gebhart/patrepeval huggingface dataset:
Selection of bacteriophage λ integrases with altered recombination specificity by in vitro compartmentalization (2009)

In vitro compartmentalization (IVC) was employed for the first time to select for novel bacteriophage lambda integrase variants displaying significantly enhanced recombination activity on a non-cognate target DNA sequence. These variants displayed up to 9-fold increased recombination activity over the parental enzyme, and one mutant recombined the chosen non-cognate substrate more efficiently than the parental enzyme recombined the wild-type DNA substrate. The in vitro specificity phenotype extended to the intracellular recombination of episomal vectors in HEK293 cells. Surprisingly, mutations conferring the strongest phenotype do not occur in the lambda integrase core-binding domain, which is known to interact directly with cognate target sequences. Instead, they locate to the N-terminal domain which allosterically modulates integrase activity, highlighting a previously unknown role for this domain in directing integrase specificity. The method we describe provides a robust, completely in vitro platform for the development of novel integrase reagent tools for in vitro DNA manipulation and other biotechnological applications.
A reinvestigation of the synthesis of cis-1,2,3,4,4a,10a-hexahydro[1,4]benzodioxino[2,3-c]pyridine and a synthesis of meso-2,3,4,5,5a,11a-hexahydro-1H-[1,4]benzodioxino[2,3-d]azepine (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA reinvestigation of the synthesis of cis-1,2,3,4,4a,10a-hexahydro[1,4]benzodioxino[2,3-c]pyridine and a synthesis of meso-2,3,4,5,5a,11a-hexahydro-1H-[1,4]benzodioxino[2,3-d]azepineNeville Finch, Louis Blanchard, and L. H. WernerCite this: J. Org. Chem. 1977, 42, 24, 3933–3937Publication Date (Print):November 1, 1977Publication History Published online1 May 2002Published inissue 1 November 1977https://pubs.acs.org/doi/10.1021/jo00444a031https://doi.org/10.1021/jo00444a031research-articleACS PublicationsRequest reuse permissionsArticle Views186Altmetric-Citations17LEARN 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
Rapid determination of <i>cis</i> and <i>trans</i> content, iodine value, and saponification number of edible oils by fourier transform near‐infrared spectroscopy (1999)

Abstract Fourier transform near‐infrared (FT‐NIR) spectroscopy was evaluated as a means of simultaneously determining the cis and trans content, iodine value (IV), and saponification number of neat fats and oils. Reference values for these parameters were obtained from oils using a previously developed mid‐FTIR Edible Oil Analysis Package. Two partial least squares calibrations were developed for a 5‐mm heated flow cell, the first a process calibration based on hydrogenated soybean samples and the second a more generalized calibration based on an oil samplematrix containing many oil types and designed to remove any correlations among the parameters measured. Each calibration performed well with its own validation samples; however, only the noncorrelated calibration was able to analyze oil samples accurately from a variety of sources. It was found that NIR analysis maintained the internal consistency between cis/trans and IV, and the accuracy and reproducibility of the predictions were on the order of ±1.5 and ±1.0 units, respectively, for all parameters evaluated. FT‐NIR is shown to be a very workable means of determining cis/trans /IV values and saponification number for edible fats and oils, and it provides a rapid alternative to the commonly used chemical and physical methods presently employed in the industry.
Small molecule probes that target Ablkinase (2009)

Two different strategies, namely a dialdehyde-based cross-linking and photo-affinity labeling, have been developed to generate small molecule activity-based probes (ABPs) for the Abelson (Abl) tyrosine kinase, of which probe 13, derived from the photo-affinity approach, showed specific labeling of Abl kinase present in a crude mammalian proteome.
HippDB: a database of readily targeted helical protein–protein interactions (2013)

arora@nyu.edu.
Perceived Value Of Educational Hypermedia: An Exploratory Study (2010)

This paper explores the idea of perceived value of educational hypermedia by extending prior research in advertising and information systems. It proposes that the value of a course support site comes from both its information content and users’ experience whenthey visit the site. The cognitive antecedents of a site’s perceived valueinclude perceived informativeness, perceived entertainment and perceived irritation. Through a field study using a course companion site and the subsequent data analysis via structural equation modeling (SEM), this study confirms that learners appreciate informative content in an entertaining format in accessing Internet-based course support. Findings of this study will help researchers and educators better understand the cognitive dimensions that enhance the perceived value of a learning technology.
Ligand-Binding PAS Domains in a Genomic, Cellular, and Structural Context (2010)

Per-Arnt-Sim (PAS) domains occur in proteins from all kingdoms of life. In the bacterial kingdom, PAS domains are commonly positioned at the amino terminus of signaling proteins such as sensor histidine kinases, cyclic-di-GMP synthases/hydrolases, and methyl-accepting chemotaxis proteins. Although these domains are highly divergent at the primary sequence level, the structures of dozens of PAS domains across a broad section of sequence space have been solved, revealing a conserved three-dimensional architecture. An all-versus-all alignment of 63 PAS structures demonstrates that the PAS domain family forms structural clades on the basis of two principal variables: (a) topological location inside or outside the plasma membrane and (b) the class of small molecule that they bind. The binding of a chemically diverse range of small-molecule metabolites is a hallmark of the PAS domain family. PAS ligand binding either functions as a primary cue to initiate a cellular signaling response or provides the domain with the capacity to respond to secondary physical or chemical signals such as gas molecules, redox potential, or photons. This review synthesizes the current state of knowledge of the structural foundations and evolution of ligand recognition and binding by PAS domains.
Laser tissue welding: a urological surgeon's perspective (1998)

Laser tissue welding has proven its efficacy in the laboratory setting when compared with more traditional modalities of tissue reapproximation. In the clinical environment, several areas including urethral reconstructive surgery have shown great promise. Several technological advancements including solder development, chromophore enhancement and temperature control have improved upon the welding process and have added more precision and reproducibility to the technique. The current potential applications for laser welding in urology are numerous. On a molecular level, growth factor supplementation has certain potential in improving upon weld site healing and wound strength. Laparoscopic surgery with its need for less cumbersome modes of tissue closure is a field that will greatly benefit from the technology of laser tissue welding. Surgical specialties outside of urology are also participating in developing the field of laser welding. In particular, cardiothoracic surgery, otolaryngology, plastic surgery, neurosurgery among others, have utilized the concept of laser tissue welding. There are many ares that have potential use for laser welding that have yet to be explored. Further investigation will likely reveal more applications for this valuable technology.
IP <sub>3</sub> Receptor Types 2 and 3 Mediate Exocrine Secretion Underlying Energy Metabolism (2005)

Type 2 and type 3 inositol 1,4,5-trisphosphate receptors (IP3R2 and IP3R3) are intracellular calcium-release channels whose physiological roles are unknown. We show exocrine dysfunction in IP3R2 and IP3R3 double knock-out mice, which caused difficulties in nutrient digestion. Severely impaired calcium signaling in acinar cells of the salivary glands and the pancreas in the double mutants ascribed the secretion deficits to a lack of intracellular calcium release. Despite a normal caloric intake, the double mutants were hypoglycemic and lean. These results reveal IP3R2 and IP3R3 as key molecules in exocrine physiology underlying energy metabolism and animal growth.
Port and Supply-Chain Security Initiatives in the United States and Abroad (2006)

Between 1990 and 2004, the value of U.S. international trade increased from $889 billion to nearly $2.2 trillion. Roughly two-thirds of this total value of trade passed through U.S. freight gateways (primarily ports) to and from countries other than Canada and Mexico. The top 50 U.S. ports accounted for about 90 percent of all maritime cargo tonnage; and 25 U.S. ports accounted for 98 percent of all container shipments. In 2004 alone, the liner shipping industry transported $1.5 billion worth of containerized goods, through U.S. ports, every day. All told, roughly 10 million loaded cargo containers entered the U.S. in 2004. Given universal recognition that cargo containers may be used to smuggle chemical, biological, radiological, or nuclear weapons, it is understandable that assuring container security has become a priority to governments and the international trade community alike to prevent incidents of mass destruction and major disruptions to the world economy. Mike Toddington, Executive Director of the International Association of Airport and Seaport Police, has noted that public officials must walk a fine line in devising methods that simultaneously secure ports and facilitate trade. Promoting both security and trade facilitation requires the examination of global supply chains. Cargo container movements, between points of origin and their ultimate destinations, are characterized by complex interactions among multiple actors, industries, regulatory agencies, modes of transportation, operating systems and legal frameworks. On behalf of the Congressional Research Service, the Lyndon B. Johnson School of Public Affairs at the University of Texas at Austin, conducted research during the 2005-06 academic year to examine the various institutional, legal and policy arrangements that have been put into place in the U.S. and abroad to enhance worldwide port and supply chain security.
Affinity-Based Protein Profiling Reveals Cellular Targets of Photoreactive Anticancer Inhibitors (2019)

Affinity-based protein profiling has proven to be a powerful method in target identification of bioactive molecules. Here, this technology was applied in two photoreactive anticancer inhibitors, arenobufagin and HM30181. Using UV irradiation, these photoreactive reagents can covalently cross-link to target proteins, leading to a covalent binding with target proteins. Moreover, the cellular on/off targets of these two molecules, including ATP1A1, MDR1, PARP1, DDX5, NOP2, RAB6A, and ERGIC1 were first identified by affinity-based protein profiling and bioimaging approaches. The protein hit, PARP1, was further validated to be involved in the function of the anticancer effects.
Achievable Rates in Gaussian MISO Channels with Secrecy Constraints (2007)

A Gaussian MISO (multiple input single output) channel is considered where a transmitter is communicating to a receiver in the presence of an eavesdropper. The transmitter is equipped with multiple antennas, while the receiver and the eavesdropper each have a single antenna. The transmitter maximizes the communication rate, while concealing the message from the eavesdropper. The channel input is restricted to Gaussian signalling, with no preprocessing of information. For these channel inputs, and under different channel fading assumptions, optimal transmission strategies are found, in terms of the input covariance matrices. It is shown that, the optimal communication strategy in all cases, is beamforming.
1-Deaza-6-methylthiopurine Ribonucleoside<sup>1</sup> (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1-Deaza-6-methylthiopurine Ribonucleoside1John A. Montgomery and Kathleen HewsonCite this: J. Med. Chem. 1966, 9, 3, 354–357Publication Date (Print):May 1, 1966Publication History Published online1 May 2002Published inissue 1 May 1966https://pubs.acs.org/doi/10.1021/jm00321a021https://doi.org/10.1021/jm00321a021research-articleACS PublicationsRequest reuse permissionsArticle Views163Altmetric-Citations28LEARN 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
Les Rendez-vous de l’histoire de Weimar « Reisen in (Un)Bekanntes/ Destination (in)connue » (2011)

Pour la deuxième année consécutive se tenait ce festival international de l’histoire que sont les Rendez-vous de l’histoire de Weimar, du 29 au 31 octobre 2010. Le thème à l’honneur pour cette édition était « Reisen in (Un)Bekanntes/ Destination (in)connue ». Plus de deux mille visiteurs, toutes générations confondues, se pressèrent aux quelque trente manifestations au programme. Les vingt films projetés dans le cadre du festival de cinéma créé spécialement pour ces Rendez-vous attirèrent prè...
One-Year Outcomes After Transcatheter Insertion of an Interatrial Shunt Device for the Management of Heart Failure With Preserved Ejection Fraction (2016)

Background— Heart failure with preserved ejection fraction has a complex pathophysiology and remains a therapeutic challenge. Elevated left atrial pressure, particularly during exercise, is a key contributor to morbidity and mortality. Preliminary analyses have demonstrated that a novel interatrial septal shunt device that allows shunting to reduce the left atrial pressure provides clinical and hemodynamic benefit at 6 months. Given the chronicity of heart failure with preserved ejection fraction, evidence of longer-term benefit is required. Methods and Results— Patients (n=64) with left ventricular ejection fraction ≥40%, New York Heart Association class II–IV, elevated pulmonary capillary wedge pressure (≥15 mm Hg at rest or ≥25 mm Hg during supine bicycle exercise) participated in the open-label study of the interatrial septal shunt device. One year after interatrial septal shunt device implantation, there were sustained improvements in New York Heart Association class ( P <0.001), quality of life (Minnesota Living with Heart Failure score, P <0.001), and 6-minute walk distance ( P <0.01). Echocardiography showed a small, stable reduction in left ventricular end-diastolic volume index ( P <0.001), with a concomitant small stable increase in the right ventricular end-diastolic volume index ( P <0.001). Invasive hemodynamic studies performed in a subset of patients demonstrated a sustained reduction in the workload corrected exercise pulmonary capillary wedge pressure ( P <0.01). Survival at 1 year was 95%, and there was no evidence of device-related complications. Conclusions— These results provide evidence of safety and sustained clinical benefit in heart failure with preserved ejection fraction patients 1 year after interatrial septal shunt device implantation. Randomized, blinded studies are underway to confirm these observations. Clinical Trial Registration— URL: https://www.clinicaltrials.gov . Unique identifier: NCT01913613.
A Wesleyan Response to the New Perfectionism (1971)

A vast undercurrent of transcendental moralizing came to the sur face in the last decade.One finds it in the most unlikely places: in Cali fornia's hippie colonies, in Timothy Leary's League of Spiritual Discovery, in Erich Fromm's projection of a Revolution ofHope, in John D. Rocker- feller, Ill's essay praising young revolutionaries, in the apparently immoral and certainly vulgar plays presented at St. Mark's East Village Episcopal parish, or in Joan Baez's essays and sketches which appeared under the title Daybreak.Fathers and teachers who have shared intimately the thoughts of a bright and sensitive youngster turned off by what he declares are the moral hypocrisies of our times have caught many glimpses of this undercurrent of ethical yearning.Its perfectionist drift both feeds upon and nurtures political radicalism.The apparent flaunting of traditional morality by such young people may constitute not simply a rejection but a prophetic judgment of those who have given chiefly Hp service to the Sermon on the Mount.Consider that now dated album of the Beatles Sergeant Pepper's Lonely Hearts Club Band.Never before in human history have so many hundreds of thousands of ordinary youngsters hstened to poetry, either good or bad, with such intense self-awareness, such groping after not only the hteral but the existential meaning of words.The meanings seemed to them, as they seemed to those of us who were older and tried to listen, ironic, paradoxical, mysteriously contradictory.Such, our braver children declared, are the names of life's game.
Auto-synthesis of series-gated emitter-coupled logic (2003)

A systematic technique for synthesizing series-gated emitter-coupled logic (ECL) for any logic function is described. The technique is applied in an auto-synthesis program whereby multilevel ECL circuit schematics are generated automatically from Boolean equation or truth table input. The resulting circuit uses a minimum number of transistors. The series gating method, minimization technique, and autosynthesis program are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<i>Cis</i> -Limited Action of the Gene-A Product of Bacteriophage ϕX174 and the Essential Bacterial Site (1972)

Parental replicative-form (RF(*)) DNA of bacteriophage varphiX174 in a replication-deficient host cell (rep(3) (-)) exhibits two characteristic features that correlate the function of viral gene A with the initiation of viral DNA replication: a specific discontinuity in the viral strand of a constant number of RF molecules and elongation of the viral strand to yield replicative-intermediate DNA forms with single-stranded tails. At high multiplicities of infection, these initiation events are limited to an average of four specifically nicked RFII molecules per cell. The limiting factor from the host cell may be related (or identical) to the essential bacterial sites known to limit the participation of parental genomes in RF replication. Double-infection experiments with wild-type phage and phage carrying an amber mutation in gene A show that the formation of gene A-specific RFII and RI is cis-limited to only the wild-type DNA. These results provide a basis at the DNA level for the known asymmetric complementation of gene A.
Characterization of Glycosylation Profiles of HIV-1 Transmitted/Founder Envelopes by Mass Spectrometry (2011)

The analysis of HIV-1 envelope carbohydrates is critical to understanding their roles in HIV-1 transmission as well as in binding of envelope to HIV-1 antibodies. However, direct analysis of protein glycosylation by glycopeptide-based mass mapping approaches involves structural simplification of proteins with the use of a protease followed by an isolation and/or enrichment step before mass analysis. The successful completion of glycosylation analysis is still a major analytical challenge due to the complexity of samples, wide dynamic range of glycopeptide concentrations, and glycosylation heterogeneity. Here, we use a novel experimental workflow that includes an up-front complete or partial enzymatic deglycosylation step before trypsin digestion to characterize the glycosylation patterns and maximize the glycosylation coverage of two recombinant HIV-1 transmitted/founder envelope oligomers derived from clade B and C viruses isolated from acute infection and expressed in 293T cells. Our results show that both transmitted/founder Envs had similar degrees of glycosylation site occupancy as well as similar glycan profiles. Compared to 293T-derived recombinant Envs from viruses isolated from chronic HIV-1, transmitted/founder Envs displayed marked differences in their glycosylation site occupancies and in their amounts of complex glycans. Our analysis reveals that the glycosylation patterns of transmitted/founder Envs from two different clades (B and C) are more similar to each other than they are to the glycosylation patterns of chronic HIV-1 Envs derived from their own clades.
What Keeps Us Awake: the Neuropharmacology of Stimulants and Wakefulness Promoting Medications (2004)

Numerous studies dissecting the basic mechanisms that control sleep regulation have led to considerable improvement in our knowledge of sleep disorders. It is now well accepted that transitions between sleep and wakefulness are regulated by complex neurobiologic mechanisms, which, ultimately, can be delineated as oscillations between two opponent processes, one promoting sleep and the other promoting wakefulness. The role of several neurotransmitter or neuromodulator systems, including noradrenergic, serotonergic, cholinergic, adenosinergic, and histaminergic systems and, more recently, the hypocretin/orexin and dopamine systems, has been clearly established. Amphetamine-like stimulants are known to increase wakefulness by blocking dopamine reuptake, by stimulating dopamine release, or by both mechanisms. Modafinil may increase wakefulness through activation of noradrenergic and dopaminergic systems, possibly through interaction with the hypocretin/orexin system. Caffeine inhibits adenosinergic receptors, which in turn can produce activation via interaction with GABAergic and dopaminergic neurotransmission. Nicotine enhances acetylcholine neurotransmission in the basal forebrain and dopamine release. Understanding the exact role of the hypocretin/orexin and dopamine systems in the physiology and pharmacology of sleep-wake regulation may reveal new insights into current and future wakefulness-promoting drugs.