gebhart/patrepeval huggingface dataset:
Characteristics of Two Forms of α-Amylases and Structural Implication (1999)

Complete (Ba-L) and truncated (Ba-S) forms of alpha-amylases from Bacillus subtilis X-23 were purified, and the amino- and carboxyl-terminal amino acid sequences of Ba-L and Ba-S were determined. The amino acid sequence deduced from the nucleotide sequence of the alpha-amylase gene indicated that Ba-S was produced from Ba-L by truncation of the 186 amino acid residues at the carboxyl-terminal region. The results of genomic Southern analysis and Western analysis suggested that the two enzymes originated from the same alpha-amylase gene and that truncation of Ba-L to Ba-S occurred during the cultivation of B. subtilis X-23 cells. Although the primary structure of Ba-S was approximately 28% shorter than that of Ba-L, the two enzyme forms had the same enzymatic characteristics (molar catalytic activity, amylolytic pattern, transglycosylation ability, effect of pH on stability and activity, optimum temperature, and raw starch-binding ability), except that the thermal stability of Ba-S was higher than that of Ba-L. An analysis of the secondary structure as well as the predicted three-dimensional structure of Ba-S showed that Ba-S retained all of the necessary domains (domains A, B, and C) which were most likely to be required for functionality as alpha-amylase.
Colloids Vs. Crystalloids—A Continuing Controversy (1984)

The crystalloid vs. colloid controversy is based on a disagreement as to the most effective, safest, and most economical method of maintaining an effective plasma volume in shock patients. This review discusses Starling's law of fluid movement, with a definition of each term in the normal physiological state, and presents examples of how each component of Starling's law differs in the two major types of pulmonary edema: (1) cardiogenic and (2) noncardiogenic. The colloid-crystalloid literature is reviewed briefly with an emphasis on the major studies that support each side, and the deficiencies in each study. The arguments supporting each side of the crystalloid-colloid debate are then listed, with a summary that demonstrates the areas of agreement between the two schools of thought on fluid resuscitation. Each major colloid (albumin, dextran, hetastarch) and a representative crystalloid (lactated Ringer's) are discussed in terms of their chemistry; pharmacology and indications; and precautions, adverse reactions, and side effects. A table is included that summarizes the available products' data regarding composition, volume expansion, duration of expansion, half-life, metabolism, elimination, precautions, adverse reactions, and dose.
Printed freeform lens arrays on multi-core fibers for highly efficient coupling in astrophotonic systems (2017)

Coupling of light into multi-core fibers (MCF) for spatially resolved spectroscopy is of great importance to astronomical instrumentation. To achieve high coupling efficiencies along with fill-fractions close to unity, micro-optical elements are required to concentrate the incoming light to the individual cores of the MCF. In this paper we demonstrate facet-attached lens arrays (LA) fabricated by two-photon polymerization. The LA provide close to 100% fill-fraction along with efficiencies of up to 73% (down to 1.4 dB loss) for coupling of light from free space into an MCF core. We show the viability of the concept for astrophotonic applications by integrating an MCF-LA assembly in an adaptive-optics test bed and by assessing its performance as a tip/tilt sensor.
Agrobacterium-Mediated Plant Transformation and its Further Applications to Plant Biology (1987)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
Synthesis and binding properties of monomeric and dimeric guanine and cytosine amine derivatives (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and binding properties of monomeric and dimeric guanine and cytosine amine derivativesJonathan L. Sessler, Darren Magda, and Hiroyuki FurutaCite this: J. Org. Chem. 1992, 57, 3, 818–826Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/jo00029a008https://doi.org/10.1021/jo00029a008research-articleACS PublicationsRequest reuse permissionsArticle Views489Altmetric-Citations37LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Improved Filtration Technique for Concentrating and Harvesting Bacteria (1980)

An improved technique is described for the filtrative concentration and harvesting of bacterial cultures. A pleated tangential flow filtration unit containing 1,000 cm of 0.2-mum-pore-size microporous membrane was used to rapidly (30 to 50 min) reduce the volume of 5 liters of bacterial culture of approximately 10 cells per ml to 0.2 to 0.5 liters of concentrated bacterial suspension. The effects of cell concentration, filtration pressure, and tangential flow rate were examined with respect to the rate of concentration and cell viability. Recovery efficiencies were between 60 and 75%, with no apparent impairment of organism viability. Cell concentration exerted the predominant effect on the filtration rate.
Rank-Constrained Solutions to Linear Matrix Equations Using PowerFactorization (2009)

Algorithms to construct/recover low-rank matrices satisfying a set of linear equality constraints have important applications in many signal processing contexts. Recently, theoretical guarantees for minimum-rank matrix recovery have been proven for nuclear norm minimization (NNM), which can be solved using standard convex optimization approaches. While nuclear norm minimization is effective, it can be computationally demanding. In this work, we explore the use of the PowerFactorization (PF) algorithm as a tool for rank-constrained matrix recovery. Empirical results indicate that incremented-rank PF is significantly more successful than NNM at recovering low-rank matrices, in addition to being faster.
The SECRET and SOUL of Marlboro (2008)

Philip Morris and other tobacco companies have been using ammonia in their manufacturing for more than half a century, and for a variety of purposes: to highlight certain flavors, to expand or "puff up" the volume of tobacco, to prepare reconstituted tobacco sheet ("recon"), to denicotinize (reduce the amount of nicotine in) tobacco, and to remove carcinogens. By the early 1960s, however, Philip Morris had also begun using ammonia to "freebase" the nicotine in cigarette smoke, creating low-yield (reduced-tar or -nicotine) cigarettes that still had the nicotine kick necessary to keep customers "satisfied" (i.e., addicted). We show that Philip Morris discovered the virtues of freebasing while analyzing the impact of the ammoniated recon used in Marlboro cigarettes. We also show how Marlboro's commercial success catalyzed efforts by the rest of the tobacco industry to discover its "secret," eventually identified as ammonia technology, and how Philip Morris later exploited the myriad uses of ammonia (e.g., for flavoring and expanding tobacco volume) to defend itself against charges of manipulating the nicotine deliveries of its cigarettes.
Estrogen receptor (ER) modulators each induce distinct conformational changes in ER α and ER β (1999)

Estrogen receptor (ER) modulators produce distinct tissue-specific biological effects, but within the confines of the established models of ER action it is difficult to understand why. Previous studies have suggested that there might be a relationship between ER structure and activity. Different ER modulators may induce conformational changes in the receptor that result in a specific biological activity. To investigate the possibility of modulator-specific conformational changes, we have applied affinity selection of peptides to identify binding surfaces that are exposed on the apo-ERs alpha and beta and on each receptor complexed with estradiol or 4-OH tamoxifen. These peptides are sensitive probes of receptor conformation. We show here that ER ligands, known to produce distinct biological effects, induce distinct conformational changes in the receptors, providing a strong correlation between ER conformation and biological activity. Furthermore, the ability of some of the peptides to discriminate between different ER alpha and ER beta ligand complexes suggests that the biological effects of ER agonists and antagonists acting through these receptors are likely to be different.
Domain Adaptation with Active Learning for Word Sense Disambiguation (2007)

When a word sense disambiguation (WSD) system is trained on one domain but applied to a different domain, a drop in accuracy is frequently observed. This highlights the importance of domain adaptation for word sense disambiguation. In this paper, we first show that an active learning approach can be successfully used to perform domain adaptation of WSD systems. Then, by using the predominant sense predicted by expectation-maximization (EM) and adopting a count-merging technique, we improve the effectiveness of the original adaptation process achieved by the basic active learning approach.
Discovery of Potent Competitive Inhibitors of Indoleamine 2,3-Dioxygenase with in Vivo Pharmacodynamic Activity and Efficacy in a Mouse Melanoma Model (2009)

A hydroxyamidine chemotype has been discovered as a key pharmacophore in novel inhibitors of indoleamine 2,3-dioxygenase (IDO). Optimization led to the identification of 5l, which is a potent (HeLa IC(50) = 19 nM) competitive inhibitor of IDO. Testing of 5l in mice demonstrated pharmacodynamic inhibition of IDO, as measured by decreased kynurenine levels (>50%) in plasma and dose dependent efficacy in mice bearing GM-CSF-secreting B16 melanoma tumors.
Characterization of progesterone receptor A and B expression in human breast cancer. (1995)

The human progesterone receptor (PR) is a ligand-activated nuclear transcription factor that mediates progesterone action in target tissues. Two PR proteins, PR-A (M(r) 81,000-83,000) and PR-B (M(r) 116,000-120,000), have been described and different physiological activities ascribed to each on the basis of in vitro studies, suggesting that their ratio of expression may control progesterone responsiveness in target cells. Presence of PR in breast tumors is an important indicator of likely responsiveness to endocrine agents. However, the relative expression of PR-A and B in breast cancer has not been described, and its clinical significance has not been addressed. Expression of PR-A and B was measured by immunoblot analysis of 202 PR-positive human breast tumor cytosols. The ratio of expression of the two PR proteins (PR-A/B) ranged from 0.04 to 179.3. The median PR-A/B ratio was 1.26, and 61.4% of samples had PR-A/B ratios between 0 and 2. PR-A/B ratios deviated significantly from a normal log distribution; tumors containing a PR-A/B ratio greater than 4 were overrepresented in the group. Linear regression analysis revealed that high PR-A/B ratios, in general, derived from a low concentration of PR-B rather than high expression of PR-A. PR-A/B protein ratios were not correlated with the age of the patient or with total PR concentration. A third PR protein band (PR78kDa) was detected in a number of samples and comprised greater than 20% of total PR protein in 52 (25.7%) of the 202 tumor samples examined. The range or frequency distribution of PR-A/B ratios in samples containing PR78kDa was not different to the overall group. In summary, in PR-positive breast tumors, the ratio of expression of PR-A and B proteins is close to unity, as is seen in a number of other progestin target tissues. However, a significant proportion of tumors expressed very low levels of PR-B and a consequently high PR-A/B ratio. Although the clinical consequence of this observation is not known, the in vitro findings that PR-A may act as a repressor of PR-B suggest that tumors containing primarily PR-A may identify a subset of patients with low or aberrant response to endocrine agents.
Single-stranded DNA and RNA origami (2017)

Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We describe a framework to design and synthesize a single DNA or RNA strand to self-fold into a complex yet unknotted structure that approximates an arbitrary user-prescribed shape. We experimentally construct diverse multikilobase single-stranded structures, including a ~10,000-nucleotide (nt) DNA structure and a ~6000-nt RNA structure. We demonstrate facile replication of the strand in vitro and in living cells. The work here thus establishes unimolecular folding as a general strategy for constructing complex and replicable nucleic acid nanostructures, and expands the design space and material scalability for bottom-up nanotechnology.
Electron delocalisation and stabilisation in substituted amino- and hydroxypropynyl radicals (1987)

A series of aminopropynes, RCCCH2NH2(R = H, Me, But, Me3Si), RCCCH2N(SiMe3)2, and hydroxypropynes RCCCH2OH (R = H, Me, But, Me3Si, CF3, and EtO2C), were prepared and the corresponding α-aminopropynyl and α-hydroxypropynyl radicals were examined by e.s.r. spectroscopy. For the first series, the C–N bond rotation barriers were determined from the exchange broadening in the spectra and hence radical stabilisation energies were estimated. The spin distribution in these series indicated an extra delocalisation in radicals with captodative substitution.
Site-directed RNA repair of endogenous Mecp2 RNA in neurons (2017)

Rett syndrome (RTT) is a debilitating neurological disorder caused by mutations in the gene encoding the transcription factor Methyl CpG Binding Protein 2 (MECP2). A distinct disorder results from <i>ME</i><i>CP2</i> gene duplication, suggesting that therapeutic approaches must restore close to normal levels of MECP2. Here, we apply the approach of site-directed RNA editing to repair, at the mRNA level, a disease-causing guanosine to adenosine (G > A) mutation in the mouse MeCP2 DNA binding domain. To mediate repair, we exploit the catalytic domain of Adenosine Deaminase Acting on RNA (ADAR2) that deaminates A to inosine (I) residues that are subsequently translated as G. We fuse the ADAR2 domain, tagged with a nuclear localization signal, to an RNA binding peptide from bacteriophage lambda. In cultured neurons from mice that harbor an RTT patient G > A mutation and express engineered ADAR2, along with an appropriate RNA guide to target the enzyme, 72% of <i>Mecp2</i> mRNA is repaired. Levels of MeCP2 protein are also increased significantly. Importantly, as in wild-type neurons, the repaired MeCP2 protein is enriched in heterochromatic foci, reflecting restoration of normal MeCP2 binding to methylated DNA. This successful use of site-directed RNA editing to repair an endogenous mRNA and restore protein function opens the door to future in vivo applications to treat RTT and other diseases.
Evolution of High-Sensitivity Microarray Technology (2003)

Microarray technology is a multiplex analytical technique for the detection of many different analytes in a mixture of biomolecules. The detection limits for each of the analytes for which the array is designed depend on a multiplicity of reaction parameters, the array itself, and profoundly on the label and detection technology employed. Significant improvements in assay sensitivity have been achieved by optimizing all steps that affect the generation of signal and noise. Nanoparticle technology brings a new dimension to this technology by providing not only higher sensitivity but also improved specificity for hybridization-based microarray assay systems.
Calcium Phosphate Mediated Gene Transfer into Established Cell Lines (2003)

DNA transfection is one of the most important techniques in molecular genetics. It is this technique that has made possible the dissection of complex eukaryotic genes and the characterization of the function of their components (1-7) as well as the isolation of particular genes on the basis of their expression in cultured cells (8-11).
Enterococci: New Aspects of an Old Organism (1999)

Enterococci are a long-known cause of bacterial endocarditis and a more recently recognized cause of nosocomial infection and superinfection. While much is known about the many antibiotic resistances of enterococci, less is known about the organism itself and how it causes disease. This article presents a brief overview of enterococci and its possible virulence factors and summarizes the authors' efforts to understand the features of this organism that may contribute to its disease potential.
THE AETIOLOGY OF OBESITY IN CHILDREN A Study of 101 Twin Pairs (1976)

The aetiology of obesity in children is studied here with the aid of a material consisting of 40 monozygotic and 61 dizygotic twins. The importance of heredity, early nutrition, and environment during preschool age is analysed. Genetic factors, studied by comparison of intra-pair differences in monozygotic and dizygotic twins, apparently play a decisive role in the origin of obesity. Analysis of the relation between birth weight and later development of subcutaneous fat in different types of twins does not show that intra-uterine nutrition is of aetiological importance. The comparison at age seven of groups of ordinary siblings and twins of different types does not support the idea that the pre-school environment is of importance in aetiology. Such influence seems to act mainly as a modifying factor.
Distinct Osteoclast Precursors in the Bone Marrow and Extramedullary Organs Characterized by Responsiveness to Toll-Like Receptor Ligands and TNF-α (2003)

Osteoclasts are derived from hemopoietic stem cells and play critical roles in bone resorption and remodeling. Multinucleated osteoclasts are attached tightly to bone matrix, whereas precursor cells with the potential to differentiate into osteoclasts in culture are widely distributed. In this study, we assessed the characteristics of osteoclast precursors in bone marrow (BM) and in extramedullary organs as indicated by their responsiveness to ligands for Toll-like receptors (TLRs) and to TNF-alpha. Development of osteoclasts from precursor cells in the BM was inhibited by CpG oligonucleotides, a ligand for TLR9, but not by LPS, a ligand for TLR4. BM osteoclasts were induced by TNF-alpha as well as receptor activator of NF-kappaB ligand in the presence of M-CSF. Splenic osteoclast precursors, even in osteoclast-deficient osteopetrotic mice, differentiated into mature osteoclasts following exposure to TNF-alpha or receptor activator of NF-kappaB ligand. However, splenic osteoclastogenesis was inhibited by both LPS and CpG. Osteoclastogenesis from peritoneal precursors was inhibited by not only these TLR ligands but also TNF-alpha. The effects of peptidoglycan, a ligand for TLR2, were similar to those of LPS. BM cells precultured with M-CSF were characterized with intermediate characteristics between those of splenic and peritoneal cavity precursors. Taken together, these findings demonstrate that osteoclast precursors are not identical in the tissues examined. To address the question of why mature osteoclasts occur only in association with bone, we may characterize not only the microenvironment for osteoclastogenesis, but also the osteoclast precursor itself in intramedullary and extramedullary tissues.
Afatinib in the treatment of head and neck squamous cell carcinoma (2013)

Phase II trials in HNSCC show that daily oral treatment with afatinib is tolerable. Most common toxicities are skin rash and diarrhea. Afatinib has clinical activity as a single agent in a subset of refractory and/or metastatic HNSCC patients. It is thought that ongoing Phase III trials should better clarify the role of this compound in the treatment of HNSCC.
Structure of an antifreeze polypeptide and its precursor from the ocean pout, Macrozoarces americanus. (1985)

Serum antifreeze polypeptides (AFP) from Newfoundland ocean pout have been resolved by ion exchange chromatography and reverse phase high performance liquid chromatography into at least 12 components. The protein sequences of three of the AFP were determined using a combination of protein Edman degradation and cDNA sequencing. The AFP precursor protein encodes for a preprotein of 87 amino acids with no obvious prosequences. Two of the AFP (SP1-A and SP1-C) were separate gene products with minor amino acid sequence differences. The protein structure of SP1-C precursor is MKSVILTGLLFVLLCVDHMTASQSVVAT QLIPINTALTPAMMEGKVTNPIGIPFAEMSQIVGKQVNTPVAKGQTLMPNMVKTYVAGK. The third AFP (SP1-B) is a post-translation modification product of SP1-C. These experiments indicate that the ocean pout AFP are a multigene family with protein structure different from any other known polypeptide antifreezes.