gebhart/patrepeval huggingface dataset:
A Backbone Linker for BOC-Based Peptide Synthesis and On-Resin Cyclization:  Synthesis of Stylostatin 1<sup>,</sup> (1999)

We have developed a new 4-alkoxybenzyl-derived linker that anchors the C-terminal amino acid to the resin through the alpha-nitrogen atom. The linker allows BOC solid-phase peptide assembly and peptide cleavage using standard HF protocols. This linking strategy provides a versatile on-resin route to cyclic peptides and avoids the diketopiperazine formation that is prominent when using FMOC chemistry on backbone linkers. The linker was prepared by forming the aryl ether from 4-hydroxybenzaldehyde and bromovaleric acid. Subsequent reductive amination of the aldehyde with an allyl-protected amino acid ester and acylation of the resulting secondary amine provided the tertiary amide. After linking the amide to the resin, standard BOC SPPS, followed by allyl deprotection, cyclization, and HF cleavage gave cyclic peptides in high purity. To exemplify the strategy, the cytotoxic heptapeptide, stylostatin 1, was synthesized from two linear precursors. For comparison purposes, the yields of the on-resin and solution-phase cyclization were determined and found to be dependent upon the linear precursor. This linker technology provides new solid-phase avenues in accessing libraries of cyclic peptides.
Nucleophilic displacements upon phenyl esters in which the direct relation between basicity of the leaving group and rate is determined by ground state conformations. Question of concerted catalysis in the hydrolysis of hexachlorophene esters (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleophilic displacements upon phenyl esters in which the direct relation between basicity of the leaving group and rate is determined by ground state conformations. Question of concerted catalysis in the hydrolysis of hexachlorophene estersThomas C. Bruice and Isao OkaCite this: J. Am. Chem. Soc. 1974, 96, 14, 4500–4507Publication Date (Print):July 1, 1974Publication History Published online1 May 2002Published inissue 1 July 1974https://pubs.acs.org/doi/10.1021/ja00821a025https://doi.org/10.1021/ja00821a025research-articleACS PublicationsRequest reuse permissionsArticle Views162Altmetric-Citations5LEARN 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
Effect of Rec <sup>−</sup> Mutations on the Activity of Colicinogenic Factors (1967)

The effect of two Rec(-) mutations (AB2463 and JC1553) on the ability of a cell to accept, maintain, and express the colicinogenic factors ColE(1), ColE(2), and ColV was examined in Escherichia coli. These mutations had no observable effect on the colicinogenic properties of the ColV factor, but prevented the spontaneous and induced production of colicins E(1) and E(2) which are determined by the ColE(1) and ColE(2) factors, respectively. The two Rec(-) mutations had no apparent effect on the ability of the cells to acquire, maintain, or transfer the ColE(1) and ColE(2) factors. These mutations did not affect the expression of immunity by any of the three Col factors. ColE(1) and ColE(2) were also shown to be indirectly induced by mating F(-) cells carrying these Col factors with ultraviolet-irradiated, non-colicinogenic, Hfr and F(+) cells. Indirect induction of colicin production occurred when either an irradiated F(+) Rec(+) or F(+) Rec(-) strain was employed as the donor strain.
Further thoughts on Newton’s zero-order rainbow (1994)

A zero-order rainbow angle may be defined as the relative minimum angle of deviation of geometrical light rays transmitted without internal reflections through a transparent particle. If the incident rays are parallel and the particle is a sphere, such a minimum does not exist. But if the incident rays are not parallel or if the particle has an elliptical rather than circular cross section, an angle of minimum deviation, hence a zero-order rainbow, can occur. For a spherical water droplet, the zero-order rainbow will occur when a point source is placed less than a droplet radius away from its surface. If a column of water with an elliptical cross section is illuminated by a plane wave, a zero-order rainbow will occur if the length of the major axis of the cross section is more than twice the length of the minor axis.
Asking the Right Questions in Crowd Data Sourcing (2012)

Crowd-based data sourcing is a new and powerful data procurement paradigm that engages Web users to collectively contribute information. In this work, we target the problem of gathering data from the crowd in an economical and principled fashion. We present Ask It!, a system that allows interactive data sourcing applications to effectively determine which questions should be directed to which users for reducing the uncertainty about the collected data. Ask It! uses a set of novel algorithms for minimizing the number of probing (questions) required from the different users. We demonstrate the challenge and our solution in the context of a multiple-choice question game played by the ICDE'12 attendees, targeted to gather information on the conference's publications, authors and colleagues.
Acute Eosinophilic Pneumonia Associated with Ranitidine (1996)

Andreu, Victoria M.D.; Bataller, Ramón M.D.; Caballería, Joan M.D.; Rodés, Joan M.D. Author Information
Low Temperature-Dependent Salmonid Alphavirus Glycoprotein Processing and Recombinant Virus-Like Particle Formation (2011)

Pancreas disease (PD) and sleeping disease (SD) are important viral scourges in aquaculture of Atlantic salmon and rainbow trout. The etiological agent of PD and SD is salmonid alphavirus (SAV), an unusual member of the Togaviridae (genus Alphavirus). SAV replicates at lower temperatures in fish. Outbreaks of SAV are associated with large economic losses of ~17 to 50 million $/year. Current control strategies rely on vaccination with inactivated virus formulations that are cumbersome to obtain and have intrinsic safety risks. In this research we were able to obtain non-infectious virus-like particles (VLPs) of SAV via expression of recombinant baculoviruses encoding SAV capsid protein and two major immunodominant viral glycoproteins, E1 and E2 in Spodoptera frugiperda Sf9 insect cells. However, this was only achieved when a temperature shift from 27°C to lower temperatures was applied. At 27°C, precursor E2 (PE2) was misfolded and not processed by host furin into mature E2. Hence, E2 was detected neither on the surface of infected cells nor as VLPs in the culture fluid. However, when temperatures during protein expression were lowered, PE2 was processed into mature E2 in a temperature-dependent manner and VLPs were abundantly produced. So, temperature shift-down during synthesis is a prerequisite for correct SAV glycoprotein processing and recombinant VLP production.
Influence of the elasticity ratio on the point of phase inversion in an immiscible polymer blend (2000)

At a shear rate of 10 s−1, a flow-induced phase inversion has been observed in-situ by optical microscopy on a blend of polydimethylsiloxane with solution of 50% of hydroxypropylcellulose in water for a range of concentrations. By increasing the shear rate up to 30 s−1, the elasticity ratio of the components can be changed without changing the viscosity ratio. The resultant steady-state morphology is not influenced by the variation of the elasticity ratio, contrary to a theoretical model.
Preparation of Radioactive CO<sub>2</sub> from BaCO<sub>3</sub> (1949)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of Radioactive CO2 from BaCO3Norman. Zwiebel, John. Turkevich, and Warren W. MillerCite this: J. Am. Chem. Soc. 1949, 71, 1, 376–377Publication Date (Print):January 1, 1949Publication History Published online1 May 2002Published inissue 1 January 1949https://pubs.acs.org/doi/10.1021/ja01169a520https://doi.org/10.1021/ja01169a520research-articleACS PublicationsRequest reuse permissionsArticle Views178Altmetric-Citations25LEARN 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
70 THz signal bandwidths through optical parametric processes in periodically poled stoichiometric lithium tantalate (2010)

Collinear broadband optical parametric generation was achieved in periodically poled Mg-doped stoichiometric lithium tantalate by picosecond pumping at 820-890 nm, i.e. close to zero group velocity ...
Modeling chemical bonding effects for protein electron crystallography: the transferable fragmental electrostatic potential (TFESP) method (2002)

This paper addresses the problem of determining the electrostatic potential of large proteins by the superposition of potentials calculated for small fragments. The use of different atomic and molecular fragments is considered for reproducing the molecular electrostatic potential of different conformations of N-acetylalanine methylamide (NAAMA) with an acceptable degree of error as measured by conventional R factors used in crystallographic structure refinement. Three different divisions of NAAMA are tested, producing fragments that incorporate increasingly more complete descriptions of molecular bonding with diminishing accuracy in geometric fit to the parent molecule: single atoms in molecules, bonded atoms in molecules and selected functional groups, such as the backbone peptide moiety, or the alpha-carbon, beta-carbon and their associated H atoms. In the resolution range 2.5-25A, the fairly straightforward use of single atoms in molecules reduces the calculated R factors by 5-15% over a free-atom superposition. No significant further improvement was found at the lowest resolutions with a superposition of single bonds in molecules and R factors were found to degrade with larger fragments at higher resolutions because of poor geometry fits to the atoms of the parent molecule. Because the potential distribution even for single atoms depends on the environment, the best accuracy will be obtained by using a library of fragment potentials calculated for each type of atom as a function of important protein conformations.
Circulating tumor DNA profiling to identify patients with metastatic colorectal cancer with improved overall survival following Sym004 treatment. (2018)

e15577 Background: Sym004, an antibody mixture targeting EGFR, has demonstrated promising activity in patients (pts) with anti-EGFR refractory metastatic colorectal cancer (mCRC). A Phase 2b trial evaluating Sym004 activity in 254 patients with mCRC was recently completed. Methods: All patients had RAS wild type tumors at the time of initial diagnosis and had responded to and subsequently relapsed on anti-EGFR antibody treatment. Baseline circulating tumor (ct)DNA profiles were obtained from 193 patients and analyzed for genomic changes using Guardant360 (Guardant Health). Results: Markers of anti-EGFR resistance such as KRAS mutations were confirmed to impact overall survival (OS) in Sym004 treated pts. A subset of pts without high allele frequency RAS mutations and BRAF V600E mutation in ctDNA termed Double Negative (DN)mCRC, was found to have an OS benefit of 3.5 months when receiving Sym004 compared to Standard of Care (SoC) (HR 0.71; p = 0.134). Further exclusion of patients with mutations in the EGFR extracellular domain (ECD) termed Triple Negative (TN) mCRC increased OS benefit of Sym004 vs. SoC to 5.5 months (HR 0.59; p = 0.044). Patients with detectable mutation in the EGFR-ECD not only had a higher number of genomic alterations but also strikingly heterogeneous and complex genomic profiles including multiple markers of anti-EGFR resistance such as subclonal BRAF, KRAS, NRAS, MAP2K1, or PIK3CA mutations, as well as ERBB2, KRAS, MET, or EGFR copy number gain/amplification. Preclinical studies demonstrated partial loss of Sym004 activity against EGFR-ECD mutated cells due to diminished binding of one of the Sym004 antibodies to the mutated receptor. Conclusions: The heterogeneous mutation landscape in patients with EGFR-ECD mutations as well as the partially impaired function of Sym004 against mutated receptors argues against the use of Sym004 for treatment of this patient subpopulation. Collectively, our data demonstrate that anti-EGFR refractory mCRC patients with DNmCRC and/or TNmCRC assessed by ctDNA are likely to benefit from Sym004 treatment, supporting a randomized registration trial in this genomically defined patient population.
Natural Convection From a Square Disk in the Intermediate Rayleigh Range (2005)

This technical brief reports on an experiment in which Ra is varied in an intermediate range. It is an interesting range because the values lie in a transition zone between laminar thin boundary layer dominated and conduction dominated natural convection. The experimental data are compared with existing correlations to check the accuracy and validity of these correlations for this transitional range of Ra. A new correlation that is only valid in this transitional zone is also proposed and compared with correlations of the same kind.
Comparison of Electrical Oscillations in Neurons with Induced or Spontaneous Cellular Rhythms due to Biochemical Regulation (1992)

Biological rhythms can be classified broadly into different categories, according to the way in which they occur. Thus, they can arise spontaneously in a given set of experimental conditions, as exemplified by rhythmic activity in nodal tissues of the heart, or they can be driven by some external periodic process. In the latter case, the biological rhythm is generally entrained in a certain range at the frequency of the forcing stimulus. Oscillations can also occur as a result of a change in external conditions that brings about the transition from a stable steady state to an oscillatory regime. The latter situations relate to different sorts of induced rhythms; indeed (see the introductory chapter by Bullock), induced rhythms are either triggered from silence or modulated from an ongoing rhythm by an external event, transient or sustained.
What Boeing Wants from Integrated Computational Materials Engineering for Metallic Materials (2012)

The steady increase in computing power and the recognition that computational models operating at different scales may begin to be combined into meso-models of materials behavior has produced a new discipline: Integrated Computational Materials Engineering (ICME). Formal recognition of this discipline has spurred research to develop and populate effective models, as well as the commercialization of codes to facilitate research and problem-solving. For research organizations, and for companies marketing commercial software platforms, guidance as to desirable model and code capabilities is critical to creation of a product that is useful and addresses problems of commercial importance. For industry, this means that ICME tools need to account for existing materials and processes, as well as those that are new and innovative. This paper examines ICME from the inside of an airframe materials organization, to clarify aspects of ICME methods and products that would be desirable for an original equipment manufacturer. This includes short-term benefits, such as assessing the impacts of process deviations, to the mid-term, such as estimation of material design allowables, to long-term benefits—the design of the next generation of airframe structural materials. The airframe industry is appropriately riskadverse, and replacement of experiential with computational methods represents a challenge that must be balanced by the creation of benefit that the ICME discipline promises. The intent of this paper is to communicate these benefits and challenges, in hopes of spurring discussion and the maturation of effective materials design tools to rival those in the structural disciplines.
INTRACELLULAR DEVELOPMENT OF POX VIRUSES (1953)

The intracellular development of viruses of the pox group is well suited to study by the electron microscope because the morphology of these viruses is so well known that they can be easily recognized whether in purified form or in thin sections of infected cells. In tissue sections, mature virus particles are always the most dense structures causing them to be conspicuous. Their shape is round to oval, although their exact size is difficult to determine in sections because the particles are not always cut at their major or minor axis. Purified virus has given values of about 210 × 260 milli-microns and the virus particles within cells are of this order of magnitude. The relative uniformity of size, shape, and density of the virus particles enable us to differentiate them from mitochondrial fragments which vary greatly in all these properties.
Immunofluorescence labeling of cell surface antigens in Dictyostelium (2013)

Immunolocalization of cellular antigens typically requires fixation and permeabilization of cells, prior to incubation with antibodies. Assessing a test protein abundantly present at the cell surface of Dictyostelium cells, we show that in fixed cells, permeabilization extracts almost completely this cell surface antigen. The extent of this artifact is variable depending on the procedure used for labeling and permeabilization, as well as on the antigen considered. An optimized protocol for labeling both surface and intracellular antigens without significant loss of labeling is proposed.
Plasmids (2002)

Abstract Plasmids are nonessential extrachromosomal genetic elements that replicate autonomously and control their own replication. Most bacterial plasmids are circular supercoiled DNA molecules that range in size from one to several hundred kilobase pairs and exist in a characteristic number of copies per cell, ranging from one to several hundred.
Synthesis and hormonal activities of 8-L-homonorleucine-vasopressin (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and hormonal activities of 8-L-homonorleucine-vasopressinMary L. Fink and Miklos BodanszykyCite this: J. Med. Chem. 1973, 16, 12, 1324–1326Publication Date (Print):December 1, 1973Publication History Published online1 May 2002Published inissue 1 December 1973https://pubs.acs.org/doi/10.1021/jm00270a002https://doi.org/10.1021/jm00270a002research-articleACS PublicationsRequest reuse permissionsArticle Views59Altmetric-Citations6LEARN 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
Wound Dressings in Diabetic Foot Disease (2004)

Wound dressings represent a part of the management of diabetic foot ulceration. Ideally, dressings should alleviate symptoms, provide wound protection, and encourage healing. No single dressing fulfills all the requirements of a diabetic patient with an infected foot ulcer. Dressings research in this area is generally poor. However, each category of dressings has particular characteristics that aid selection. Nonadhesive dressings are simple, inexpensive, and well tolerated. Foam and alginate dressings are highly absorbent and effective for heavily exuding wounds. Hydrogels facilitate autolysis and may be beneficial in managing ulcers containing necrotic tissue. Dressings containing inidine and silver may aid in managing wound infection. Occlusive dressings should be avoided for infected wounds. All dressings require frequent change for wound inspection. Heavily exudating ulcers require frequent change to reduce maceration of surrounding skin. Dressing choice should be guided by the characteristics of the ulcer, the requirements of the patient, and costs.
Learning and use of sensorimotor schemata maps (2009)

In this paper we present a framework for the learning and use of sensorimotor schemata. Therefore, we introduce the concept of a schema as a compact representation of an attractor dynamic and discuss how schemata, if embedded into the proposed architecture, can be used to produce, simulate, or recognize goal-directed behaviors. We further present a first implementation of the framework which incorporates well-founded biological principles. Firstly, we apply population coding for the representation of schemata in a neural map and, secondly, we use basis functions as flexible intermediate representations for sensorimotor transformations. Simulation results show that during an initial motor babbling phase the system is able to autonomously develop schemata which correspond to generic behaviors. Moreover, the learned sensorimotor schemata map is topologically ordered insofar as neighboring schemata represent similar behaviors. In accordance with biological findings on the motor system of vertebrates the schemata form a set of behavior primitives which can be flexibly combined to yield more complex behaviors.