gebhart/patrepeval huggingface dataset:
Limited reaction processing: Silicon epitaxy (1985)

We introduce a new technique, limited reaction processing, in which radiant heating is used to provide rapid, precise changes in the temperature of a substrate to control surface reactions. This process was used to fabricate thin layers of high quality epitaxial silicon. Abrupt transitions in doping concentration at the epitaxial layer/substrate interface were achieved for undoped films deposited on heavily doped substrates.
sal1 determines the number of aleurone cell layers in maize endosperm and encodes a class E vacuolar sorting protein (2003)

A microscopy-based screen of a large collection of maize Mutator (Mu) transposon lines identified the supernumerary aleurone layers 1-1 (sal1-1) mutant line carrying up to seven layers of aleurone cells in defective kernel endosperm compared with only a single layer in wild-type grains. Normal, well filled endosperm that is homozygous for the sal1-1 mutant allele contains two to three layers of aleurone cells. Cloning of the sal1 gene was accomplished by using Mu tagging, and the identity of the cloned gene was confirmed by isolating an independent sal1-2 allele by reverse genetics. Homozygous sal1-2 endosperm has two to three layers of aleurone cells in normal, well filled grains. In situ hybridization experiments reveal that the sal1 gene is ubiquitously expressed in vegetative as well as zygotic grain tissues, with no difference being detected between aleurone cells and starchy endosperm cells. Northern blot analysis failed to detect the sal1-2 transcript in leaves of homozygous plants, suggesting that the allele is a true sal1 knockout allele. The sal1 gene encodes a homologue of the human Chmp1 gene, a member of the conserved family of the class E vacuolar protein sorting genes implicated in membrane vesicle trafficking. In mammals, CHMP1 functions in the pathway targeting plasma membrane receptors and ligands to lysosomes for proteolytic degradation. Possible roles for the function of the sal1 gene in aleurone signaling, including a defect in endosome trafficking, are discussed.
De novo sterologenesis in the skin. II. Regulation by cutaneous barrier requirements. (1985)

Recent studies suggest: that the epidermis and pilosebaceous epithelium are important sites of de novo sterol synthesis, and that the rate of cutaneous cholesterol synthesis does not change with alterations in circulating sterol levels. Since cutaneous sterols may be important for permeability barrier function, we studied the effect of experimentally altered barrier function on de novo sterologenesis in the epidermal and dermal layers of the skin. Epidermal sterologenesis appeared to be modulated by the skin's barrier requirements because topical detergent and acetone treatment stimulated de novo synthesis of nonsaponifiable lipids in the epidermis, but not in the dermis. Synthetic activity paralleled both the return of barrier function toward normal and the extent of prior damage to the barrier. Moreover, plastic-wrap occlusion of solvent-treated sites simultaneously corrected both the barrier abnormality and normalized sterol synthesis, further linking increased epidermal sterologenesis to barrier requirements. Whereas topical applications of a variety of other topical lipids did not down-regulate synthesis, epicutaneously applied 25-hydroxycholesterol appeared to diminish synthesis. These results suggest that maintenance of barrier function is one purpose of epidermal de novo nonsaponifiable lipid synthesis, and demonstrate further that, despite a lack of low density lipoprotein receptors, epidermis can regulate its lipid-synthetic apparatus in response to certain specific requirements.
Hydroxyl radical cleavage of tRNA in the ribosomal P site. (1992)

Hydroxyl radical is a useful probe of the accessibility of the sugar moiety of nucleic acids to solvent. Here we compare the accessibility of free and ribosome-bound yeast tRNA(Phe), Escherichia coli tRNA(Phe), and E. coli tRNA(Leu2) to attack by hydroxyl radicals generated from Fe(2+)-EDTA. When bound to the P site of 30S ribosomal subunits, a discrete region, corresponding almost precisely to the anticodon stem-loop, is strongly protected; weaker protection is observed in the 3' strand of the D stem and in the variable loop. The protected nucleotides constitute a well-defined substructure, corresponding to the lower half of the anticodon-D loop coaxial arm of the tRNA crystal structure. This result suggests that the 30S P site contains a pocket that becomes inaccessible to the Fe(2+)-EDTA complex when tRNA is bound, whose minimum dimensions can be inferred from the boundaries of the protected region of tRNA. When bound to the P site of 70S ribosomes, the entire tRNA backbone becomes inaccessible to hydroxyl radicals. Since previous studies have shown that virtually the entire footprint of a P-site tRNA on 16S and 23S rRNAs is mimicked by the extremities of the tRNA (the anticodon stem-loop plus the 3'-terminal aminoacyl-pentanucleotide), protection of the entire tRNA was unexpected. We conclude that protection of the elbow of tRNA is due either to interactions with ribosomal proteins or to enclosure in an inaccessible site formed by association of the two ribosomal subunits.
Winged helix domains with unknown function in Hel308 and related helicases (2011)

Hel308 is a superfamily 2 helicase/translocase that is conserved throughout archaea and in some eukaryotes for repair of genotoxic lesions such as ICLs (interstrand DNA cross-links). Atomic structures of archaeal Hel308 have allowed mechanistic insights into ATPase and helicase functions, but have also highlighted structures that currently lack a known function, such as an unexpected WH (winged helix) domain. This domain and similar overall protein structural organization was also identified in other superfamily 2 helicases that process RNA molecules in eukaryotes: Brr2, Mtr4 and Prp43p. We survey the structure of Hel308 with regard to its WH domain in particular and its function(s) in maintaining structural integrity of the overall Hel308 ring structure, and possibly during interactions of Hel308 with other proteins and/or forked DNA.
Liquid–liquid phase separation in supersaturated lysozyme solutions and associated precipitate formation/crystallization (1997)

Using cloud point determinations, the phase boundaries (binodals) for metastable liquid–liquid (L–L) separation in supersaturated hen egg white lysozyme solutions with 3%, 5%, and 7% (w/v) NaCl at pH=4.5 and protein concentrations c between 40 and 400 mg/ml were determined. The critical temperature for the binodal increased approximately linearly with salt concentration. The coexisting liquid phases both remained supersaturated but differed widely in protein concentration. No salt repartitioning was observed between the initial and the two separated liquid phases. After the L–L separation, due to the presence of the high protein concentration phase, crystallization occurred much more rapidly than in the initial solution. At high initial protein concentrations, a metastable gel phase formed at temperatures above the liquid binodal. Both crystal nucleation and gel formation were accelerated in samples that had been cycled through the binodal. Solutions in the gel and L–L regions yielded various types of precipitates. Based on theoretical considerations, previous observations with other proteins, and our experimental results with lysozyme, a generic phase diagram for globular proteins is put forth. A limited region in the (T,c) plane favorable for the growth of protein single crystals is delineated.
A Novel Anti-sTn Monoclonal Antibody 3P9 Inhibits Human Xenografted Colorectal Carcinomas (2012)

The aim of this study is to raise tumor-suppressing monoclonal antibodies (mAbs) against colorectal carcinomas. Here, we generated a novel mAb 3P9, targeted a cancer-associated carbohydrate antigen sialyl-Tn (sTn), which showed significant inhibitory effect on proliferation and migration of sTn cells and tumor growth by inducing apoptosis. We also demonstrated that mAb 3P9 showed higher sensitivity and specificity in immunohistochemistry assay on colonic adenocarcinoma than the broadly used commercial anti-sTn antibody B72.3. These results provide the first evidence that mAb 3P9 has potential applications, not only for diagnosis but also for antibody-based tumor therapy.
A pharmacokinetic perspective on medicament noncompliance (1993)

Clinical Pharmacology and Therapeutics (1993) 54, 242–244; doi:10.1038/clpt.1993.143
Cloning, sequencing, and characterization of multicopy suppressors of a mukB mutation in Escherichia coli (1994)

The mukB gene codes for a 177 kDa protein, which might be a candidate for a force-generating enzyme in chromosome positioning in Escherichia coli. The mukB106 mutant produces normal-sized, anucleate cells and shows a temperature-sensitive colony formation. To identify proteins interacting with the MukB protein, we isolated three multicopy suppressors (msmA, msmB, and msmC) to the temperature-sensitive colony formation of the mukB106 mutation. The msmA gene, which could not suppress the production of anucleate cells, was found to be identical to the dksA gene. The msmB and msmC genes suppressed the production of anucleate cells as well as the temperature-sensitive colony formation. However, none of them could suppress both phenotypes in a mukB null mutation. DNA sequencing revealed that the msmB gene was identical to the cspC gene and that the msmC gene had not been described before. A homology search revealed that the amino acid sequences of both MsmB and MsmC possessed high similarity to proteins containing the cold-shock domain, such as CspA of E. coli and the Y-box binding proteins of eukaryotes; this suggests that MsmB and MsmC might be DNA-binding proteins that recognize the CCAAT sequence. Hence, the msmB and msmC genes were renamed cspC and cspE, respectively. Possible mechanisms for suppression of the mukB106 mutation are discussed.
Efficiency of electrically small antennas combined with matching networks (1977)

The efficiency of an antenna combined with a matching network constructed from elements with finite <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</tex> is determined by applying the principle of conservation of energy. The conditions which must be satisfied to obtain maximum efficiency are examined. An analysis shows that for many electrically small antennas the conditions for maximum efficiency can be met using a simple L section as the matching network. Examples are presented to show the importance of including the matching network in efficiency calculations for electrically small antennas.
Solution‐Processed Metallic Conducting Polymer Films as Transparent Electrode of Optoelectronic Devices (2012)

The conductivity of PEDOT:PSS films was significantly enhanced from 0.3 S cm(-1) to 3065 S cm(-1) through a treatment with dilute sulfuric acids. PEDOT:PSS films with a sheet resistance of 39 Ω sq(-1) and transparency of around 80% at 550 nm are obtained. These PEDOT:PSS films with conductivity and transparency comparable to ITO can replace ITO as the transparent electrode of optoelectronic devices.
Influence of Cyclosporine A on Molecular Interactions in Lyotropic Reverse Hexagonal Liquid Crystals (2010)

We present a dielectric study of H(II) mesophases (H(II)) based on a GMO/tricaprylin/phosphatidylcholine/water system seeded with the peptide Cyclosporine A (CSA). The study covers a frequency range 0.01 Hz to 1 MHz and a temperature range of 293 to 319 K, with a 3 K temperature step. Three dielectric relaxation processes are observed and discussed. This picture is further elucidated by comparison with a dielectric study of the empty H(II) mesophase system, previously published, where the same three processes were involved. A complex picture emerges whereby the CSA is intercalated between the surfactant tails yet protrudes into the interface as well. Whereas the CSA remains hydrophobic, it still influences the relaxation behavior of the GMO head and counterion movement along the interface in a nontrivial manner. The third dipolar species, the tricaprylin molecule, is also influenced by the presence of CSA. A critical temperature T(0) = 307 K is recognized and identified as the dehydration temperature of the surfactant heads. This induces a conformal transition in the CSA, drastically changing its effect on the three dielectric processes evident in the raw data. The implications of this behavior are discussed in detail.
Incomplete processing of progastrin expressed by human colon cancer cells: role of noncarboxyamidated gastrins (1994)

Gastrin is mitogenic for several colon cancers. To assess a possible autocrine role of gastrin in colon cancers, we examined human colon cancer cell lines for expression of gastrin mRNA and various forms of gastrin. Gastrin mRNA was not detected in the majority of colon cancer cell lines by Northern hybridization but was detected in all human colon cancer lines by the sensitive method of reverse transcriptase-polymerase chain reaction (PCR). Gastrin mRNA was quantitated by the competitive PCR method. The majority of cell lines expressed very low levels of gastrin mRNA (< 1-5 copies/cell); only one cell line expressed > 20 copies/cell. The mature carboxyamidated form of gastrin was not detected in any of the cell lines by radioimmunoassay or immunocytochemistry. Results suggested that either gastrin mRNA expressed by colon cancer cells was altered (mutated) or posttranslational processing of progastrin was incomplete. Gastrin cDNA from all the colon cancer cell lines had an identical sequence to the published sequence of human gastrin cDNA. Specific antibodies against precursor forms of gastrin were used, and significant concentrations of nonamidated (glycine-extended) and prepro forms of gastrin were measured in tumor extracts of representative colon cancer cell lines. The presence of precursor forms of gastrin suggested a lack of one or more of the processing enzymes and/or cofactors. Significant concentrations of the processing enzyme (peptidylglycine alpha-amidating monooxygenase) were detected in colon cancer cells by immunocytochemistry. Therefore, lack of other cofactors or enzymes may be contributing to incomplete processing of precursor forms of gastrin, which merits further investigation. Since low levels of gastrin mRNA were expressed by the majority of human colon cancer cell lines and progastrin was incompletely processed, it seems unlikely that gastrin can function as a viable autocrine growth factor for colon cancer cells. High concentrations of glycine-extended gastrin-17 (GG) (> 10(-6) M) were mitogenic for a gastrin-responsive human colon cancer (DLD-1) cell line in vitro. It remains to be seen if GG or other precursor forms of gastrin are similarly mitogenic in vivo, which may then lend credibility to a possible autocrine role of gastrinlike peptides in colon cancers.
Spectral analysis for long-term robotic mapping (2014)

This paper presents a new approach to mobile robot mapping in long-term scenarios. So far, the environment models used in mobile robotics have been tailored to capture static scenes and dealt with the environment changes by means of `memory decay'. While these models keep up with slowly changing environments, their utilization in dynamic, real world environments is difficult. The representation proposed in this paper models the environment's spatio-temporal dynamics by its frequency spectrum. The spectral representation of the time domain allows to identify, analyse and remember regularly occurring environment processes in a computationally efficient way. Knowledge of the periodicity of the different environment processes constitutes the model predictive capabilities, which are especially useful for long-term mobile robotics scenarios. In the experiments presented, the proposed approach is applied to data collected by a mobile robot patrolling an indoor environment over a period of one week. Three scenarios are investigated, including intruder detection and 4D mapping. The results indicate that the proposed method allows to represent arbitrary timescales with constant (and low) memory requirements, achieving compression rates up to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> . Moreover, the representation allows for prediction of future environment states with ~ 90% precision.
Vitamin A Metabolites Induce Gut-Homing FoxP3+ Regulatory T Cells (2007)

In this study, we report a novel biological function of vitamin A metabolites in conversion of naive FoxP3- CD4+ T cells into a unique FoxP3+ regulatory T cell subset (termed "retinoid-induced FoxP3+ T cells") in both human and mouse T cells. We found that the major vitamin A metabolite all-trans-retinoic acid induces histone acetylation at the FoxP3 gene promoter and expression of the FoxP3 protein in CD4+ T cells. The induction of retinoid-induced FoxP3+ T cells is mediated by the nuclear retinoic acid receptor alpha and involves T cell activation driven by mucosal dendritic cells and costimulation through CD28. Retinoic acid can promote TGF-beta1-dependent generation of FoxP3+ regulatory T cells but decrease the TGF-beta1- and IL-6-dependent generation of inflammatory Th17 cells in mouse T cells. Retinoid-induced FoxP3+ T cells can efficiently suppress target cells and, thus, have a regulatory function typical for FoxP3+ T cells. A unique cellular feature of these regulatory T cells is their high expression of gut-homing receptors that are important for migration to the mucosal tissues particularly the small intestine. Taken together, these results identify retinoids as positive regulatory factors for generation of gut-homing FoxP3+ T cells.
Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans (2001)

Double-stranded RNAs can suppress expression of homologous genes through an evolutionarily conserved process named RNA interference (RNAi) or post-transcriptional gene silencing (PTGS). One mechanism underlying silencing is degradation of target mRNAs by an RNP complex, which contains approximately 22 nt of siRNAs as guides to substrate selection. A bidentate nuclease called Dicer has been implicated as the protein responsible for siRNA production. Here we characterize the Caenorhabditis elegans ortholog of Dicer (K12H4.8; dcr-1) in vivo and in vitro. dcr-1 mutants show a defect in RNAi. Furthermore, a combination of phenotypic abnormalities and RNA analysis suggests a role for dcr-1 in a regulatory pathway comprised of small temporal RNA (let-7) and its target (e.g., lin-41).
The role of the Y chromosome in male infertility (2001)

It was suggested by Ronald Fisher in 1931 that genes that benefit the male (including those required for spermatogenesis) would accumulate on the Y chromosome. Following the discovery that microdeletions of the Y chromosome were associated with diverse spermatogenic phenotypes, at least three intervals that contain one or more genes controlling male germ-cell differentiation have been identified in humans. These intervals, named AZFa , AZFb and AZFc , have been mapped, cloned and examined in detail for the presence of functional genes. In this review, I have discussed the genes that map to the AZF intervals and the evidence indicating which ones are the most likely candidates underlying Y-linked male infertility. In addition, I have considered the analysis of key intervals on the mouse Y chromosome, where it provides comparative data supporting the role of a candidate gene in an infertility phenotype.
Finding maximal link disjoint paths in a multigraph (2002)

The problem of fast restoration of lost transport facilities between nodes of the growing high-capacity fiber network has recently emerged as a principle concern of both network operators and their customers. At the same time, there is increasing use of intelligent cross-connects in the telephone network. It should be possible to use the computing and connection capacity of cross-connects to recover from facility outages by enabling the cross-connects to automatically reroute traffic in the event of facility damage or loss. An algorithm by which a network node might be able to establish as many paths as required (up to the theoretical maximum) between itself and another node with which it has lost part or all of its directly connecting transmission facilities is presented. The algorithm has been simulated on a Sun 3/60 workstation and is able to find all four paths of the example network in under one second.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Deep Contextualized Word Representations (2018)

Matthew E. Peters, Mark Neumann, Mohit Iyyer, Matt Gardner, Christopher Clark, Kenton Lee, Luke Zettlemoyer. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers). 2018.
WW domain containing oxidoreductase gene expression is altered in non-small cell lung cancer. (2003)

WWOX (WW domain containing oxidoreductase), a putative tumor suppressor gene that maps to the common fragile site FRA16D on chromosome 16q23.3-24.1, is altered in breast, esophageal, and ovarian cancer. Because the FRA3B/FHIT locus at 3p14.2 is a preferential target for genetic changes caused by tobacco smoke, we intended to evaluate the status of the FRA16D/WWOX gene in non-small cell lung cancer; we have analyzed 27 paired normal and tumor lung tissues and 8 lung cancer cell lines for WWOX alterations by reverse transcriptase-PCR, loss of heterozygosity, and mutation analysis. Transcripts missing WWOX exons were detected in 7 primary tumors (7 of 27; 25.9%) and 5 of 8 cell lines. In addition, loss of heterozygosity at the WWOX locus was observed in 10 primary tumors (10 of 27; 37.0%). We conclude that WWOX alterations occur in a significant fraction of lung cancers and may contribute to the pathogenesis of non-small cell lung cancer.
Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. (1993)

The accuracy by which organisms duplicate their DNA is of considerable interest. At least three mechanisms operate, serially, to secure high fidelity: base selection, exonucleolytic proofreading, and postreplicative mismatch correction. To obtain insights into the efficiency and specificity of these steps in the bacterium Escherichia coli, we have performed DNA sequence analysis of mutations occurring in the bacterial lacI gene in a series of strains genetically disabled in one or more of these error avoidance pathways. The base selection efficiency was estimated from mutagenesis occurring in a mutDmutL strain, which is deficient in both proofreading (mutD5) and mismatch repair (mutL). The proofreading efficiency was derived comparing the mutD5 mutL strain to the mismatch repair-deficient mutL strain. The efficiency of mismatch repair was derived comparing the mutL strain to the wild-type strain. The results show that base selection discriminates against errors by 200,000-2,000,000-fold, proofreading by 40-200-fold, and mismatch repair by 20-400-fold, each depending on the type of error. Base selection and proofreading act more strongly against transversions than transitions, whereas mismatch repair does the opposite. The data are based on 866 sequenced lacI mutations in a target that allows the scoring of at least 127 different mutations in 76 distinct DNA sequence contexts in vivo. They may therefore have general significance.