced cord blood cells suggests that TEL-AML1 functions as a first-hit mutation by endowing this preleukemic cell with altered self-renewal and survival properties.
Structural analysis of human apolipoprotein A-I variants. Amino acid substitutions are nonrandomly distributed throughout the apolipoprotein A-I primary structure. (1990)

In the course of an electrophoretic mutation screening program of 32,000 dried blood samples from newborns, 17 genetic variants of apolipoprotein A-I (apoA-I) were found and structurally analyzed. The following defects were identified by the combined use of high performance liquid chromatography, time-of-flight secondary ion mass spectrometry, and sequence analysis: Pro3----Arg (1 x), Pro4----Arg (1 x), Asp89----Glu (1 x), Lys107----0 (4 x), Lys107----Met (2 x), Glu139----Gly (2 x), Glu147----Val (1 x), Pro165----Arg (4 x), and Glu198----Lys (1 x). The distribution of point mutations in the apoA-I gene leading to these 9 and 11 other variants of apoA-I reported previously was statistically analyzed. Substitutions are overrepresented in the 10 amino-terminal amino acids (p less than 0.001, chi 2-test) and in residues 103-177 (p less than 0.025, chi 2-test) or residues 103-198 (p less than 0.05, chi 2-test), respectively. We further noted the following. (i) Prolines were substituted by arginine or histidine residues at a frequency much higher than expected on the basis of random nucleotide substitutions (5 out of 18 "electrically non-neutral" amino acid substitutions, p less than 0.001, chi 2-test). These substitutions are the result of transversions of cytosines contained within stretches of at least 5 consecutive cytosines in the apoA-I gene. The observed hypervariability of the apoA-I amino terminus, therefore, might be caused by a hot spot for mutation formed by the 7 subsequent cytosines in codons 3, 4, and 5. (ii) CpG dinucleotides were overrepresentatively affected by C----T transitions (5 out of 18 electrically nonneutral amino acid substitution, p less than 0.001, chi 2-test). The hypervariability of the apoA-I alpha-helical domain might therefore be caused by CpG dinucleotides predominantly occurring in codons 120-208 of apoA-I (82 out of 125). (iii) Comparison of mutation sites in the human apoA-I gene with sites of nonsynonymous substitutions revealed that amino acid substitutions found in human apoA-I were predominantly localized in areas that were little conserved during mammalian evolution. These regions may therefore represent areas of less structural constraint for the function of apoA-I.
Encoding Electronic Properties by Synthesis of Axial Modulation-Doped Silicon Nanowires (2005)

We describe the successful synthesis of modulation-doped silicon nanowires by achieving pure axial elongation without radial overcoating during the growth process. Scanning gate microscopy shows that the key properties of the modulated structures-including the number, size, and period of the differentially doped regions-are defined in a controllable manner during synthesis, and moreover, that feature sizes to less than 50 nanometers are possible. Electronic devices fabricated with designed modulation-doped nanowire structures demonstrate their potential for lithography-independent address decoders and tunable, coupled quantum dots in which changes in electronic properties are encoded by synthesis rather than created by conventional lithography-based techniques.
Compartmental analysis of technetium-99m-teboroxime kinetics employing fast dynamic SPECT at rest and stress. (1994)

We conclude that quantitative compartmental analysis of 99mTc-teboroxime kinetics provides a sensitive indicator for changes in response to adenosine-induced coronary vasodilation.
Core Sequences and a Cleavage Site Wobble Pair Required for HDV Antigenomic Ribozyme Self-Cleavage (1996)

The secondary structures proposed for the cis-acting hepatitis delta virus (HDV) ribozymes contain four duplex regions, three sequences joining the duplexes and two hairpin loops. The core and active site of the ribozyme could be formed by portions of the joining sequences, J1/4 and J4/2, together with one of the hairpin loops, L3. To establish the core region and define essential bases within this putative active site 28 single base changes at 15 positions were made and tested for effects on ribozyme cleavage. At 14 of the 15 positions all of the changes resulted in detectable decreased rates of cleavage. At seven of the positions one or more of the changes resulted in a 500-fold or greater decrease in the observed rate constant for cleavage. Mutations that resulted in 10(3)-fold effects were found in all three regions hypothesized to form the core. At the cleavage site substitutions of the cytosine 5' of the site of cleavage did not provide strong support for a sequence-specific interaction involving this nucleotide. In contrast, an A-C combination was the most effective substitution for a potential G-U pair 3' of the cleavage site, suggesting a requirement for a wobble pair at that position.
How effective is suffixing? (1991)

The interaction of suffixing algorithms and ranking techniques in retrieval performance, particularly in an online environment, was investigated. Three general purpose suffixing algorithms were used for retrieval on the Cranfield 1400, Medlars, and CACM test collections, with no significant improvement in performance shown for any of the algorithms. A failure analysis suggested three modifications to ranking techniques: variable weighting of term variants, selective stemming depending on query length, and selective stemming depending on term importance. None of these modifications improved performance. Recommendations are made regarding the uses of suffixing in an online environment. © 1991 John Wiley & Sons, Inc.
Novel genetic association of TNF-α-238 and PDCD1-7209 polymorphisms with long-term non-progressive HIV-1 infection (2013)

The novel genetic associations between allelic variants of genes TNF-α-238 and PDCD1-7209 with the LTNP condition underline the importance of host genetic factors in the progression of HIV-1 infection and in immunological preservation.