gebhart/patrepeval huggingface dataset:
Identification of Sequence Motifs Causing Band Compressions on Human cDNA Sequencing (1996)

In order to characterize DNA sequences leading to band compressions in an automated dideoxy-DNA sequencing system which uses fluorescent dye primers, we compiled DNA sequences at compression sites from accumulated sequence data of human cDNAs (about 205 kb in total length). The results clearly showed that almost all the 3'-end regions at the compression sites (> 98%) carried two types of common sequence motifs. The predominant one (about 68%) contained a sequence of 5'-Y'GN1-2AR'-3' (Y' and R': pyrimidine and purine residues capable of base pairing). The remainder (about 32%) carried a hairpin motif with a relatively stable GC-rich stem (> or = 3 bp) connected by a loop consisting of 3 or 4 nucleotides. The occurrence of compressions at these motif sites was further confirmed by using synthetic DNAs with random sequences (about 58 kb in total length). Since DNA sequences at compression sites analyzed so far shared either of the type of motifs in the sequencing system employed here, it was possible to predict the nucleotide residue to be located at a compression site by carefully checking the sequence preceding the site.
Expression of genes transferred into monocot and dicot plant cells by electroporation. (1985)

We have developed a general method for electrically introducing DNA into plant cells. Gene transfer occurs when a high-voltage electric pulse is applied to a solution containing protoplasts and DNA. Carrot protoplasts were used as a model system to optimize gene-transfer efficiency, which was measured 24-48 hr after electroporation by the amount of chloramphenicol acetyltransferase activity resulting from the expression of the introduced chimeric plasmids. Gene-transfer efficiency increased with the DNA concentration and was affected by the amplitude and duration of the electric pulse as well as by the composition of the electroporation medium. Our optimized gene-transfer conditions were effective when applied to tobacco and maize protoplasts, demonstrating that the method is applicable to both monocot and dicot protoplasts.
Use of contexts in language model interpolation and adaptation (2009)

Language models (LMs) are often constructed by building multiple individual component models that are combined using context independent interpolation weights. By tuning these weights, using either perplexity or discriminative approaches, it is possible to adapt LMs to a particular task. This paper investigates the use of context dependent weighting in both interpolation and test-time adaptation of language models. Depending on the previous word contexts, a discrete history weighting function is used to adjust the contribution from each component model. As this dramatically increases the number of parameters to estimate, robust weight estimation schemes are required. Several approaches are described in this paper. The first approach is based on MAP estimation where interpolation weights of lower order contexts are used as smoothing priors. The second approach uses training data to ensure robust estimation of LM interpolation weights. This can also serve as a smoothing prior for MAP adaptation. A normalized perplexity metric is proposed to handle the bias of the standard perplexity criterion to corpus size. A range of schemes to combine weight information obtained from training data and test data hypotheses are also proposed to improve robustness during context dependent LM adaptation. In addition, a minimum Bayes' risk (MBR) based discriminative training scheme is also proposed. An efficient weighted finite state transducer (WFST) decoding algorithm for context dependent interpolation is also presented. The proposed technique was evaluated using a state-of-the-art Mandarin Chinese broadcast speech transcription task. Character error rate (CER) reductions up to 7.3% relative were obtained as well as consistent perplexity improvements.
Deficiency of lymphocyte function-associated antigen 3 (LFA-3) in paroxysmal nocturnal hemoglobinuria. Functional correlates and evidence for a phosphatidylinositol membrane anchor. (1987)

Lymphocyte function-associated antigen 3 (LFA-3) is a widely distributed cell surface glycoprotein that binds to the T lymphocyte CD2 surface glycoprotein. This interaction mediates CTL-target cell conjugate formation and adhesion of thymocytes to thymic epithelial cells. CD2 is also the E rosette receptor of T lymphocytes and mediates rosetting with autologous E by binding to LFA-3. We describe deficient expression of LFA-3 on E from paroxysmal nocturnal hemoglobinuria (PNH) patients. PNH is an acquired defect affecting phosphatidylinositol-anchored membrane proteins, of which decay-accelerating factor (DAF) is most important in the clinical symptoms of PNH. LFA-3-negative, weakly positive, and positive populations were found among PNH E. There was a good correlation with DAF deficiency. PNH E exhibited decreased binding of 125I-CD2 and rosetting with a human T lymphoma cell line. PNH E readily incorporated purified LFA-3, restoring LFA-3 expression and the CD2 binding and rosetting activity to normal levels. The expression of DAF was not restored after the incorporation of purified LFA-3 into PNH E, showing that LFA-3 and DAF are different molecules. Phosphatidylinositol-specific phospholipase C (PIPLC) treatment of a B lymphoma cell line released 35% of the cell surface LFA-3 and 62% of DAF. LFA-3 on E was resistant to PIPLC. However, when LFA-3 purified from human E was reconstituted in sheep E or human E and subjected to PIPLC treatment, 40-50% of LFA-3 was released from the cell membrane. The results show that LFA-3 is attached to the cell membrane by a phosphatidylinositol glycolipid moiety, and confirm previous findings (37-41) that LFA-3 is a cell adhesion molecule that mediates adhesion by interacting with CD2 antigen.
Speckle reduction in optical coherence tomography by matrix completion using bilateral random projection (2014)

Speckle noise is problematic in optical coherence tomography (OCT) and often obscures the structure details. In this paper, we propose a new method to reduce speckle noise from multiply scanned OCT slices. The proposed method registers the OCT scans using a global alignment followed by a local alignment based on global and local motion estimation. Then low rank matrix completion using bilateral random projection is utilized to estimate the noise and recover the clean image. Experimental results show that the proposed method archives average contrast to noise ratio 14.90, better than 13.78 by the state-of-the-art method used in current OCT machines. The technology can be embedded into current OCT machines to enhance the image quality.
THE PINEAL GLAND AND MELATONIN: Molecular and Pharmacologic Regulation (1999)

The pineal gland expresses a group of proteins essential for rhythmic melatonin production. This pineal-specific phenotype is the consequence of a temporally and specially controlled program of gene expression. Understanding of pineal circadian biology has been greatly facilitated in recent years by a number of molecular studies, including the cloning of N-acetyltransferase, the determination of the in vivo involvement of the cAMP-inducible early repressor in the regulation of N-acetyltransferase, and the identification of a pineal transcriptional regulatory element and its interaction with the cone-rod homeobox protein. Likewise, appreciation the physiological roles of melatonin has increased dramatically with the cloning and targeted knockout of melatonin receptors. With these molecular tools in hand, we can now address more specific questions about how and why melatonin is made in the pineal at night and about how it influences the rest of the body.
Tetramer visualization of gut-homing gluten-specific T cells in the peripheral blood of celiac disease patients (2007)

Tetramers of MHC-peptide complexes are used for detection and characterization of antigen-specific T cell responses, but they require knowledge about both antigenic peptide and the MHC restriction element. The successful application of these reagents in human diseases involving CD4+ T cells is limited. Celiac disease, an intestinal inflammation driven by mucosal CD4+ T cells recognizing wheat gluten peptides in the context of disease-associated HLA-DQ molecules, is an ideal model to test the potential clinical use of these reagents. We investigated whether gluten-specific T cells can be detected in the peripheral blood of celiac disease patients using DQ2 tetramers. Nine DQ2+ patients and six control individuals on a gluten-free diet were recruited to the study. Participants consumed 160 g of gluten-containing bread daily for 3 days. After bread-challenge, gluten-specific T cells were detectable in the peripheral blood of celiac patients but not controls both directly by tetramer staining and indirectly by enzyme-linked immunospot. These T cells expressed the beta(7) integrin indicative of gut-homing properties. Most of the cells had a memory phenotype, but many other phenotypic markers showed a heterogeneous pattern. Tetramer staining of gluten-specific T cells has the potential to be used for diagnosis of celiac disease.
Non-Invasive Prenatal Chromosomal Aneuploidy Testing - Clinical Experience: 100,000 Clinical Samples (2014)

NIPT has been commercially offered for just over 2 years and the clinical use by patients and clinicians has increased significantly. The risks associated with invasive testing have been substantially reduced by providing another assessment of aneuploidy status in high-risk patients. The accuracy and NIPT assay positivity rate are as predicted by clinical validations and the test demonstrates improvement in the current standard of care.
Engineered Recombinant Peanut Protein and Heat-Killed Listeria monocytogenes Coadministration Protects Against Peanut-Induced Anaphylaxis in a Murine Model (2003)

Peanut allergy (PNA) is the major cause of fatal and near-fatal anaphylactic reactions to foods. Traditional immunotherapy using peanut (PN) protein is not an option for PNA therapy because of the high incidence of adverse reactions. We investigated the effects of s.c. injections of engineered (modified) recombinant PN proteins and heat-killed Listeria monocytogenes (HKLM) as an adjuvant on anaphylactic reactions in a mouse model of PN allergy. PN-allergic C3H/HeJ mice were treated s.c. with a mixture of the three major PN allergens and HKLM (modified (m)Ara h 1-3 plus HKLM). The effects on anaphylactic reactions following PN challenge and the association with Ab levels and cytokine profiles were determined. Although all mice in the sham-treated groups exhibited anaphylactic symptoms with a median symptom score of 3, only 31% of mice in the mAra h 1-3 plus HKLM group developed mild anaphylaxis, with a low median symptom score of 0.5. Alterations in core body temperature, bronchial constriction, plasma histamine, and PN-specific IgE levels were all significantly reduced. This protective effect was markedly more potent than in the mAra h 1-3 protein alone-treated group. HKLM alone did not have any protective effect. Reduced IL-5 and IL-13, and increased IFN-gamma levels were observed only in splenocytes cultures from mAra h 1-3 plus HKLM-treated mice. These results show that immunotherapy with modified PN proteins and HKLM is effective for treating PN allergy in this model, and may be a potential approach for treating PNA.
Dendroscope: An interactive viewer for large phylogenetic trees (2007)

Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets.
Targeted disruption of the surfactant protein B gene disrupts surfactant homeostasis, causing respiratory failure in newborn mice. (1995)

Surfactant protein B (SP-B) is an 8.7-kDa, hydrophobic protein that enhances the spreading and stability of surfactant phospholipids in the alveolus. To further assess the role of SP-B in lung function, the SP-B gene was disrupted by homologous recombination in murine mouse embryonic stem cells. Mice with a single mutated SP-B allele (+/-) were unaffected, whereas homozygous SP-B -/- offspring died of respiratory failure immediately after birth. Lungs of SP-B -/- mice developed normally but remained atelectatic in spite of postnatal respiratory efforts. SP-B protein and mRNA were undetectable and tubular myelin figures were lacking in SP-B -/- mice. Type II cells of SP-B -/- mice contained no fully formed lamellar bodies. While the abundance of SP-A and SP-C mRNAs was not altered, an aberrant form of pro-SP-C, 8.5 kDa, was detected, and fully processed SP-C peptide was markedly decreased in lung homogenates of SP-B -/- mice. Ablation of the SP-B gene disrupts the routing, storage, and function of surfactant phospholipids and proteins, causing respiratory failure at birth.
Boric acid recovery using polymer filtration: Studies with alkyl monool, diol, and triol containing polyethylenimines (2005)

Abstract Three water‐soluble polymers containing linear alkyl monool, 1,2‐diol, and 1,2,3‐triol groups, mostly on the primary amines of polyethylenimine, were synthesized, characterized, and tested for their ability to recover boric acid. The boron‐binding capacities of these polymers and the backbone polyethylenimine were determined by titration, ultrafiltration, and inductively coupled plasma/atomic emission spectroscopy analysis. At low boron concentrations, the 1,2,3‐triol polymer performed better than the 1,2‐diol, whereas at high boron concentrations, the 1,2‐diol outperformed the 1,2,3‐triol. 11 B‐NMR spectroscopy and retention studies with various salt concentrations indicated that boron interacted with these two polymers by means of ion pairing with the protonated amines and by borate ester formation. For the monool and the polyethylenimine backbone, the mechanism for boron binding was ion pairing only. These polymers are under consideration for the selective recovery and recycling of enriched boric acid used in the primary coolant loop of pressurized water nuclear reactors. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 97: 1590–1604, 2005
Interleukin 13 induces interleukin 4-independent IgG4 and IgE synthesis and CD23 expression by human B cells. (1993)

Recently the cDNA encoding interleukin 13 (IL-13), a T-cell-derived cytokine, was cloned and expressed. The present study demonstrates that IL-13 induces IgG4 and IgE synthesis by human B cells. IL-13-induced IgG4 and IgE synthesis by unfractionated peripheral blood mononuclear cells and highly purified B cells cultured in the presence of activated CD4+ T cells or their membranes. IL-13-induced IgG4 and IgE synthesis is IL-4-independent, since it was not affected by neutralizing anti-IL-4 monoclonal antibody. Highly purified, surface IgD+ B cells could also be induced to produce IgG4 and IgE by IL-13, indicating that the production of these isotypes reflected IgG4 and IgE switching and not a selective outgrowth of committed B cells. IL-4 and IL-13 added together at optimal concentrations had no additive or synergistic effect, suggesting that common signaling pathways may be involved. This notion is supported by the observation that IL-13, like IL-4, induced CD23 expression on B cells and enhanced CD72, surface IgM, and class II major histocompatibility complex antigen expression. In addition, like IL-4, IL-13 induced germ-line IgE heavy-chain gene transcription in highly purified B cells. Collectively, our data indicate that IL-13 is another T-cell-derived cytokine that, in addition to IL-4, efficiently directs naive human B cells to switch to IgG4 and IgE production.
A Radical Demise: Toxins and Trauma Share Common Pathways in Hair Cell Death (1999)

The pathologic similarities noted after ototoxic and/or traumatic injury to the cochlea as well as the key features of the cochlea that make it susceptible to reactive oxygen species (ROS) damage are reviewed. Recent evidence linking ROS to cochlear damage associated with both ototoxins and/or trauma are presented. Mechanisms of generation of ROS in the cochlea and how these metabolites damage the cochlea and impair function are also reviewed. Finally, examples of novel therapeutic strategies to prevent and reverse hearing loss due to noise and/or ototoxins are presented to illustrate the clinical relevance of these new findings.
Simvastatin Increases Endothelial Nitric Oxide Synthase and Ameliorates Cerebral Vasospasm Resulting From Subarachnoid Hemorrhage (2002)

Simvastatin treatment before or after SAH attenuated cerebral vasospasm and neurological deficits in mice. The mechanism may be attributable in part to eNOS upregulation.
Email Task Management: An Iterative Relational Learning Approach. (2005)

Today’s email clients were designed for yesterday’s email. Originally, email was merely a communication medium. Today, people engage in a variety of complex behaviours using email, such as project management, collaboration, meeting scheduling, to-do tracking, etc. Our goal is to develop automated techniques to help people manage complex activities or tasks in email. The central challenge is that most activities are distributed over multiple messages, yet email clients allow users to manipulate just isolated messages. We describe machine learning approaches to identifying tasks and relations between individual messages in a task (i.e., finding cause-response links between emails) and for semantic message analysis (i.e., extracting metadata about how messages within a task relate to the task progress). Our key innovation compared to related work is that we exploit the relational structure of these two problems. Instead of attacking them separately, in our synergistic iterative approach, relations identification is used to assist semantic analysis, and vice versa. Our experiments with real-world email corpora demonstrate an improvement compared to nonrelational benchmarks.
A Survey of Adaptive Optimization in Virtual Machines (2005)

Virtual machines face significant performance challenges beyond those confronted by traditional static optimizers. First, portable program representations and dynamic language features, such as dynamic class loading, force the deferral of most optimizations until runtime, inducing runtime optimization overhead. Second, modular program representations preclude many forms of whole-program interprocedural optimization. Third, virtual machines incur additional costs for runtime services such as security guarantees and automatic memory management. To address these challenges, vendors have invested considerable resources into adaptive optimization systems in production virtual machines. Today, mainstream virtual machine implementations include substantial infrastructure for online monitoring and profiling, runtime compilation, and feedback-directed optimization. As a result, adaptive optimization has begun to mature as a widespread production-level technology. This paper surveys the evolution and current state of adaptive optimization technology in virtual machines.
Normal moveout revisited; inhomogeneous media and curved interfaces (1988)

Abstract The equation of normal moveout, t 2 = t 20 + x 2 /V 2a , is valid for a reflection from the base of a single homogeneous and isotropic bed, but is only an approximation in the real world of multilayered, inhomogeneous media and curved interfaces. Using the theory of geometrical optics, we can find another second-order equation which represents hyperbolas that are also symmetrical about the time axis. However, the centers of these hyperbolas do not coincide with the center of coordinates, but are shifted along the time axis. The equation describing this second type of hyperbola is (t + t p - t 0 ) 2 = t 2p + x 2 /V 21 , where t p is the time of focusing depth and V 1 , the velocity of the input medium. This equation is not only more accurate than the usual normal moveout, but its use is more economical on a vector computer because the traditional dynamic correction is a static correction in the t p analysis. This procedure makes it possible to compute velocities for all the samples of all the stacked traces and produces a velocity section. t p analysis can also be used to build a stacked section without any manual picking of velocities.The same concepts can be extended to the section after stack, allowing recognition of the geometrical patterns of the reflectors.
Membrane transport and information storage, advances in membrane fluidity, vol. 4 (1991)

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Detection ofEGFRGene Mutation in Lung Cancer by Mutant-Enriched Polymerase Chain Reaction Assay (2006)

Our results indicate that EGFR mutations are readily detectable by mutant-enriched PCR in various clinical samples. Thus, mutant-enriched PCR may provide a valuable method of potentially detecting a small fraction of mutant genes in heterogeneous specimens, indicating its possible use in clinical application for NSCLC.
Effects of latrunculin B on outflow facility, intraocular pressure, corneal thickness, and miotic and accommodative responses to pilocarpine in monkeys. (2004)

In ocular normotensive monkeys, 0.005/0.01% LAT-B administered topically increases outflow facility and/or decreases IOP, but does not affect the cornea. Multiple doses reduce IOP more than a single dose. LAT-B dose-dependently relaxes the iris sphincter and ciliary muscle, with some separation of the miotic and accommodative effects.
Role of Folylpolyglutamate Synthetase and Folylpolyglutamate Hydrolase in Methotrexate Accumulation and Polyglutamylation in Childhood Leukemia (1999)

Inefficient polyglutamylation is a mechanism of resistance to methotrexate (MTX) in childhood T-lineage acute lymphoblastic leukemia (T-ALL) and in acute myeloid leukemia (AML) in comparison with childhood c/preB-ALL. We analyzed the profile of MTX polyglutamylation in childhood c/preB-ALL, T-ALL, and AML (n = 45, 15, and 14, respectively), the activity of the MTX-polyglutamate synthesizing enzyme folylpolyglutamate synthetase (FPGS) (n = 39, 11, and 19, respectively) and of the MTX-polyglutamate breakdown enzyme folylpolyglutamate hydrolase (FPGH) (n = 98, 25, and 34, respectively). MTX-Glu4-6 accumulation after 24 hours exposure to 1 μmol/L [3H]-MTX in vitro was lower in T-ALL (threefold) and AML (fourfold) compared with c/preB-ALL (P ≤ .001). The FPGS activity was twofold lower in T-ALL and AML than in c/preB-ALL samples (P &lt; .01). FPGH activity was not different between c/preB-ALL and T-ALL, but threefold higher in AML (P &lt; .001). FPGS, FPGH, and the ratio FPGS/FPGH were correlated with MTX-Glu4-6 accumulation (r = .49, r = −.34 and r = .61, respectively). Multivariate analysis showed that FPGS, but not FPGH, was an independent contributor for MTX-Glu1-6 accumulation, but not for MTX-Glu4-6 accumulation. In conclusion, low FPGS activity is associated with low accumulation of MTX-Glu4-6 in T-ALL and AML. For the group of AML as compared with the group of ALL, a high FPGH activity can play an additional role.