gebhart/patrepeval huggingface dataset:
Recent developments in the MAFFT multiple sequence alignment program (2008)

The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater challenges in both scalability and accuracy than those of 5 years ago. As increasing amounts of sequence data are being generated by large-scale sequencing projects, scalability is now critical in many situations. The requirement of accuracy has also entered a new stage since the discovery of functional noncoding RNAs (ncRNAs); the secondary structure should be considered for constructing a high-quality alignment of distantly related ncRNAs. To deal with these problems, in 2007, we updated MAFFT to Version 6 with two new techniques: the PartTree algorithm and the Four-way consistency objective function. The former improved the scalability of progressive alignment and the latter improved the accuracy of ncRNA alignment. We review these and other techniques that MAFFT uses and suggest possible future directions of MSA software as a basis of comparative analyses. MAFFT is available at http://align.bmr.kyushu-u.ac.jp/mafft/software/.
A brief introduction to boosting (1999)

Boosting is a general method for improving the accuracy of any given learning algorithm. This short paper introduces the boosting algorithm AdaBoost, and explains the underlying theory of boosting, including an explanation of why boosting often does not suffer from overfitting. Some examples of recent applications of boosting are also described. Background Boosting is a general method which attempts to &amp;quot;boost&amp;quot; the accuracy of any given learning algorithm. Boosting has its roots in a theoretical framework for studying machine learning called the &amp;quot;PAC&amp;quot; learning model, due to Valiant [37]; see Kearns and Vazirani [24] for a good introduction to this model. Kearns and Valiant [22, 23] were the first to pose the question of whether a &amp;quot;weak&amp;quot; learning algorithm which performs just slightly better than random guessing in the PAC model can be &amp;quot;boosted&amp;quot; into an arbitrarily accurate &amp;quot;strong&amp;quot; learning algorithm. Schapire [30] came up with the first provable polynomial-time boosting algorithm in ...
Integration of ERG gene mapping and gene‐expression profiling identifies distinct categories of human prostate cancer (2008)

Expression profiling of prostate cancer samples containing single patterns of ERG alterations can provide novel insights into the mechanism of prostate cancer development, and support the view that factors other than ERG status are the major determinants of poor clinical outcome.
Risk of Iron Overload among Middle-aged Women (2000)

Iron overload, expressed as increased body iron stores, has been recognized as a potential hazard because it promotes the generation of oxygen radicals. We analyzed factors associated with serum ferritin levels (an indicator of body iron stores) among middle-aged women with a high prevalence of nutrient supplement use. Serum ferritin concentrations were determined on automated immunoassay for 487 healthy women with the mean age of 57 years who participated in the New York University Women's Health Study. The mean serum ferritin concentration in postmenopausal women was more than twice that in premenopausal women. Serum ferritin concentrations progressively increased with advancing age, but adjustment for menopausal status considerably weakened this association. Among non-dietary factors, nonwhite ethnicity, obesity and cigarette smoking were positively associated with serum ferritin concentrations. After adjustment for these factors and for menopausal status, serum ferritin levels were positively associated with meat intake and multivitamin use and inversely associated with breakfast cereal consumption. However, none of these lifestyle factors positively associated with serum ferritin levels had a significant impact on serum ferritin levels above 100 ng/ml (approximately equal to median concentration). Our results suggest that iron overload seems unlikely among middle aged women through their diet and nutritional supplements.
Cellular Genes Derived from Gypsy/Ty3 Retrotransposons in Mammalian Genomes (2009)

Gypsy/Ty3 retrotransposons, a group of long terminal repeat retrotransposons related to vertebrate retroviruses, are found in the genome of many fungi, plants, and animals. Although multiple families of such retroelements are present in fish, active Gypsy/Ty3 retrotransposons have all been eliminated from the lineage leading to mammals at least 180 million years ago. However, over 50 cellular genes related to Gypsy/Ty3 retrotransposons have been identified in mammalian genomes, indicating recurrent "molecular domestication" of these elements by their host during evolution. Most retrotransposon-derived proteins are conserved in divergent mammalian species and show sequence similarity to Gag proteins, major structural proteins for retroelement particle formation. Among the proposed and demonstrated biological functions for gag-derived genes, placenta formation in the mouse requires two gag-derived genes from the same family. Some forms of epigenetic regulation of gag-related genes might derive from host genome defense mechanisms that repelled retrotransposon ancestors. Together, such observations support a major role for transposable elements as a source of new coding sequences allowing important genetic innovations during evolution.
Influence of fine structure of lipid A on Limulus amebocyte lysate clotting and toxic activities (1984)

We examined the relationship between the fine structure of lipid A and the toxicity of endotoxin or lipopolysaccharides as measured by the Limulus amebocyte lysate (LAL), rabbit pyrogenicity, chicken embryo lethal dose, and dermal Shwartzman reaction tests. Lipid A and lipid A-like compounds obtained from deep-rough mutants of Salmonella spp. and Escherichia coli had a wide range of structural variations. These compounds included native lipopolysaccharides, diphosphoryl and monophosphoryl lipid A's, and lipid X (a monosaccharide). The LAL test was positive for all lipids tested with lysates from Travenol Laboratories and from Associates of Cape Cod (2.9 X 10(3) to 2.6 X 10(7) endotoxin units per mg), except for O-deacylated and dephosphorylated lipid X, which were negative. The Mallinckrodt lysate gave negative tests for lipid X. In the rabbit pyrogenicity and chicken embryo lethal dose tests, only native lipopolysaccharide and diphosphoryl lipid A's were judged toxic. The Shwartzman reaction was positive for a specific purified diphosphoryl lipid A (thin-layer chromatography-3 fraction) but negative for the purified monophosphoryl lipid A (also a thin-layer chromatography-3 fraction). These results show that the LAL test is not a valid measure of all parameters of toxicity of a lipid A or lipid A-like compound and can yield false-positive results. However, these findings are not in conflict with the widespread use of the LAL assay for pyrogens in the pharmaceutical industry since a good correlation exists between LAL results and pyrogenicity when undegraded endotoxin is evaluated in parallel assays.
G4 Resolvase 1 Binds Both DNA and RNA Tetramolecular Quadruplex with High Affinity and Is the Major Source of Tetramolecular Quadruplex G4-DNA and G4-RNA Resolving Activity in HeLa Cell Lysates (2008)

Quadruplex structures that result from stacking of guanine quartets in nucleic acids possess such thermodynamic stability that their resolution in vivo is likely to require specific recognition by specialized enzymes. We previously identified the major tetramolecular quadruplex DNA resolving activity in HeLa cell lysates as the gene product of DHX36 (Vaughn, J. P., Creacy, S. D., Routh, E. D., Joyner-Butt, C., Jenkins, G. S., Pauli, S., Nagamine, Y., and Akman, S. A. (2005) J. Biol Chem. 280, 38117-38120), naming the enzyme G4 Resolvase 1 (G4R1). G4R1 is also known as RHAU, an RNA helicase associated with the AU-rich sequence of mRNAs. We now show that G4R1/RHAU binds to and resolves tetramolecular RNA quadruplex as well as tetramolecular DNA quadruplex structures. The apparent K(d) values of G4R1/RHAU for tetramolecular RNA quadruplex and tetramolecular DNA quadruplex were exceptionally low: 39 +/- 6 and 77 +/- 6 Pm, respectively, as measured by gel mobility shift assay. In competition studies tetramolecular RNA quadruplex structures inhibited tetramolecular DNA quadruplex structure resolution by G4R1/RHAU more efficiently than tetramolecular DNA quadruplex structures inhibited tetramolecular RNA quadruplex structure resolution. Down-regulation of G4R1/RHAU in HeLa T-REx cells by doxycycline-inducible short hairpin RNA caused an 8-fold loss of RNA and DNA tetramolecular quadruplex resolution, consistent with G4R1/RHAU representing the major tetramolecular quadruplex helicase activity for both RNA and DNA structures in HeLa cells. This study demonstrates for the first time the RNA quadruplex resolving enzymatic activity associated with G4R1/RHAU and its exceptional binding affinity, suggesting a potential novel role for G4R1/RHAU in targeting in vivo RNA quadruplex structures.
Perceptron Trees: A Case Study in Hybrid Concept Representations (1989)

Abstract This article presents a case study in examining the bias of two particular formalisms: decision trees and linear threshold units. The immediate result is a new hybrid representation, called a ‘perceptron tree’, and an associated learning algorithm called the ‘percepton tree error correction procedure’. The longer term result is a model for exploring issues related to understanding representational bias and constructing other useful hybrid representations.
Immunological screening method to detect specific translation products. (1978)

We describe a very sensitive method to detect as antigens the presence of specific proteins within phage plaques or bacterial colonies. We coat plastic sheets with antibody molecules, expose the sheet to lysed bacteria so that a released antigen can bind, and then label the immobilized antigen with radioiodinated antibodies. Thus, the antigen is sandwiched between the antibodies attached to the plastic sheet and those carrying the radioactive label. Autoradiography then shows the positions of antigen-containing colonies or phage plaques. A few molecules of antigen released from each bacterial cell generatean adequate signal.
The epidemiology of autism: a review (1999)

Based on recent surveys, a minimum estimate of 18.7/10000 for all forms of pervasive developmental disorders was derived, which outlines the needs in special services for a large group of children.
Detoxification of organophosphate nerve agents by immobilizedEscherichia coli with surface-expressed organophosphorus hydrolase (1999)

An improved whole-cell technology for detoxifying organophosphate nerve agents was recently developed based on genetically engineered Escherichia coli with organophosphorus hydrolase anchored on the surface. This article reports the immobilization of these novel biocatalysts on nonwoven polypropylene fabric and their applications in detoxifying contaminated wastewaters. The best cell loading (256 mg cell dry weight/g of support or 50 mg cell dry weight/cm2 of support) and subsequent hydrolysis of organophosphate nerve agents were achieved by immobilizing nongrowing cells in a pH 8, 150 mM citrate-phosphate buffer supplemented with 1 mM Co2+ for 48 h via simple adsorption, followed by organophosphate hydrolysis in a pH 8, 50 mM citrate-phosphate buffer supplemented with 0.05 mM Co2+ and 20% methanol at 37 degrees C. In batch operations, the immobilized cells degraded 100% of 0.8 mM paraoxon, a model organophosphate nerve agent, in approximately 100 min, at a specific rate of 0.160 mM min-1 (g cell dry wt)-1. The immobilized cells retained almost 100% activity during the initial six repeated cycles and close to 90% activity even after 12 repeated cycles, extending over a period of 19 days without any nutrient supplementation. In addition to paraoxon, other commonly used organophosphates, such as diazinon, coumaphos, and methylparathion were hydrolyzed efficiently. The cell immobilization technology developed here paves the way for an efficient, simple, and cost-effective method for detoxification of organophosphate nerve agents.
Extracellular Cations Sensitize and Gate Capsaicin Receptor TRPV1 Modulating Pain Signaling (2005)

Transient receptor potential (TRP) channels detect diverse sensory stimuli, including alterations in osmolarity. However, a molecular detector of noxious hypertonic stimuli has not yet been identified. We show here that acute pain-related behavior evoked by elevated ionic strength is abolished in TRP vanilloid subtype 1 (TRPV1)-null mice and inhibited by iodoresiniferatoxin, a potent TRPV1 antagonist. Electrophysiological recordings demonstrate a novel form of ion channel modulation by which extracellular Na+, Mg2+, and Ca2+ ions sensitize and activate the capsaicin receptor, TRPV1. At room temperature, increasing extracellular Mg2+ (from 1 to 5 mM) or Na+ (+50 mM) increased ligand-activated currents up to fourfold, and 10 mM Mg2+ reduced the EC50 for activation by capsaicin from 890 to 450 nM. Moreover, concentrations of divalent cations >10 mM directly gate the receptor. These effects occur via electrostatic interactions with two glutamates (E600 and E648) formerly identified as proton-binding residues. Furthermore, phospholipase C-mediated signaling enhances the effects of cations, and physiological concentrations of cations contribute to the bradykinin-evoked activation of TRPV1 and the sensitization of the receptor to heat. Thus, the modulation of TRPV1 by cationic strength may contribute to inflammatory pain signaling.
Intra Coding of the HEVC Standard (2012)

This paper provides an overview of the intra coding techniques in the High Efficiency Video Coding (HEVC) standard being developed by the Joint Collaborative Team on Video Coding (JCT-VC). The intra coding framework of HEVC follows that of traditional hybrid codecs and is built on spatial sample prediction followed by transform coding and postprocessing steps. Novel features contributing to the increased compression efficiency include a quadtree-based variable block size coding structure, block-size agnostic angular and planar prediction, adaptive pre- and postfiltering, and prediction direction-based transform coefficient scanning. This paper discusses the design principles applied during the development of the new intra coding methods and analyzes the compression performance of the individual tools. Computational complexity of the introduced intra prediction algorithms is analyzed both by deriving operational cycle counts and benchmarking an optimized implementation. Using objective metrics, the bitrate reduction provided by the HEVC intra coding over the H.264/advanced video coding reference is reported to be 22% on average and up to 36%. Significant subjective picture quality improvements are also reported when comparing the resulting pictures at fixed bitrate.
Immunotherapy Can Reject Intracranial Tumor Cells without Damaging the Brain despite Sharing the Target Antigen (2010)

Although vaccines targeting tissue differentiation Ags represent a promising strategy for cancer immunotherapy, the risk of triggering autoimmune damage to normal tissues remains to be determined. Immunizing against a melanoma-associated Ag, dopachrome tautomerase (DCT), which normal melanocytes and glial cells also express, allowed concurrent analysis of autoimmune consequences in multiple tissues. We show that vaccination with recombinant adenovirus expressing DCT elicited a strong CTL response in C57BL/6 mice, leading to protection against intracranial challenge with B16-F10 melanoma cells. Both histological analysis and behavioral testing indicated that there was no evidence of neuropathology in vaccinated animals and long-term survivors. Although vitiligo or demyelination could be induced by additional stimuli (i.e., surgery or inflammation) in DCT-vaccinated mice, it did not extend beyond the inflammatory area, suggesting that there is self-regulatory negative feedback in normal tissues. These results demonstrate that it is possible to vaccinate against a tumor embedded in a vital organ that shares the target Ag.
Optimal Huffman Coding of DCT Blocks (2004)

It is a well-observed characteristic that, when a discrete cosine transform block is traversed in the zigzag order, ac coefficients generally decrease in size and the runs of zero coefficients increase in length. This paper presents a minor modification to the Huffman coding of the JPEG baseline compression algorithm to exploit this characteristic. During the run-length coding, instead of pairing a nonzero ac coefficient with the run-length of the preceding zero coefficients, our encoder pairs it with the run-length of subsequent zeros. This small change makes it possible for our codec to code a pair using a separate Huffman code table optimized for the position of the nonzero coefficient denoted by the pair. These position-dependent code tables can be encoded efficiently without incurring a sizable overhead. Experimental results show that our encoder produces a further reduction in the ac coefficient Huffman code size by about 10%-15%.
Ontology Learning from Text: A Survey of Methods (2005)

After the vision of the Semantic Web was broadcasted at the turn of the millennium, ontology became a synonym for the solution to many problems concerning the fact that computers do not understand human language: if there were an ontology and every document were marked up with it and we had agents that would understand the markup, then computers would finally be able to process our queries in a really sophisticated way. Some years later, the success of Google shows us that the vision has not come true, being hampered by the incredible amount of extra work required for the intellectual encoding of semantic mark-up – as compared to simply uploading an HTML page. To alleviate this acquisition bottleneck, the field of ontology learning has since emerged as an important sub-field of ontology engineering. It is widely accepted that ontologies can facilitate text understanding and automatic processing of textual resources. Moving from words to concepts not only mitigates data sparseness issues, but also promises appealing solutions to polysemy and homonymy by finding non-ambiguous concepts that may map to various realizations in – possibly ambiguous – words. Numerous applications using lexical-semantic databases like WordNet (Miller, 1990) and its non-English counterparts, e.g. EuroWordNet (Vossen, 1997) or CoreNet (Choi and Bae, 2004) demonstrate the utility of semantic resources for natural language processing. Learning semantic resources from text instead of manually creating them might be dangerous in terms of correctness, but has undeniable advantages: Creating resources for text processing from the texts to be processed will fit the semantic component neatly and directly to them, which will never be possible with general-purpose resources. Further, the cost per entry is greatly reduced, giving rise to much larger resources than an advocate of a manual approach could ever afford. On the other hand, none of the methods used today are good enough for creating semantic resources of any kind in a completely unsupervised fashion, albeit automatic methods can facilitate manual construction to a large extent. The term ontology is understood in a variety of ways and has been used in philosophy for many centuries. In contrast, the notion of ontology in the field of computer science is younger – but almost used as inconsistently, when it comes to the details of the definition. The intention of this essay is to give an overview of different methods that learn ontologies or ontology-like structures from unstructured text. Ontology learning from other sources, issues in description languages, ontology editors, ontology merging and ontology evolving transcend the scope of this article. Surveys on ontology learning from text and other sources can be found in Ding and Foo (2002) and Gomez-Perez
Effect of Dose on Immune Response in Patients Vaccinated With an HER-2/neu Intracellular Domain Protein—Based Vaccine (2004)

The HER-2/neu ICD protein vaccine was well tolerated and effective in eliciting HER-2/neu-specific T-cell and antibody immunity in the majority of breast and ovarian cancer patients who completed the vaccine regimen. Although the dose of vaccine did not impact the magnitude of T-cell or antibody immunity elicited, patients receiving the highest dose developed HER-2/neu-specific immunity more rapidly than those who received the lowest dose.
Security Analysis of RFID Based on Multiple Readers (2007)

As a new auto-identifying technique, RFID has been widely applied to supply-chain and retailing. However the specialties and limitation of RFID system and device will incur lots of security problems especially when the system contains a lot of tags and many readers , the traditional methods become helpless. Here we present and analyze an improved hash key technique based on multiple readers.
Targets for Antiinflammatory Drugs (1995)

Aspirin-like nonsteroidal antiinflammatory agents, corticosteroids, and methotrexate are the mainstays of therapy in rheumatoid arthritis and other inflammatory diseases. It is now clear that these agents share at least one characteristic: All of these agents diminish the adhesive interactions required for the accumulation of white blood cells at an inflamed site. We discuss the biochemical and functional mechanisms by which these drugs alter the inflammatory response, and the potential for development of new antiinflammatory agents based upon these pharmacological actions.
Population pharmacokinetics and exposure-safety relationship of nanoliposomal irinotecan (MM-398, nal-IRI) in patients with solid tumors. (2015)

e13588 Background: MM-398 is a nanoliposomal irinotecan (nal-IRI). This study characterized the population PK and exposure–response with MM-398 in patients with solid tumors. Methods: Population PK analysis was performed for total irinotecan (IRI) and its active metabolite SN-38 in 353 patients administered MM-398 60-120 mg/m2 in 6 studies. Covariates include body size (BSA), hepatic and renal functions (UGT1A1*28 7/7, bilirubin, liver metastasis, AST, ALT, albumin, CrCl), demographics (sex, race, age), and external factors (co-treatment with 5-FU, manufacturing site). Exposure-safety (neutropenia, diarrhea, and anemia) relationships were evaluated from 6 studies. Predictions of incidence rates of AEs were obtained from exposure-safety and predicted exposure with a dose of 80mg/m2. Results: Population PK of IRI was described as a 2-compartmental model, and SN-38 as a 1-compartmental model. Significant covariates to IRI were race and BSA; covariates to SN-38 were baseline bilirubin and BSA. No other covariates were significant; association with UGT1A1*28 was not significant. Compared to 120 mg/m2 q3w, MM398 80 mg/m2 q2w had similar average (Cavg), and 1.5-fold lower Cmax for both IRI and SN-38. SN-38 Cmax was associated with incidence of G ≥ 3 neutropenia and anemia, and IRI Cmax was associated with incidence of G ≥ 3 diarrhea. Compared to Caucasians, Asians had 0.5-fold lower IRI Cmax, corresponding to 5% lower predicted G ≥ 3 diarrhea. In contrast, Asians had 1.5-fold higher SN-38 Cmax than Caucasians, corresponding to 7% higher predicted G ≥ 3 neutropenia. Compared to patients with bilirubin < 1 mg/dL, patients with bilirubin 1-2 mg/dL had 1.4-fold higher SN-38. Conclusions: MM-398 at a lower dose, given more frequently, was predicted to have similar Cavg and lower Cmax. IRI Cmax was associated with diarrhea and SN-38 Cmax was associated with neutropenia and anemia. Asians had lower IRI levels, but higher SN-38. Increasing baseline bilirubin was associated with higher SN-38 levels. Clinical trial information: NCT01494506.