gebhart/patrepeval huggingface dataset:
Analysis of xylem formation in pine by cDNA sequencing (1998)

Secondary xylem (wood) formation is likely to involve some genes expressed rarely or not at all in herbaceous plants. Moreover, environmental and developmental stimuli influence secondary xylem differentiation, producing morphological and chemical changes in wood. To increase our understanding of xylem formation, and to provide material for comparative analysis of gymnosperm and angiosperm sequences, ESTs were obtained from immature xylem of loblolly pine (Pinus taeda L.). A total of 1,097 single-pass sequences were obtained from 5' ends of cDNAs made from gravistimulated tissue from bent trees. Cluster analysis detected 107 groups of similar sequences, ranging in size from 2 to 20 sequences. A total of 361 sequences fell into these groups, whereas 736 sequences were unique. About 55% of the pine EST sequences show similarity to previously described sequences in public databases. About 10% of the recognized genes encode factors involved in cell wall formation. Sequences similar to cell wall proteins, most known lignin biosynthetic enzymes, and several enzymes of carbohydrate metabolism were found. A number of putative regulatory proteins also are represented. Expression patterns of several of these genes were studied in various tissues and organs of pine. Sequencing novel genes expressed during xylem formation will provide a powerful means of identifying mechanisms controlling this important differentiation pathway.
Timed-sequential induction therapy improves postremission outcome in acute myeloid leukemia: a report from the Children's Cancer Group (1996)

Timed sequencing of cycles of induction chemotherapy in acute myeloid leukemia (AML) has been proposed as a way to achieve maximal leukemic cell kill through recruitment and synchronization of residual neoplastic cells. Furthermore, whether intensive induction therapy should be continued in the presence of profound myelosuppression is an important question. The Children's Cancer Group (CCG) conducted a prospective randomized trial in which 589 patients with AML were randomized at diagnosis to one of two induction approaches involving a 4-day cycle of five active chemotherapeutic agents, with the second cycle administered either 10 days after the first cycle, despite low or dropping blood counts (intensive timing), or 14 days or later from the beginning of the first cycle, depending on bone marrow status (standard timing). All patients achieving remission received a total of four cycles of induction therapy. They were then allocated to allogeneic bone marrow transplantation (BMT) if a compatible family donor was present or randomized to aggressive nonmyeloablative therapy or to myeloablative therapy with purged autologous BMT rescue. The three postremission arms remain coded. Induction success and median days to complete induction were similar for the 295 patients randomized to the intensive timing arm (75%, 99 days) compared with the 294 patients randomized to the standard timing arm (70%, 105 days; P = .18 for remission). However, a marked improvement in outcome was demonstrated in patients randomized to the intensive timing arm, with an actuarial event-free survival at 3 years of 42% +/- 7% (95% confidence interval [CI]) versus 27% +/- 6% for patients on the standard timing arm (P = .0005). Disease-free survival results at 3 years from the end of induction were superior for patients receiving intensively timed induction therapy (N = 211), 55% +/- 9% versus 37% +/- 9% for standard timing patients (N = 195, P = .0002), with a median follow-up from achieving remission of 28 months. Superior results were documented for patients receiving intensive timing irrespective of the postremission therapy to which they were allocated. Intensively timed induction therapy for patients with AML markedly improves event-free survival, even for patients undergoing myeloablative therapy with BMT rescue. Without controlling for the type of induction therapy received, results of various BMT studies in AML comparing different preparative regimens will be difficult to interpret.
Quantum limits on noise in linear amplifiers (1982)

How much noise does quantum mechanics require a linear amplifier to add to a signal it processes? An analysis of narrow-band amplifiers (single-mode input and output) yields a fundamental theorem for phase-insensitive linear amplifiers; it requires such an amplifier, in the limit of high gain, to add noise which, referred to the input, is at least as large as the half-quantum of zero-point fluctuations. For phase-sensitive linear amplifiers, which can respond differently to the two quadrature phases ("$cos\ensuremath{\omega}t$" and "$sin\ensuremath{\omega}t$"), the single-mode analysis yields an amplifier uncertainty principle---a lower limit on the product of the noises added to the two phases. A multimode treatment of linear amplifiers generalizes the single-mode analysis to amplifiers with nonzero bandwidth. The results for phase-insensitive amplifiers remain the same, but for phase-sensitive amplifiers there emerge bandwidth-dependent corrections to the single-mode results. Specifically, there is a bandwidth-dependent lower limit on the noise carried by one quadrature phase of a signal and a corresponding lower limit on the noise a high-gain linear amplifier must add to one quadrature phase. Particular attention is focused on developing a multimode description of signals with unequal noise in the two quadrature phases.
Infection dynamics in a traveller with persistent shedding of Zika virus RNA in semen for six months after returning from Haiti to Italy, January 2016 (2016)

We describe the dynamics of Zika virus (ZIKV) infection in a man in his early 40s who developed fever and rash after returning from Haiti to Italy, in January 2016. Follow-up laboratory testing demonstrated detectable ZIKV RNA in plasma up to day 9 after symptom onset and in urine and saliva up to days 15 and 47, respectively. Notably, persistent shedding of ZIKV RNA was demonstrated in semen, still detectable at 181 days after onset.
Bronchioloalveolar Pathologic Subtype and Smoking History Predict Sensitivity to Gefitinib in Advanced Non–Small-Cell Lung Cancer (2004)

Our data suggest that individuals in whom gefitinib is efficacious are more likely to have adenocarcinomas of the bronchioloalveolar subtype and to be never smokers. These observations may provide clues to mechanisms determining sensitivity to this agent and suggest that NSCLC has a different biology in patients who never smoked and those with bronchioloalveolar carcinoma.
INTERLEUKIN-1 MEDIATES INCREASED PLASMA LEVELS OF EICOSANOIDS AND CYTOKINES IN PATIENTS WITH SEPSIS SYNDROME (1995)

The purpose of this was to study evaluate the effects of interleukin-1 (IL-1) inhibition by human recombinant IL-1 receptor antagonist (IL-1ra) on plasma prostaglandin, leukotriene, and cytokine levels in sepsis syndrome. As part of a multisite, prospective, randomized, double-blind, placebo-controlled clinical trial, 19 septic patients received IL-1ra in a 100 mg bolus followed by 2.0 mg/kg/h i.v. for 72 h (n = 10) or placebo (n = 9). Plasma thromboxane B2 (TXB2), prostaglandin 6-keto-F1 alpha (PGI), leukotriene B4 (LTB4), leukotrienes C4D4E4 (LTC4D4E4), IL-1 beta, IL-6, and tumor necrosis factor alpha (TNF) were measured by ELISA before study drug infusion (baseline) and at 24, 48, 72, and 96 h after the beginning of the study drug infusion. Differences between placebo and IL-1-ra for plasma LTB4 and TNF were not significant. Plasma TXB2, PGI, LTC4D4E4, and IL-6, expressed as % baseline, were significantly lower in patients receiving IL-1ra than in the placebo group (p < .05), while plasma IL-1 was increased significantly. IL-1 may be a necessary mediator of increased circulating PGI, TXB2, LTC4D4E4, and IL-6 levels in patients with sepsis syndrome. Plasma IL-1 is increased with infusion of IL-1ra. The clinical significance of IL-1 in modifying circulating eicosanoid and cytokine concentrations in clinical sepsis is not clear from the data.
Thymic Selection Generates a Large T Cell Pool Recognizing a Self-Peptide in Humans (2002)

The low frequency of self-peptide-specific T cells in the human preimmune repertoire has so far precluded their direct evaluation. Here, we report an unexpected high frequency of T cells specific for the self-antigen Melan-A/MART-1 in CD8 single-positive thymocytes from human histocompatibility leukocyte antigen-A2 healthy individuals, which is maintained in the peripheral blood of newborns and adults. Postthymic replicative history of Melan-A/MART-1-specific CD8 T cells was independently assessed by quantifying T cell receptor excision circles and telomere length ex vivo. We provide direct evidence that the large T cell pool specific for the self-antigen Melan-A/MART-1 is mostly generated by thymic output of a high number of precursors. This represents the only known naive self-peptide-specific T cell repertoire directly accessible in humans.
Serum concentrations of free and total insulin‐like growth factor‐I, IGF binding proteins ‐1 and‐3 and IGFBP‐3 protease activity in boys with normal or precocious puberty (1996)

We conclude that easily dissociable and ultrafiltrated free IGF-I serum levels are increased in boys with normal and precocious puberty and suggest that the increased free IGF-I serum concentration in puberty primarily reflects changes in total concentrations of IGF-I and IGFBPs secondary to increased GH secretion, but that it is not influenced by changes in IGFBP-3 proteolysis.
Transfer of a dominant-acting tumor-inducing oncogene from human prostatic carcinoma cells to cloned rat embryo fibroblast cells by DNA-transfection. (1992)

The mechanism by which normal human prostate cells develop into prostatic carcinoma cells is not presently known. In the present study we have tested the hypothesis that specific prostatic carcinomas develop as a consequence of activation of a cellular gene(s) with transforming and tumorigenic potential. To test this possibility, high molecular weight DNA was extracted from the human prostatic carcinoma cell line, LNCaP, and cotransfected with a dominant acting neomycin resistance gene, pSV2-neo, into a subclone of Fischer rat embryo fibroblast (CREF) cells, CREF-Trans 6, and NIH-3T3 cells. Cells were selected for growth in G418 and pooled resistant colonies, which were morphologically normal, were injected subcutaneously into athymic nude mice. Tumors developed in several of the animals inoculated with LNCaP DNA-transfected CREF-Trans 6 cells and they were established in monolayer culture. In contrast, no tumors developed in nude mice injected with untransfected CREF-Trans 6 cells, pSV2-neo transfected CREF-Trans 6 cells or LNCaP plus pSV2-neo DNA-transfected NIH-3T3 cells. DNA from the first cycle tumor-derived CREF-Trans 6 cell lines, which were morphologically transformed in monolayer culture, was cotransfected with pSV2-neo a second time into CREF-Trans 6 cells and transfected cells, which were still morphologically normal, were injected into nude mice. Tumors developed in animals and they were again established in tissue culture. Secondary transfectants isolated from animals were morphologically transformed and grew with high efficiency in agar. Both primary and secondary LNCaP-transfected-nude mouse tumor derived-CREF-Trans 6 cells contained human repetitive (Alu) sequences. Although the pattern of Alu integration in the tumor derived CREF-Trans 6 cells were different for different tumors, both primary and secondary tumors contained a single apparently common-sized Alu fragment. The present study indicates that the human prostatic carcinoma cell line, LNCaP, contains a dominant-acting tumor-inducing oncogene which does not induce morphological transformation of CREF-Trans 6 or NIH-3T3 cells in monolayer culture. In addition, the CREF-Trans 6 cell line can detect this tumor-inducing gene function, whereas this activity is not observed in DNA-transfected NIH-3T3 cells.
Endothal and cantharidin analogs: relation of structure to herbicidal activity and mammalian toxicity (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEndothal and cantharidin analogs: relation of structure to herbicidal activity and mammalian toxicityMasafumi Matsuzawa, Michael J. Graziano, and John E. CasidaCite this: J. Agric. Food Chem. 1987, 35, 5, 823–829Publication Date (Print):September 1, 1987Publication History Published online1 May 2002Published inissue 1 September 1987https://pubs.acs.org/doi/10.1021/jf00077a045https://doi.org/10.1021/jf00077a045research-articleACS PublicationsRequest reuse permissionsArticle Views345Altmetric-Citations43LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
5-Methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation. (1995)

Methylation of cytosine residues in DNA plays an important role in regulating gene expression during vertebrate embryonic development. Conversely, disruption of normal patterns of methylation is common in tumors and occurs early in progression of some human cancers. In vertebrates, it appears that the same DNA methyltransferase maintains preexisting patterns of methylation during DNA replication and carries out de novo methylation to create new methylation patterns. There are several indications that inherent signals in DNA structure can act in vivo to initiate or block de novo methylation in adjacent DNA regions. To identify sequences capable of enhancing de novo methylation of DNA in vitro, we designed a series of oligodeoxyribonucleotide substrates with substrate cytosine residues in different sequence contexts. We obtained evidence that some 5-methylcytosine residues in these single-stranded DNAs can stimulate de novo methylation of adjacent sites by murine DNA 5-cytosine methyltransferase as effectively as 5-methylcytosine residues in double-stranded DNA stimulate maintenance methylation. This suggests that double-stranded DNA may not be the primary natural substrate for de novo methylation and that looped single-stranded structures formed during the normal course of DNA replication or repair serve as "nucleation" sites for de novo methylation of adjacent DNA regions.
Synthetic Studies on Pyrroloquinolines. I. Syntheses of 2, 3-Dihydro-1H-pyrrolo [2, 3-<I>b</I>] quinoline Derivatives (1972)

2, 3-Dihydro-4-hydroxy-1H-pyrrolo [2, 3-b] quinolines (III) were prepared by reactions of 4-chloro-2, 3-dihydrofuro [3, 2-c] quinolines (1) with ammonia or primary amines. 4-Chloro-2, 3-dihydro-1H-pyrrolo [2, 3-b] quinolines (VIII) were also prepared by the same amination of 2, 4-dichloro-3-(β-chloroethyl)-quinolines (II) accompanied with various minor products.The structures of these compounds were mainly confirmed by chemical methods.
Location of crossovers during gene targeting with insertion and replacement vectors. (1993)

Gene targeting was used to introduce nonselectable genetic changes into chromosomal loci in mouse embryo-derived stem cells. The nonselectable markers were linked to a selectable marker in both insertion- and replacement-type vectors, and the transfer of the two elements to the Hprt locus was assayed. When insertion vectors were used as substrates, the frequency of transfer was highly dependent upon the distance between the nonselectable marker and the double-strand break in the vector. A marker located close to the vector ends was frequently lost, suggesting that a double-strand gap repair activity is involved in vector integration. When replacement vectors were used, cotransfer of a selectable marker and a nonselectable marker 3 kb apart was over 50%, suggesting that recombination between vector and target often occurs near the ends of the vector. To illustrate the use of replacement vectors to transfer specific mutations to the genome, we describe targeting of the delta F508 mutation to the CFTR gene in mouse embryo-derived stem cells.
Evaluation of the eZono 4000 with eZGuide for ultrasound-guided procedures (2014)

Ultrasound-guided procedures are increasingly common in a variety of acute care settings, such as the operating room, critical care unit and emergency room. However, accurate judgment of needle tip position using traditional ultrasound technology is frequently difficult, and serious injury can result from inadvertently advancing beyond or through the target. Needle navigation is a recent innovation that allows the clinician to visualize the needle position and trajectory in real time as it approaches the target. A novel ultrasound machine has recently been introduced that is portable and designed for procedural guidance. The eZono 4000™ features an innovative needle navigation technology that is simple to use and permits the use of a wide range of commercially available needles, avoiding the inconvenience and cost of proprietary equipment. This article discusses this new ultrasound machine in the context of other currently available ultrasound machines featuring needle navigation.
A comparison of profile hidden Markov model procedures for remote homology detection (2002)

Profile hidden Markov models (HMMs) are amongst the most successful procedures for detecting remote homology between proteins. There are two popular profile HMM programs, HMMER and SAM. Little is known about their performance relative to each other and to the recently improved version of PSI-BLAST. Here we compare the two programs to each other and to non-HMM methods, to determine their relative performance and the features that are important for their success. The quality of the multiple sequence alignments used to build models was the most important factor affecting the overall performance of profile HMMs. The SAM T99 procedure is needed to produce high quality alignments automatically, and the lack of an equivalent component in HMMER makes it less complete as a package. Using the default options and parameters as would be expected of an inexpert user, it was found that from identical alignments SAM consistently produces better models than HMMER and that the relative performance of the model-scoring components varies. On average, HMMER was found to be between one and three times faster than SAM when searching databases larger than 2000 sequences, SAM being faster on smaller ones. Both methods were shown to have effective low complexity and repeat sequence masking using their null models, and the accuracy of their E-values was comparable. It was found that the SAM T99 iterative database search procedure performs better than the most recent version of PSI-BLAST, but that scoring of PSI-BLAST profiles is more than 30 times faster than scoring of SAM models.
Characterization of a pollen‐specific cDNA from sunflower encoding a zinc finger protein. (1992)

Summary We have isolated, via differential hybridization screening of a floral cDNA library from sunflower, a cDNA clone that hybridizes to a 1100 nucleotide‐long mRNA found exclusively in mature pollen grains. The cDNA encodes a 219 amino acid‐long polypeptide containing two potential zinc fingers alternating with two basic domains. A similar organization is found in the erythroid‐specific transcription factor Eryf1 from chicken and its murine homolog GF‐1. The C‐terminus of the protein contains a sixfold repeat of the pentapeptide sequence (S,T,A)(E,D)TQN. These features suggest that the SF3 protein is a transcription factor required for the expression of late pollen genes. The SF3 gene is a member of a multicopy gene family. A genomic copy of the gene has been isolated and sequenced; it is split by four short, AT‐rich introns.
Nutrition of Myxococcus xanthus, a fruiting myxobacterium (1978)

The minimal requirements for vegetative growth of Myxococcus xanthus have been sought. Isoleucine, leucine, and valine were required, and vitamin B12 was needed for the synthesis of methionine. Pyruvate was an excellent energy source and an efficient source of cellular carbon. Acetate, aspartate, glutamate, and most tricarboxylic acid cycle intermediates could also be utilized, but were less efficient sources of carbon and energy than was pyruvate. Many mono- and disaccharides were tested, but, in agreement with earlier results, none served as carbon-energy sources. A minimal medium (A1) has been devised that includes the essential amino acids and vitamin B12, with pyruvate and aspartate as carbon-energy sources. In this medium, M. xanthus could propagate indefinitely, and on it vegetative cells formed colonies with greater than 75% efficiency; hence, it is likely that no organic cofactors other than those present in A1 are required in more than trace amounts.
High‐resolution time of arrival estimation for OFDM‐based transceivers (2015)

A novel algorithm for time of arrival (TOA) estimation for OFDM‐based transceivers is presented. The algorithm processes the sampled baseband signal to obtain a high‐resolution estimate of the TOA of the OFDM symbol. In the first step, the algorithm obtains a sample‐resolution estimate of the TOA by finding the peak of the absolute value of the cross‐correlation of the in‐phase and quadrature received signals with the known transmitted symbol. In the second step, the algorithm refines this estimate to sub‐sample resolution by estimating the phase delay of the received signal based on the gradient of a linear fit to the phase difference between the transmitted and received sub‐carriers (in the frequency domain). The algorithm was applied to the long training sequence (LTS) symbol of the IEEE wireless local area network (WLAN) 802.11 g preamble. In real‐world experiments, the algorithm was found to achieve a mean TOA estimation error of 49 cm in a low multi‐path line‐of‐sight environment for ranges of 1–7 m.
Human computer interactions using language based technology (2002)

Spoken language offers an attractive alternative for human computer interface, since speech is the most natural, efficient, flexible, and economical means of communication among humans. To provide this interface, however, speech recognition technology must be combined with natural language processing technology, so that the verbal input can not only be recognized, but also understood, and appropriate actions can be taken. This paper provides an overview of recent research in spoken language understanding, focusing on the activities in the United States sponsored by the Advanced Research Projects Agency of the Department of Defense. Some of the future research directions are also summarized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optical Fiber Amplifiers: Design and System Applications (1993)

Manufacturing of active fibers properties of rare-earth ions in glass host materials characterization measurements for rare-earth-doped fibers basics of 1550-nm fiber amplifiers optimization of er-doped fiber pump wavelength choice for 1550-nm amplifiers improved 1550-nm amplifiers in advanced configurations the 1300-nm amplifiers in advanced configurations the 1300-nm fiber amplifier fiber amplifiers in digital direct detection systems distributed fiber amplifiers amplifiers for AM-modulated systems.