gebhart/patrepeval huggingface dataset:
The synthesis of oligonucleotides containing an aliphatic amino group at the 5′ terminus: synthesis of fluorescent DNA primers for use in DNA sequence analysis (1985)

A rapid and versatile method has been developed for the synthesis of oligonucleotides which contain an aliphatic amino group at their 5' terminus. This amino group reacts specifically with a variety of electrophiles, thereby allowing other chemical species to be attached to the oligonucleotide. This chemistry has been utilized to synthesize several fluorescent derivatives of an oligonucleotide primer used in DNA sequence analysis by the dideoxy (enzymatic) method. The modified primers are highly fluorescent and retain their ability to specifically prime DNA synthesis. The use of these fluorescent primers in DNA sequence analysis will enable DNA sequence analysis to be automated.
Evaluation of Subjective Assessments and Objective Diagnostic Tests for Diagnosing Tear-Film Disorders Known to Cause Ocular Irritation (1998)

Subjective assessments and objective diagnostic tests have clinical utility as diagnostic tools in tear-film disorders. ATD is correlated with ocular-surface disease. An algorithm summarizing the diagnostic utility of these tests is included.
The Phosphotyrosine Binding-like Domain of Talin Activates Integrins (2002)

Cellular regulation of the ligand binding affinity of integrin adhesion receptors (integrin activation) depends on the integrin beta cytoplasmic domains (tails). The head domain of talin binds to several integrin beta tails and activates integrins. This head domain contains a predicted FERM domain composed of three subdomains (F1, F2, and F3). An integrin-activating talin fragment was predicted to contain the F2 and F3 subdomains. Both isolated subdomains bound specifically to the integrin beta3 tail. However, talin F3 bound the beta3 tail with a 4-fold higher affinity than talin F2. Furthermore, expression of talin F3 (but not F2) in cells led to activation of integrin alpha(IIb)beta3. A molecular model of talin F3 indicated that it resembles a phosphotyrosine-binding (PTB) domain. PTB domains recognize peptide ligands containing beta turns, often formed by NPXY motifs. NPX(Y/F) motifs are highly conserved in integrin beta tails, and mutations that disrupt this motif interfere with both integrin activation and talin binding. Thus, integrin binding to talin resembles the interactions of PTB domains with peptide ligands. These resemblances suggest that the activation of integrins requires the presence of a beta turn at NPX(Y/F) motifs conserved in integrin beta cytoplasmic domains.
Core based trees (CBT) (1993)

One of the central problems in one-to-many wide-area communications is forming the delivery tree - the collection of nodes and links that a multicast packet traverses. Significant problems remain to be solved in the area of multicast tree formation, the problem of scaling being paramount among these.In this paper we show how the current IP multicast architecture scales poorly (by scale poorly, we mean consume too much memory, bandwidth, or too many processing resources), and subsequently present a multicast protocol based on a new scalable architecture that is low-cost, relatively simple, and efficient. We also show how this architecture is decoupled from (though dependent on) unicast routing, and is therefore easy to install in an internet that comprises multiple heterogeneous unicast routing algorithms.
Internal friction in polymer systems (1989)

Internal friction is an effective mechanism for dissipating energy in polymer systems. Of particular interest is the ability to dampen and absorb unwanted acoustic and mechanical vibrations. The use of internal friction will become more effective when detailed geometric, thermodynamic, and kinetic models are developed for the physical phenomena producing the vibration damping. A model that relates the viscoelastic properties of polymeric systems to their molecular level structures has been developed. This model considers the nature of the temperature and frequency dependences of the storage and loss components of the complex moduli of polymers. It provides correct and internally consistent correlations. Therefore, it constitutes a first step in an attempt to bridge the gap between the results of application of an external stress (such as acoustic or mechanical vibration) and the molecular level properties of the polymers.
Nucleic acid related compounds. 6. Sugar-modified N6-(3-methyl-2-butenyl)adenosine derivatives, N6-benzyl analogs, and cytokinin-related nucleosides containing sulfur or formycin (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleic acid related compounds. 6. Sugar-modified N6-(3-methyl-2-butenyl)adenosine derivatives, N6-benzyl analogs, and cytokinin-related nucleosides containing sulfur or formycinMorris J. Robins and E. M. TripCite this: Biochemistry 1973, 12, 12, 2179–2187Publication Date (Print):June 1, 1973Publication History Published online1 May 2002Published inissue 1 June 1973https://pubs.acs.org/doi/10.1021/bi00736a001https://doi.org/10.1021/bi00736a001research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations36LEARN 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
Manipulating the Immune System with Immune Globulin (1992)

ALMOST as soon as a therapeutically useful concentrated immune globulin product became available for intramuscular use, it was obvious that a preparation that could be administered intravenously would be advantageous.1 , 2 However, many years of immunochemical research were required before a concentrated, biologically active, and safe preparation of immune globulin suitable for intravenous use became available. In the past decade, chemists have learned how to prevent protein aggregation while concentrating immune globulin. Purification can be achieved by chromatography, and stabilization of the intact immune globulin is then promoted by acidification with pepsin or the addition of sugars, amino acids, or both. . . .
Specific inhibition of HIV‐1 replication by short hairpin RNAs targeting human cyclin T1 without inducing apoptosis (2005)

RNA interference (RNAi), a sequence-specific RNA degradation mechanism mediated by small interfering RNA (siRNA), can be used not only as a research tool but also as a therapeutic strategy for viral infection. We demonstrated that intracellular expression of short hairpin RNA (shRNA) targeting human cyclin T1 (hCycT1), a cellular factor essential for transcription of messenger and genomic RNAs from the long terminal repeat promoter of provirus of human immunodeficiency virus type 1 (HIV-1), could effectively suppress the replication of HIV-1. We also showed that downregulation of hCycT1 did not cause apoptotic cell death, therefore, targeting cellular factor hCycT1 by shRNAs may provide an attractive approach for genetic therapy of HIV-1 infection in the future.
Expression and Self-Assembly of Norwalk Virus Capsid Protein from Venezuelan Equine Encephalitis Virus Replicons (2002)

The Norwalk virus (NV) capsid protein was expressed using Venezuelan equine encephalitis virus replicon particles (VRP-NV1). VRP-NV1 infection resulted in large numbers of recombinant NV-like particles that were primarily cell associated and were indistinguishable from NV particles produced from baculoviruses. Mutations located in the N-terminal and P1 domains of the NV capsid protein ablated capsid self-assembly in mammalian cells.
Inhibition of β2 Integrin–mediated Leukocyte Cell Adhesion (2001)

Many integrins mediate cell attachment to\nthe extracellular matrix by recognizing short tripeptide sequences such as arginine–glycine–aspartic acid and\nleucine–aspartate–valine. Using phage display, we have now found that the leukocyte-specific b2 integrins bind\nsequences containing a leucine–leucine–glycine (LLG)\ntripeptide motif. An LLG motif is present on intercellular adhesion molecule (ICAM)-1, the major b2 integrin ligand, but also on several matrix proteins, including von Willebrand factor. We developed a novel b2 integrin\nantagonist peptide CPCFLLGCC (called LLG-C4), the structure of which was determined by nuclear magnetic resonance. The LLG-C4 peptide inhibited leukocyte adhesion\nto ICAM-1, and, interestingly, also to von Willebrand factor. When immobilized on plastic, the LLG-C4 sequence supported the\nb2 integrin–mediated leukocyte adhesion, but not b1 or b3 integrin–mediated cell adhesion.\nThese results suggest that LLG sequences exposed on ICAM-1 and on von Willebrand factor at sites of vascular injury play a role in the binding of leukocytes, and LLG-C4 and peptidomimetics derived from it could provide a therapeutic approach to inflammatory reactions.
Power issues related to branch prediction (2004)

This paper explores the role of branch predictor organization in power/energy/performance tradeoffs for processor design. We find that as a general rule, to reduce overall energy consumption in the processor it is worthwhile to spend more power in the branch predictor if this results in more accurate predictions that improve running time. Two techniques, however, provide substantial reductions in power dissipation without harming accuracy. Banking reduces the portion of the branch predictor that is active at any one time. And a new on-chip structure, the prediction probe detector (PPD), can use pre-decode bits to entirely eliminate unnecessary predictor and branch target buffer (BTB) accesses. Despite the extra power that must be spent accessing the PPD, it reduces local predictor power and energy dissipation by about 45% and overall processor power and energy dissipation by 5-6%.
Immunodeficiency Disorders (2002)

Primary immunodeficiency diseases are genetically determined impairments of immune response. Our knowledge of these disorders dates only to the 1950s, when Colonel Ogden Bruton applied electrophoretic analysis to the serum of a young boy with recurrent pneumonia. No γ-globulin band was present. Antibody activity had been localized to the γ-globulin band only a decade previously. Bruton's case linked susceptibility to infection to absent γ-globulin and to absent antibody. Since then, a large number of syndromes of immunodeficiency have been described. As few as 15 years ago, we knew the molecular and genetic basis for no more than a handful of these diseases. Now many more than 20 disorders have established genetic causes.KeywordsAtopic DermatitisRespiratory BurstChronic Granulomatous DiseasePneumocystis Carinii PneumoniaKiller WhaleThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
A New Structure of Silicon-on-Insulator Metal-Oxide-Semiconductor Field Effect Transistor to Suppress the Floating Body Effect (2003)

Considering that the silicon-on-insulator (SOI) devices have an inherent floating body effect, which may cause substantial influences in the performance of SOI device and circuit, we propose a novel device structure to suppress the floating body effect. In the new structure there is a buried p+ region under the n+ source and that region is extended to outside of the source, and this additional p+ region provides a path for accumulated holes to flow out of the body. Numerical simulations were carried out with Medici, and the output characteristics and gate characteristics were compared with those of conventional SOI counterparts. The simulated results show the suppression of floating body effect in the novel SOI device as expected.
16세기 동양과 서양의 공동체 이념에 대한 비교 연구 (2011)

이 글은 낡은 것이 의심되고 새로운 공동체의 이상이 제기되었던 역사적 이행기 16세기에 서구와 한국에서 나타났던 ``자치공동체``의 이념적 상과 실현 원리를 비교하고 그것이 가진 차이를 드러내는 데 그 목적이 있었다. 서구의 재세례파운동과 조선의 향약운동은 그것을 주도한 계층과 그 귀결에 있어서 일정한 차이를 가짐에도 불구하고 당시의 국가적 형태의 정치운동과 갈등하며 제기되었거나 혹은 새로운 정치체를 지향하며 제기되었다는 점에서 근대 국가의 정치와는 구분되는 ``자치공동체``의 이념적 상을 가지고 있기 때문이다. 재세례파(anabaptist)의 ``기독교적 자치공동체`` 이념과 향약(鄕約)의 ``유교적 자치공동체`` 이념의 가장 근본적인 차이는 그들이 지향한 공동체와 군주의 관계, 그리하여 국가와 공동체의 관계를 바라보는 관점과 실제적 태도에 놓여 있었다. 16세기 역사적 변동기에 재세례파운동이 꿈꾸었던 기독교적 자치공동체의 이념과 향약운동이 꿈꾸었던 유교적 자치공동체의 이념은 모두 각자 자치도시의 원리와 마을공동체의 자치를 위해 참여와 대표의 범위를 넓히려 했으며 그 공동체의 윤리적 구심점을 본래의 기독교 정신으로 돌아간 신앙적 실천으로, 본래의 유자의 정신을 구현한 도덕적 실천으로 모색했지만, 그들이 현실의 종교세력, 현실의 군주, 현실의 국가에 취한 태도는 동일하지 않았기 때문이다. 재세례파운동은 대부분 그 지역의 군주에 대해, 또한 로마의 가톨릭교회에 대해 반대했을 뿐 아니라 기독교적 공동체의 ``자치도시``가 근본적으로 세속의 ``국가``와 양립할 수 없다고 본 반면, 향약운동은 유교적 공동체의 ``마을공동체``가 군주와 국가 아래에 양립가능하며 군주를 유자로 만듦으로써 ``자치공동체``와 ``국가``가 긴밀히 연관될 수 있다고 보았다. 그러므로 향약운동이 초기에 취했던 비판적 태도를 점차 잃고 체제 내화되어갔던 보다 근본적인 까닭은 그들의 자치 공동체 이념이 다만 특정한 국가 권력인 훈구 세력에 대한 비판일 뿐 군주나 국가 자체로부터 자립적인 정치적 자치를 의미한 것은 아니었던 데 놓여 있다. 만일 향약이 국가와는 구분되는 정치적 자치체로서 ``유자의 공동체``를 구상하고자 했다면, 그러한 정치원리가 자족적인 경제적 토대와 관련되어야 할 필요성이 대두되었을 것이며 따라서 경제 개혁의 구호만이 아니라 실제적인 비판과 실천으로 나아갈 수 있었을 것이다. 그렇기에 공동체가 자치적이기 위해 가져야 할 보다 근본적인 조건은 그 공동체 내부의 자치 규약이나 원리에 있는 것이 아니라, 그 공동체가 공동체 외부와 가지는 독립성과 비판성에 놓여 있다고 할 수 있을 것이다.
Dietary selenium affects methylation of the wobble nucleoside in the anticodon of selenocysteine tRNA([Ser]Sec) (1993)

We reported previously that the presence of selenium in culture media of mammalian cells influences both the steady-state levels and distributions of two tRNA isoacceptors involved in the insertion of selenocysteine into protein in response to certain UGA codons. In this study, we demonstrate an increase in the levels of these isoacceptors in rats fed a selenium-adequate diet compared to animals fed a selenium-deficient diet, as well as a shift in the relative distribution toward the tRNA which elutes later from an RPC-5 column. These effects were found to occur in a tissue-specific manner. Both selenocysteine tRNAs were isolated from rat liver, sequenced, analyzed by mass spectrometry, and shown to differ only by ribose 2'-O-methylation of 5-methylcarboxymethyluridine that occurs in the wobble position of the anticodon. This modified nucleoside has been documented previously only in yeast tRNA while the corresponding 2'-O-methylribose derivative has not been observed. The structure of these nucleosides was established by mass spectrometry and confirmed by chemical synthesis. Although the role of methylation of the wobble nucleotide is not known, the differences in elution properties from RPC-5 columns are consistent with other experimental observations indicating that a change in tRNA conformation accompanies this methylation.
Enhanced Nasal Delivery of Luteinizing Hormone Releasing Hormone Agonist Buserelin by Oleic Acid Solubilized and Stabilized in Hydroxypropyl-.BETA.-cyclodextrin. (1995)

The potential use of three 2-hydroxypropyl ether derivatives of cyclodextrins (HP-alpha-, HP-beta- and HP-gamma-CyDs) as biocompatible solubilizers and stabilizers for oleic acid, a lipophilic absorption enhancer, was assessed in the nasal absorption of buserelin, an agonist of luteinizing hormone-releasing hormone, in rats. HP-CyDs increased the aqueous solubility of oleic acid and protected it against oxidation through the formation of inclusion complexes with the efficacy increasing in the order: HP-gamma-CyD << HP-alpha-CyD < HP-beta- CyD. The bend structure due to a cis-double bond halfway along the acyl chain of oleic acid provided a better fit into the cavity of HP-beta-CyD, in which the double bond appears to be buried, and hence becomes less susceptible to oxidation. The rate and extent of nasal bioavailability of buserelin were remarkably increased by coadministration of oleic acid and HP-beta-CyD, compared with the sole use of the enhancer. This enhancement was ascribable to the lowering of both the enzymatic and physical barriers of the nasal epithelium to the peptide, probably through the facilitated transmucosal penetration of oleic acid solubilized in HP-beta-CyD.
Defective interfering type A equine influenza virus (H3N8) protects mice from morbidity and mortality caused by homologous and heterologous subtypes of influenza A virus (1994)

Intranasal administration of defective interfering A/equine/Newmarket/7339/79 (H3N8) influenza virus (DI EQV) protected mice from otherwise lethal intranasal infection with homologous virus (EQV) or with the heterologous subtypes A/WSN (H1N1) or A/PR/8/34 (H1N1). Such protected mice showed little or no sign of clinical disease. Disease with only low mortality resulting from a 'low' dose of WSN was completely prevented with a 100-fold lower dose of DI EQV (4 haemagglutinating units/ml or 12 ng virus/mouse), indicating that there was a roughly proportional relationship between the protective dose of DI virus and the infecting inoculum. DI EQV-protected mice continued to gain weight at the normal rate, whereas those treated with inactivated DI EQV ceased putting on weight for about 7 days and were still underweight nearly 3 weeks later. Unlike DI WSN, DI EQV inhibited multiplication of infectious WSN in the lungs by 20 to 60-fold. Intranasal DI EQV on its own gave little protection to mice challenged 24 days later with EQV suggesting that it was only weakly immunogenic. DI EQV afforded significant protection when given up to 5 days before live virus challenge indicating that the DI genome remained active in the respiratory tract for this period of time.
Vector Predictive Coding of Speech at 16 kbits/s (1985)

Vector quantization, in its simplest form, may be regarded as a generalization of PCM (independent quantization of each sample of a waveform) to what might be called "vector PCM," where a block of consecutive samples, a vector, is simultaneously quantized as one unit. In theory, a performance arbitrarily close to the ultimate rate-distortion limit is achievable with waveform vector quantization if the dimension of the vector, <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</tex> , is large enough. The main obstacle in effectively using vector quantization is complexity. A vector quantizer of dimension <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</tex> operating at a rate of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</tex> bits/sample requires a number of computations on the order of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k2^{kr}</tex> and a memory of the same order. However, a low-dimensional vector quantizer (dimensions 4-8) achieves a remarkable improvement over scalar quantization (PCM). Consequently, using the vector quantizer as a building block and imbedding it with other waveform data compression techniques may lead to the development of a new and powerful class of waveform coding systems. This paper proposes and analyzes a waveform coding system, adaptive vector predictive coding (AVPC), in which a low-dimensionality vector quantizer is used in an adaptive predictive coding scheme. In the encoding process, a locally generated prediction of the current input vector is subtracted from the current vector, and the resulting error vector is coded by a vector quantizer. Each frame consisting of many vectors is classified into one of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</tex> statistical types. This classification determines which one of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</tex> fixed predictors and of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</tex> vector quantizers will be used for encoding the current frame.
The N-terminus of hepcidin is essential for its interaction with ferroportin: structure-function study (2005)

Hepcidin is the principal iron-regulatory hormone. It acts by binding to the iron exporter ferroportin, inducing its internalization and degradation, thereby blocking cellular iron efflux. The bioactive 25 amino acid (aa) peptide has a hairpin structure stabilized by 4 disulfide bonds. We synthesized a series of hepcidin derivatives and determined their bioactivity in a cell line expressing ferroportin-GFP fusion protein, by measuring the degradation of ferroportin-GFP and the accumulation of ferritin after peptide treatment. Bioactivity was also assayed in mice by the induction of hypoferremia. Serial deletion of N-terminal amino acids caused progressive decrease in activity which was completely lost when 5 N-terminal aa's were deleted. Synthetic 3-aa and 6-aa N-terminal peptides alone, however, did not internalize ferroportin and did not interfere with ferroportin internalization by native hepcidin. Deletion of 2 C-terminal aa's did not affect peptide activity. Removal of individual disulfide bonds by pairwise substitution of cysteines with alanines also did not affect peptide activity in vitro. However, these peptides were less active in vivo, likely because of their decreased stability in circulation. G71D and K83R, substitutions previously described in humans, did not affect hepcidin activity. Apart from the essential nature of the N-terminus, hepcidin structure appears permissive for mutations.
MethylSig: a whole genome DNA methylation analysis pipeline (2014)

Supplementary data are available at Bioinformatics online.
Protocols for dry DNA storage and shipment at room temperature (2013)

The globalization of DNA barcoding will require core analytical facilities to develop cost-effective, efficient protocols for the shipment and archival storage of DNA extracts and PCR products. We evaluated three dry-state DNA stabilization systems: commercial Biomatrica(®) DNAstable(®) plates, home-made trehalose and polyvinyl alcohol (PVA) plates on 96-well panels of insect DNA stored at 56 °C and at room temperature. Controls included unprotected samples that were stored dry at room temperature and at 56 °C, and diluted samples held at 4 °C and at -20 °C. PCR and selective sequencing were performed over a 4-year interval to test the condition of DNA extracts. Biomatrica(®) provided better protection of DNA at 56 °C and at room temperature than trehalose and PVA, especially for diluted samples. PVA was the second best protectant after Biomatrica(®) at room temperature, whereas trehalose was the second best protectant at 56 °C. In spite of lower PCR success, the DNA stored at -20 °C yielded longer sequence reads and stronger signal, indicating that temperature is a crucial factor for DNA quality which has to be considered especially for long-term storage. Although it is premature to advocate a transition to DNA storage at room temperature, dry storage provides an additional layer of security for frozen samples, protecting them from degradation in the event of freezer failure. All three forms of DNA preservation enable shipment of dry DNA and PCR products between barcoding facilities.