gebhart/patrepeval huggingface dataset:
Assembling Genomic DNA Sequences with PHRAP (2007)

The PHRAP assembly program provides rapid comparison, alignment, and assembly of large sets of DNA sequences. PHRAP compares sequences by searching for pairs of perfectly matching "words" or sequence regions that meet certain criteria. If a match is found, PHRAP then tries to extend the alignment into overlapping sections called contigs. PHRAP uses quality values produced by the PHRED basecaller to strike a balance between tolerance of discrepancies and prevention of stacking repeat sequences. The PHRAP assembly algorithm is generally used as part of the PHRED/PHRAP/Consed software suite for sequence analysis. This unit presents instructions for basic usage of the PHRAP assembler, including preparation of the input files (Support Protocols 1 and 2) and explanation of output files (Basic Protocols 1 and 2). Several command line options for changing the PHRAP assembly parameters are also discussed (Basic Protocol 3).
Thermal Analysis of Polyurethane Block Polymers (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermal Analysis of Polyurethane Block PolymersRobert W. Seymour and Stuart L. CooperCite this: Macromolecules 1973, 6, 1, 48–53Publication Date (Print):January 1, 1973Publication History Published online1 May 2002Published inissue 1 January 1973https://pubs.acs.org/doi/10.1021/ma60031a008https://doi.org/10.1021/ma60031a008research-articleACS PublicationsRequest reuse permissionsArticle Views4173Altmetric-Citations496LEARN 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
Cancer Immunotherapy: Selected Targets and Small‐Molecule Modulators (2016)

There is a significant amount of excitement in the scientific community around cancer immunotherapy, as this approach has renewed hope for many cancer patients owing to some recent successes in the clinic. Currently available immuno-oncology therapeutics under clinical development and on the market are mostly biologics (antibodies, proteins, engineered cells, and oncolytic viruses). However, modulation of the immune system with small molecules offers several advantages that may be complementary and potentially synergistic to the use of large biologicals. Therefore, the discovery and development of novel small-molecule modulators is a rapidly growing research area for medicinal chemists working in cancer immunotherapy. This review provides a brief introduction into recent trends related to selected targets and pathways for cancer immunotherapy and their small-molecule pharmacological modulators.
Twenty-four hour canine renal preservation by pulsatile perfusion, hypothermic storage, and combinations of the two methods. (1977)

A comparison of the effectiveness of two renal preservation techniques was studied in 30 cannine renal pairs. In the absence of warm ischemia, 24-hr preservation by pulsatile perfusion was not significantly superior to hypothermic storage. When 15 min of warm ischemia was added as an additional insult, pulsatile perfusion afforded significantly better early function than cold storage. Combinations of pulsatile perfusion and hypothermic storage following 15 min of warm ischemia were superior to hypothermic storage alone, but inferior to pulsatile perfusion. Kidneys initially perfused for 6 hr and then cold-stored functioned slightly better than kidneys perfused for 18 hr after initial cold storage.
3D DRAM Design and Application to 3D Multicore Systems (2009)

Editor's note:From a system architecture perspective, 3D technology can satisfy the high memory bandwidth demands that future multicore/manycore architectures require. This article presents a 3D DRAM architecture design and the potential for using 3D DRAM stacking for both L2 cache and main memory in 3D multicore architecture.—Yuan Xie, Pennsylvania State University
Ex Situ and In Situ Stability of Platinum Supported on Niobium-Doped Titania for PEMFCs (2009)

The stability and activity of niobium-doped titania were compared to those of commercial catalyst (HiSpec 4000), both ex situ and in a proton exchange membrane fuel cell. The stability test involved holding the cell at for . Fuel cell polarization curves were obtained both before and after the potential holds. Cyclic voltammogram data showed that the Pt surface area was stable for even after holding for at . A significant drop in the Pt surface area was observed, however, for after at . The high potential hold test showed significantly higher stability of the membrane electrode assembly with compared to that with .
Turbulence-free space-time quantum imaging (2013)

We experimentally demonstrate turbulence-free space-time quantum imaging. Quantum images of remote objects are produced with two sensors measuring at different space-time points under turbulent conditions. The quantum images generated move depending on the time delay between the two sensor measurements and the speed of a rotating ground glass that is part of a chaotic laser light source. For small delay times turbulence has virtually no adverse affect on the moving quantum images. The experimental setup and findings contribute to understanding the fundamentals of multi-photon quantum interference in complex media. Furthermore, the space-time memory demonstrated in our research provides important new pathways for investigating quantum imaging, quantum information storage and quantum computing. The turbulence-free space-time quantum imaging procedure greatly increases the information content of each photon measured. The moved quantum images are in fact new images that are stored in a space-time virtual memory process. The images are stored within the same quantum imaging data sets and thus quantum imaging can produce more information per photon measured than was previously realized.
Characterization of FRA6E and its potential role in autosomal recessive juvenile parkinsonism and ovarian cancer (2003)

Abstract Characterization of FRA6E (6q26), the third most frequently observed common fragile site (CFS) in the human population, determined that aphidicolin‐induced instability at FRA6E extends over a very large region (3.6 Mb). Sequence analysis identified eight genes ( IGF2R , SLC22A1 , SLC22A2 , SLC22A3 , PLG , LPA , MAP3K4 , and PARK2 ) as mapping within the large FRA6E region. PARK2 , the gene associated with autosomal recessive juvenile parkinsonism (ARJP), accounts for more than half of the CFS. Homozygous deletions and large heterozygous deletions have been observed in PARK2 in ARJP patients. RT‐PCR analysis of the eight genes localizing to FRA6E indicated that 50% of the genes, including PARK2 , were down‐regulated in one or more of the primary ovarian tumors analyzed. PARK2 expression was down‐regulated in 60.0% of the primary ovarian tumors analyzed. Additionally, we found tumor‐specific alternative transcripts of PARK2 . Loss of heterozygosity analysis of primary ovarian tumors by use of polymorphic markers in the 6q26 region demonstrated 72% LOH in the center of the PARK2 gene, the highest of any of the markers tested. FRA6E shares many similarities with FRA3B (3p14.2) and FRA16D (16q23.2) in representing a large region of genomic instability and containing an extremely large gene that may play a role in the development of ovarian and many other cancers. © 2003 Wiley‐Liss, Inc.
Polymer-supported alkyl azodicarboxylates for Mitsunobu reactions (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymer-supported alkyl azodicarboxylates for Mitsunobu reactionsLee D. Arnold, Hanaa I. Assil, and John C. VederasCite this: J. Am. Chem. Soc. 1989, 111, 11, 3973–3976Publication Date (Print):May 1, 1989Publication History Published online1 May 2002Published inissue 1 May 1989https://pubs.acs.org/doi/10.1021/ja00193a032https://doi.org/10.1021/ja00193a032research-articleACS PublicationsRequest reuse permissionsArticle Views1079Altmetric-Citations67LEARN 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
Structural Consequences of Histidine Phosphorylation: NMR Characterization of the Phosphohistidine Form of Histidine-Containing Protein from Bacillus subtilis and Escherichia coli (1994)

The bacterial phosphoenolpyruvate:sugar phosphotransferase system involves a series of reactions in which phosphoprotein intermediates are formed. Histidine-containing protein (HPr) is phosphorylated on the N delta 1 position of the imidazole ring of His15 by enzyme I and acts as a phosphoryl donor to the sugar-specific enzymes IIA. The structure of phosphorylated HPr from Bacillus subtilis, primarily, and from Escherichia coli has been studied by nuclear magnetic resonance (NMR) spectroscopy. Phosphorylation of His15 results in large downfield shifts in amide proton and nitrogen resonances for residues 16 and 17 but results in only modest or no shifts in other backbone resonances. The exchange rates of these two amide groups are decreased more than 10-fold upon phosphorylation. Analysis of the coupling constants 3JNH alpha revealed no significant changes throughout the protein, indicating that backbone phi dihedral angles do not change detectably. 3J alpha beta and 3JN beta patterns determined from P.E.COSY and HNHB spectra, respectively, revealed a change in one side chain, that of conserved Arg17. Analysis of NOESY spectra revealed a limited number of changes in NOEs involving protons in Ser12, His15, Arg71, and Pro18 in B. subtilis HPr. The NMR results indicate that the Arg17 side chain becomes limited in its conformational range in the phosphorylated protein, taking on a conformation that points its guanidinium group toward the phosphoryl group on His15. In addition, the tautomeric and ionization states of His15 have been determined using 15N and 31P NMR. At neutral pH, the imidazole is predominantly in the protonated form and the phosphoryl group is in the dianionic form in P-His15. Altogether, the results indicate that phosphorylation of His15 yields only a local effect on the protein's structure. The data are consistent with a small change in the disposition of the histidine side chain, allowing phosphoryl group oxygens to serve as hydrogen bond acceptors for the amide protons of residues Ala16 and Arg17, which constitute the first two residues of an alpha-helix. Thus, similar to many proteins that bind phosphoryl moieties noncovalently, the phosphoryl group in P-His15-HPr is situated to allow for a favorable electrostatic interaction at the N-terminal end of an alpha-helix.
Abdominal Obesity and Dyslipidemia in the Metabolic Syndrome: Importance of Type 2 Diabetes and Familial Combined Hyperlipidemia in Coronary Artery Disease Risk (2004)

Regional body fat distribution has an important influence on metabolic and cardiovascular risk factors. Increased abdominal (visceral) fat accumulation is a risk factor for coronary artery disease (CAD), dyslipidemia, hypertension, stroke, and type 2 diabetes. The recent emphasis on treatment of the dyslipidemia of the metabolic syndrome (hypertriglyceridemia, reduced high-density lipoprotein, and increased small, dense low-density lipoprotein particle number) has compelled practitioners to consider lipid-lowering therapy in a greater number of their patients, as one in two individuals over age 50 has the metabolic syndrome. Individuals with the metabolic syndrome typically have normal low-density lipoprotein cholesterol levels, and current lipid-lowering guidelines may underestimate their cardiovascular risk. Two subgroups of patients with the metabolic syndrome are at particularly high risk for premature CAD. One, individuals with type 2 diabetes, accounts for 20-30% of early cardiovascular disease. The second, familial combined hyperlipidemia, accounts for an additional 10-20% of premature CAD. Familial combined hyperlipidemia is characterized by the metabolic syndrome in addition to a disproportionate elevation of apolipoprotein B levels. The measurement of fasting glucose and apolipoprotein B, in addition to the fasting lipid profile, can help to estimate CAD risk in patients with the metabolic syndrome.
Tumor-associated macrophages (2015)

Tumor-associated macrophages (TAMs) are key cells in tumor-associated chronic inflammation, and can promote tumor growth, proliferation, angiogenesis, invasion, metastasis and chemotherapy resistance. Under different circumstances, macrophages can be polarized into classically activated macrophages (M1) and alternatively activated macrophages (M2). Cyclooxygenase 2, nuclear factor-κB, Toll like receptor (TLR) signaling pathway, anoxia, the protooncogene MYC, Notch signaling pathway and cytokines are all involved in the transition of TAMs from M1 to M2 phenotype. The phenotype and function of TAMs vary with tumor progression, so antitumor drug therapies targeting macrophages should depend on the stage of tumors.


Key words: 
Macrophages; Neoplasms; Phenotype
Biological control of onion neck rot (Botrytis aclada): Protection of wounds made by leaf topping (1991)

The efficacy of fungal antagonists in protecting onions from neck rot caused by Botrytis aclada was investigated. Leaf wounds made by topping of onions during harvest, which are considered as important entrance sites for B. aclada, were treated with conidial suspensions (5 × 107 conidia ml‐1) of antagonists. In field experiments with artificial inoculation with conidia of B. aclada, applications of Trichoderma viride during harvest reduced the incidence of neck rot, assessed after three months’ storage of the onions at 9° C, from 35% to 24% in 1989 and from 28% to 18% in 1990, when onions initially had been stored under favourable conditions for fungal development. Comparable results were obtained with T. hamatum and Gliocladium roseum. A bioassay based on wound treatment of detached onion leaves was developed to select further antagonists. From 40 candidate antagonists tested, 20 strains gave similar or better control than the strain of T. viride applied in the field experiments. Effective antagonists could be found amongst strains of Trichoderma spp. Gliocladium spp. and Penicillium spp. as well as amongst fungi such as Aureobasidium pullulans and yeasts isolated from green leaves of onion or rye.
A Versatile Viral System for Expression and Depletion of Proteins in Mammalian Cells (2009)

The ability to express or deplete proteins in living cells is crucial for the study of biological processes. Viral vectors are often useful to deliver DNA constructs to cells that are difficult to transfect by other methods. Lentiviruses have the additional advantage of being able to integrate into the genomes of non-dividing mammalian cells. However, existing viral expression systems generally require different vector backbones for expression of cDNA, small hairpin RNA (shRNA) or microRNA (miRNA) and provide limited drug selection markers. Furthermore, viral backbones are often recombinogenic in bacteria, complicating the generation and maintenance of desired clones. Here, we describe a collection of 59 vectors that comprise an integrated system for constitutive or inducible expression of cDNAs, shRNAs or miRNAs, and use a wide variety of drug selection markers. These vectors are based on the Gateway technology (Invitrogen) whereby the cDNA, shRNA or miRNA of interest is cloned into an Entry vector and then recombined into a Destination vector that carries the chosen viral backbone and drug selection marker. This recombination reaction generates the desired product with >95% efficiency and greatly reduces the frequency of unwanted recombination in bacteria. We generated Destination vectors for the production of both retroviruses and lentiviruses. Further, we characterized each vector for its viral titer production as well as its efficiency in expressing or depleting proteins of interest. We also generated multiple types of vectors for the production of fusion proteins and confirmed expression of each. We demonstrated the utility of these vectors in a variety of functional studies. First, we show that the FKBP12 Destabilization Domain system can be used to either express or deplete the protein of interest in mitotically-arrested cells. Also, we generate primary fibroblasts that can be induced to senesce in the presence or absence of DNA damage. Finally, we determined that both isoforms of the AT-Rich Interacting Domain 4B (ARID4B) protein could induce G1 arrest when overexpressed. As new technologies emerge, the vectors in this collection can be easily modified and adapted without the need for extensive recloning.
Transport of a soft cargo on a nanoscale ratchet (2011)

Surface ratchets can guide droplet transport for microfluidic systems. Here, we demonstrated the actuation of microgels encapsulated in droplets using a unidirectional nanotextured surface, which moves droplets with low vibration amplitudes by a ratcheting mechanism. The nanofilm carries droplets along the ratchets with minimal drop shape deformation to move the encapsulated soft cargo, i.e., microscale hydrogels. The tilted nanorods of the nanofilm produce unidirectional wetting, thereby enabling droplet motion in a single direction. Maximum droplet translation speed on the nanofilm was determined to be 3.5 mm∕s, which offers a pathway towards high throughput microgel assembly applications to build complex constructs.
Selective Ion Passage through Functionalized Graphene Nanopores (2008)

We design functionalized nanopores in graphene monolayers and show by molecular dynamics simulations that they provide highly selective passage of hydrated ions. Only ions that can be partly stripped of their hydration shells can pass through these ultrasmall pores with diameters of ∼5 Å. For example, a fluorine−nitrogen-terminated pore allows the passage of Li+, Na+, and K+ cations with the ratio 9:14:33, but it blocks the passage of anions. The hydrogen-terminated pore allows the passage of F−, Cl−, and Br− anions with the ratio 0:17:33, but it blocks the passage of cations. These nanopores could have potential applications in molecular separation, desalination, and energy storage systems.
Novel Fold and Putative Receptor Binding Site of Granulocyte-Macrophage Colony-Stimulating Factor (1991)

Granulocyte-macrophage colony-stimulating factor (GM-CSF) stimulates the development of and the cytotoxic activity of white blood cells. Recombinant human GM-CSF has proven useful in the treatment of blood disorders. The structure of GM-CSF, which was determined at 2.4 angstrom resolution by x-ray crystallography, has a novel fold combining a two-stranded antiparallel beta sheet with an open bundle of four alpha helices. Residues implicated in receptor recognition, which are distant in the primary sequence, are on adjacent alpha helices in the folded protein. A working model for the receptor binding site is presented.
Beam shaping concepts with aspheric surfaces (2015)

Employing aspherical lenses to reduce aberrations to improve focusing qualities is a well-known concept. But the potpourri of aspheric surfaces offers way more possibilities, even the chance for flexible beam shaping setups. Since these are refractive optical elements the beam shaping is robust with respect to wavelength changes. Being able to generate ring shaped light distributions is interesting for various applications. Here the most uncommon aspheric surface – an axicon – is utilized. Axicons are glass cones, which convert the incoming light into Bessel beams. Those are characterized by their concentric ring structure and long depth of focus, which makes them very interesting for material processing. Above that, combining such an axicon with a focusing lens leads to a ring focus. Its size is not only determined by the choice of the axicon angle and the lens properties, but also through the diameter of the incoming beam. Thus, for optimal usage a flexible beam expander, which leaves the beam quality unaltered is mandatory. The remarkable properties of these beam shaping set-ups are shown in theory and experimentally. Furthermore, a configuration consisting of two axicons and interchangeable focusing lenses is presented. For one thing, this set-up allows for tuning of the working distance in any required way for optimal material processing. For another thing, the induced chromatic focal shift of the focusing lens that occurs by a change of wavelength can be compensated for by adapting the distance of the axicons and leaving the working distance unchanged.
Limiting Current Enhancement by Self‐Induced Redox Cycling on a Micro‐Macro Twin Electrode (1991)

The current arising from a reversible redox reaction involving soluble species occurring at a microelectrode may be increased by moving a large electrode at open circuit close to the microelectrode. This phenomena is readily explained. The product of the electrochemical reaction at the microelectrode diffuses the short distance to the nearest part of the macroelectrode and alters the concentration of the redox species at this location on the macroelectrode, compared to other locations at the electrode surface. In this situation, the macroelectrode behaves as a shorted concentration cell and attempts to reduce the concentration aberration caused by the reaction occurring at the microelectrode. This is accomplished by producing more of the original reactant for the microelectrode. This, in turn, increases the flux of reactant to the microelectrode and, therefore, also the current at the microelectrode.
Boron-containing inhibitors of synthetases (2011)

The use of boron in small-molecule pharmaceuticals is increasing. Boron's ubiquitous occurrence in nature and the recent success of a boronic acid drug (Velcade®) in the clinic have alleviated many concerns over its use in pharmaceuticals. In addition, the unique physicochemical properties of boronic acids make them an attractive addition to the medicinal chemists toolbox. This tutorial review will discuss these properties and potential benefits for anyone interested in finding novel enzyme inhibitors. An exceptional class of boronic acids, the oxaboroles, will be highlighted and their properties and uses will be discussed in detail. Finally, the current paradigm for the reaction of boronic acids with enzyme nucleophiles will be summarized.