gebhart/patrepeval huggingface dataset:
JSmol and the Next‐Generation Web‐Based Representation of 3D Molecular Structure as Applied to Proteopedia (2013)

Abstract Although Java does not run on some handheld devices, e.g., iPads and iPhones, JavaScript does. The development of JSmol, a JavaScript‐only version of Jmol, is described, and its use in Proteopedia is demonstrated. A key aspect of JSmol is that it includes the full implementation of the entire set of Jmol functionalities, including file reading and writing, scripting, and rendering. The relative performances of Java‐based Jmol and JavaScript‐only JSmol are discussed. We can now confirm that the guiding principles of Java programming can be completely and relatively straightforwardly transformed directly into JavaScript, requiring no Java applet, and producing identical graphical results. JSmol is thus the first full‐featured molecular viewer, and the first ever viewer for proteins, which can be utilized with an internet browser on handheld devices lacking Java. Since the MediaWiki features of Proteopedia have been modified to optionally use JSmol, the wealth of crowd‐sourced content in Proteopedia is now directly available on such devices, without the need to download any additional applet.
A New One-Pot Synthesis of Alkynylphosphonates (2000)

A method for the palladium-catalyzed synthesis of alkynylphosphonates from 1,1-dibromo-1-alkenes has been developed. In general, the best catalyst system for this transformation was found to be Pd(OAc)(2), dppf, H-phosphonate, propylene oxide, DMF, 80 degrees C. The reaction appears tolerant of a range of functional groups in both the 1,1-dibromo-1-alkene and H-phosphonate coupling partners. The synthesis of a backbone-modified thymidine dimer is used to illustrate the application of this methodology in the synthesis of complex target molecules.
CEllular Local Area Radio Network: CELARN (2002)

The cellular local area radio network (CELARN), which is suitable for transmitting data to indoor mobiles, such as forklifts in factories and warehouses, is proposed. CELARN consists of some radio networks and a wired network which integrates the radio networks. The base stations are connected to one another by the wired network in a logical ring. A data-frame makes the round of the base stations to transmit data. Moreover, the data-frame behaves as a token of the common radio control channel to prevent collisions. The transmission delay performance of CELARN in a car manufacturing factory is analyzed for the practical use.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Linguistic features weighting for a text-to-speech system without prosody model (2005)

This paper presents a Non-Uniform Units selection-based Text-To-Speech synthesizer. Nowadays, systems use prosodic models that do not allow the prosody to vary as far as we should hope, involving a listening comfort degradation. Our system has the advantage to avoid the using of prosodic model. Speech units selection builds its features set exclusively from the linguistic information generated by the natural language analysis. We also present an original method to automatically weight these features. Therefore, selected units are not restricted by a predetermined prosody. With only using linguistic features, we obtain a various prosody and the units concatenation is performed without resort to heavy signal processing
Lipase specificities : potential application in lipid bioconversions (1997)

Les nouvelles utilisations des lipases dans une large gamme de synthèses organiques et la modification des huiles et corps gras ont considérablement augmenté au cours des dernières années, à cause de la disponibilité croissante de lipases d'origines microbiennes, agents catalyseurs des interfaces hydrophiles/hydrophobes. Cet article aborde deux sujets majeurs : la caractérisation et la détermination des spécificités des lipases et l'emploi des lipases aux propriétés sélectionnées pour des applications déterminées comme la bioconversion des huiles et corps gras
Imaging receptor for advanced glycation end product expression in mouse model of hind limb ischemia (2013)

These data show the feasibility of imaging and quantifying the effect of diabetes on RAGE expression in limb ischemia.
Injectable In Situ –Forming pH/Thermo-Sensitive Hydrogel for Bone Tissue Engineering (2008)

We developed a novel pH- and thermo-sensitive hydrogel as a scaffold for autologous bone tissue engineering. We synthesized this polymer by adding pH-sensitive sulfamethazine oligomers (SMOs) to both ends of a thermo-sensitive poly(epsilon-caprolactone-co-lactide)-poly(ethylene glycol)-poly(epsilon-caprolactone-co-lactide) (PCLA-PEG-PCLA) block copolymer, yielding a pH/thermo-sensitive SMO-PCLA-PEG-PCLA-SMO block copolymer. The synthesized block copolymer solution rapidly formed a stable gel under physiological conditions (pH 7.4 and 37 degrees C), whereas it formed a sol at pH 8.0 and 37 degrees C, making it injectable. This pH/thermo-sensitive hydrogel exhibited high biocompatibility in a Dulbecco's modified Eagle's medium extract test. Under physiological conditions, the hydrogel easily encapsulated human mesenchymal stem cells (hMSCs) and recombinant human bone morphogenetic protein-2 (rhBMP-2), with encapsulating efficiencies of about 90% and 85%, respectively. To assay for ectopic bone formation in vivo, we subcutaneously injected a polymer solution containing hMSCs and rhBMP-2 into the back of mice, after which we could observe hMSC differentiation for up to 7 weeks. Histological studies revealed mineralized tissue formation and high levels of alkaline phosphatase activity in the mineralized tissue. Therefore, this pH/thermo-sensitive SMO-PCLA-PEG-PCLA-SMO block copolymer demonstrated potential as an injectable scaffold for bone tissue engineering, with in situ formation capabilities.
On the interaction of promiscuous antigenic peptides with different DR alleles. Identification of common structural motifs (1991)

We have investigated the interaction between DR1 molecules and the two antigenic peptides, tetanus toxoid 830-843 and hemagglutinin 307-319, previously known to bind most DR alleles (degenerate binding) and to be recognized by the same T cell clones in the context of different DR alleles (promiscuous T cell recognition). The DR1 affinity of these two peptides was compared with that of two other different T cell epitopes (pertussis toxin 30-42 and ragweed allergen Ra3 51-65). It was found that degeneracy and promiscuity were associated with high affinity interactions, whereas binding and T cell selectivity were associated with weaker interactions. Thus, the selectivity of DR-peptide interactions, as is commonly observed with the antibody molecule, appears to be inversely correlated to affinity. Several singly substituted analogs of the hemagglutinin 307-319 determinant have also been tested for capacity to bind various DR alleles (DR1, DR2, DR5, and DR7). The results obtained suggest that this determinant may bind the different DR alleles in a similar orientation. Similar conclusions were reached when the interaction between the tetanus toxoid 830-843 determinant and three different DR alleles (DR1, DR2, and DR7) was studied following the same experimental approach. When crucial DR-binding residues of the two peptides were compared, it was found that they were very similar in both chemical nature and spacing in the peptide primary structure, suggesting that the two peptides may bind DR in a very similar orientation. Finally, a putative motif has been derived and shown to be present in a majority of the DR binders tested, but only in a minority of the non-DR binding peptides.
Quantitative Proteomic Analysis Using a MALDI Quadrupole Time-of-Flight Mass Spectrometer (2001)

We describe an approach to the quantitative analysis of complex protein mixtures using a MALDI quadrupole time-of-flight (MALDI QqTOF) mass spectrometer and isotope coded affinity tag reagents (Gygi, S. P.; et al. Nat. Biotechnol. 1999, 17, 994-9.). Proteins in mixtures are first labeled on cysteinyl residues using an isotope coded affinity tag reagent, the proteins are enzymatically digested, and the labeled peptides are purified using a multidimensional separation procedure, with the last step being the elution of the labeled peptides from a microcapillary reversed-phase liquid chromatography column directly onto a MALDI sample target. After addition of matrix, the sample spots are analyzed using a MALDI QqTOF mass spectrometer, by first obtaining a mass spectrum of the peptides in each sample spot in order to quantify the ratio of abundance of pairs of isotopically tagged peptides, followed by tandem mass spectrometric analysis to ascertain the sequence of selected peptides for protein identification. The effectiveness of this approach is demonstrated in the quantification and identification of peptides from a control mixture of proteins of known relative concentrations and also in the comparative analysis of protein expression in Saccharomyces cerevisiae grown on two different carbon sources.
Extended Boolean information retrieval (1983)

article Free Access Share on Extended Boolean information retrieval Authors: Gerard Salton Cornell Univ., Ithaca, NY Cornell Univ., Ithaca, NYView Profile , Edward A. Fox International Institute for Tropical Agriculture, Ibadan, Nigeria International Institute for Tropical Agriculture, Ibadan, NigeriaView Profile , Harry Wu ITT Programming Technology Center, Stratford, CT ITT Programming Technology Center, Stratford, CTView Profile Authors Info & Claims Communications of the ACMVolume 26Issue 11Nov. 1983pp 1022–1036https://doi.org/10.1145/182.358466Published:01 November 1983Publication History 729citation5,833DownloadsMetricsTotal Citations729Total Downloads5,833Last 12 Months624Last 6 weeks142 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
From Hydrophobic to Superhydrophobic and Superhydrophilic Siloxanes by Thermal Treatment (2014)

The cross-influence effects of treatment temperature and time on the wettability of a siloxane elastomer is investigated in detail, through static and tilt contact angle measurements. The material is heated at 400, 500, 600, 650, 700, and 800 °C for various periods, ranging from 1 to 300 s. The siloxane surface is subjected to multiple wettability transitions with treatment time: from intrinsic hydrophobicity to superhydrophobicity (and water repellency) and then through intermediate stages (hydrophobicity and hydrophilicity) to superhydrophilicity. For the time scale used herein (1-300 s), this scenario is recorded for treatment at 650, 700, and 800 °C. For treatment at lower temperatures (400, 500, and 600 °C) only the first transition, from intrinsic hydrophobicity to superhydrophobicity, is recorded. Scanning electron microscopy, micro-Fourier transform infrared (micro-FTIR), and micro-Raman spectroscopies are employed to correlate the aforementioned wettability transitions with structural and chemical changes of the siloxane surface, developed during thermal treatment. It is shown that the first transition from intrinsic hydrophobicity to superhydrophobicity is accompanied by a severe surface-structure evolution that increases surface roughness. Once superhydrophobicity is achieved, the surface structure reaches a saturation point and it is not subjected to any other change with further thermal treatment. FTIR spectroscopy shows that the intensity of the O-H/C-H peaks increases/decreases with treatment time, and Raman measurements show that the C-Si-C vibrations gradually disappear with treatment time. The evaporation of a droplet resting on a superhydrophobic, water-repellent siloxane surface, which was produced after appropriate thermal treatment, is monitored. It is shown that droplet evaporation initially follows the constant contact area mode. At later evaporation stages, a transition to the constant contact angle mode is recorded. Finally, it is demonstrated that the superhydrophobic and water-repellent siloxane surfaces exhibit self-cleaning properties, good durability, and furthermore do not practically affect the optical transparency of glass substrates.
Polyphosphate and omptins: novel bacterial procoagulant agents (2009)

Derangement of the blood clotting system contributes strongly to multiple organ failure in severe sepsis. In this review, we examine two microbial modulators of the clotting system: polyphosphates and omptins. Polyphosphates are linear polymers of inorganic phosphate that are abundant in the acidocalcisomes of prokaryotes and unicellular organisms as well as in the dense granules of human platelets. Polyphosphates modulate haemostasis by: (1) triggering clotting via the contact pathway; (2) accelerating the activation of coagulation factor V (a key cofactor in blood clotting) and (3) causing fibrin to form clots whose fibrils are thicker and more resistant to fibrinolysis. While polyphosphates are found in all prokaryotes, omptins have a more limited distribution among certain Gram-negative species. Omptins are outer membrane aspartyl proteases which were recently found to proteolytically inactivate tissue factor pathway inhibitor (TFPI), the main inhibitor of the initiation phase of blood clotting. Omptin activity against TFPI requires lipopolysaccharide without O-antigen (rough LPS) such as is found on the surface of Yersinia pestis, the etiologic agent of plague. Interestingly, expression of Pla, the Yersinia pestis omptin, has a demonstrated virulence role in converting plasminogen into the fibrinolytic enzyme plasmin, which would seemingly antagonize any procoagulant effect of TFPI inactivation. However, since the rate of TFPI inactivation is much higher than the rate of plasminogen activation, we suggest that Pla may have a dual function in supporting the bubonic form of plague which is unique to Yersinia pestis.
202. The hydrogenation of furfuraldehyde to furfuryl alcohol and sylvan (2-methylfuran) (1947)

The first page of this article is displayed as the abstract.
Development of a macrophage-based nanoparticle platform for antiretroviral drug delivery (2006)

Complex dosing regimens, costs, side effects, biodistribution limitations, and variable drug pharmacokinetic patterns have affected the long-term efficacy of antiretroviral medicines. To address these problems, a nanoparticle indinavir (NP-IDV) formulation packaged into carrier bone marrow-derived macrophages (BMMs) was developed. Drug distribution and disease outcomes were assessed in immune-competent and human immunodeficiency virus type 1 (HIV-1)-infected humanized immune-deficient mice, respectively. In the former, NP-IDV formulation contained within BMMs was adoptively transferred. After a single administration, single-photon emission computed tomography, histology, and reverse-phase-high-performance liquid chromatography (RP-HPLC) demonstrated robust lung, liver, and spleen BMMs and drug distribution. Tissue and sera IDV levels were greater than or equal to 50 microM for 2 weeks. NP-IDV-BMMs administered to HIV-1-challenged humanized mice revealed reduced numbers of virus-infected cells in plasma, lymph nodes, spleen, liver, and lung, as well as, CD4(+) T-cell protection. We conclude that a single dose of NP-IDV, using BMMs as a carrier, is effective and warrants consideration for human testing.
Cytotoxic activity of the recombinant anti-mesothelin immunotoxin, SS1(dsFv)PE38, towards tumor cell lines established from ascites of patients with peritoneal mesotheliomas. (2004)

High expression of mesothelin is seen on tumor cells of patients with peritoneal mesothelioma and correlates with sensitivity to SS1(dsFv)PE38. Clinical studies of SS1(dsFv)PE38 in patients with peritoneal mesotheliomas are ongoing.
Development of an Automatic Aircraft Collision Avoidance System for Fighter Aircraft (2013)

The U.S. Department of Defense has identified midair mishaps as a leading cause of loss of life, lost combat capability, and financial cost in fighter/attack aircraft operations. In the past, losses from midair mishaps were mitigated through training. Now, an Automatic Air Collision Avoidance System (Auto ACAS) has been identified as a technology that could significantly reduce midair accidents. Auto ACAS is not a pilot advisory system or a deconfliction system; rather, Auto ACAS performs an automatic, aggressive maneuver to avoid collisions with other aircraft and returns control to the pilot as soon as the collision is prevented. The system coordinates maneuver trajectories between aircraft, determines which combination of maneuvers provides the best separation, and initiates maneuvers when a collision is imminent.
Antagonism exerted by an association of a Bacteroides thetaiotaomicron strain and a Fusobacterium necrogenes strain against Clostridium perfringens in gnotobiotic mice and in fecal suspensions incubated in vitro (1989)

Antagonism between an association of Bacteroides thetaiotaomicron and Fusobacterium necrogenes strains and two strains of Clostridium perfringens was evidenced both in vivo in gnotobiotic mice and ex vivo in fecal suspensions incubated for 22 h at 37 degrees C. Several features of this antagonism were similar in and ex vivo. (i) An obligate and continuous synergy between B. thetaiotaomicron and F. necrogenes was required; (ii) the two C. perfringens strains did not respond to the same extent to this antagonism; and (iii) expression of the antagonism was host and diet dependent. Neither diffusible nor soluble inhibitory substances were detectable in feces of gnotobiotic mice, nor could depletion of nutrients be identified as causing antagonism in both in and ex vivo experiments. Our findings support the hypothesis that a reversible bacteriostasis induced by the inhibitory strains acting together continuously, and hindering the target strain from utilizing available nutrients, was responsible for this antagonism.
Introducing Collaborative Communities With Edge and Vitality (2009)

Professional learning communities (PLCs) are rapidly gaining momentum in schools and school districts. Based on widespread and multifarious policies, implementations, and examples that have sprung up across North America, the PLC idea is certainly a timely subject for investigation. We believe that this potent strategy for educational change, and specifically school improvement, shows promise of becoming "contagious." Persons at all levels of the educational system concerned about school improvement have an invested interest in this staff development model. Stakeholder groups include state department personnel, intermediate service agency staff, district and campus administrators, teacher-leaders, parents, local school community members, university scholars, clinical faculty members, and higher-education administrators. In fact, the development of PLCs is "currently in vogue" as a vehicle for school-wide change and improvement (Dufour, 2004, p. 6) and is becoming more aligned with student learning and achievement (Mullen & Hutinger, 2008; Murphy & Lick, 2005). The concept of a learning community is a commonplace idea, and the PLC is fast approaching on its heels. In fact, the concept has become so popular that the PLC initiative has probably become something of an educational movement—it will likely reach a "tipping point" where an idea "sticks," culturally speaking, and has staying power (Gladwell, 2002).KeywordsProfessional DevelopmentLearning CommunityProfessional LearningEducational ChangeSchool ImprovementThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Noninvasive Detection of Concealed Liquid Explosives Using Raman Spectroscopy (2007)

We present a Raman spectroscopic method for the noninvasive detection of liquid explosives within bottles, and other packaging, of substantially higher sensitivity and wider applicability than that currently available via conventional Raman spectroscopy. The approach uses a modification of the spatially offset Raman spectroscopy (SORS) concept, which permits the interrogation of a wide range of containers, including transparent, colored, and diffusely scattering plastic and glass beverage, medicine, and cosmetic bottles, with no change in experimental geometry. The enhanced sensitivity is achieved by the technique's inherent ability to effectively suppress fluorescence and Raman contributions originating from the wall of the container. The application is demonstrated on the noninvasive detection of hydrogen peroxide solution, a critical component of a number of liquid explosives. In contrast to conventional Raman spectroscopy, the modified SORS concept enables the detection of concealed hydrogen peroxide solution in all the studied cases.
Efficient sum-frequency upconversion in a resonantly pumped Nd:YAG laser (1992)

An efficient, 459-nm, resonantly pumped Nd:YAG sum-frequency upconversion laser is described. The pump beam from a single-frequency 805-nm laser diode was resonantly enhanced inside the laser cavity and summed with the 1064-nm circulating field. A blue output of 1.2 mW was obtained at an input power of 50 mW.
Targeting Antibodies to Carbon Nanotube Field Effect Transistors by Pyrene Hydrazide Modification of Heavy Chain Carbohydrates (2012)

Many carbon nanotube field-effect transistor (CNT-FET) studies have used immobilized antibodies as the ligand binding moiety. However, antibodies are not optimal for CNT-FET detection due to their large size and charge. Their size can prevent ligands from reaching within the Debye length of the CNTs and a layer of charged antibodies on the circuits can drown out any ligand signal. In an attempt to minimize the antibody footprint on CNT-FETs, we examined whether pyrene hydrazide modification of antibody carbohydrates could reduce the concentration required to functionalize CNT circuits. The carbohydrates are almost exclusively on the antibody Fc region and this site-specific modification could mediate uniform antibody orientation on the CNTs. We compared the hydrazide modification of anti- E. coli O157:H7 polyclonal antibodies to pyrenebutanoic acid succinimidyl ester-coated CNTs and carbodiimide-mediated antibody CNT attachment. Our results show that the pyrene hydrazide modification was superior to those methods with respect to bacteria detection and less than 1 nM labeled antibody was required to functionalize the circuits.
Positron Emission Tomography in Evaluation of Dementia (2001)

In patients presenting with cognitive symptoms of dementia, regional brain metabolism was a sensitive indicator of AD and of neurodegenerative disease in general. A negative PET scan indicated that pathologic progression of cognitive impairment during the mean 3-year follow-up was unlikely to occur.
Microscopic nonlinearities of two-component organic crystals (2001)

We determine the molecular first-order hyperpolarizability β of the highly nonlinear organic salt 4-N,N-dimethylamino-4′-N′-methyl stilbazolium tosylate (DAST, βzzz=(1540±250)×10-40 m4/V at λ = 1542 nm) and the cocrystal 4-{2-[1-(2-hydroxyethyl)-4-pyridylidene]-ethylidene}-cyclo-hexa-2,5-dien-1-one)–(methyl 2,4-dihydroxybenzoate) (M2-MDB, βzzz=(1510±250)×10-40 m4/V at λ = 1907 nm) in solution. These values are compared with the molecular first-order hyperpolarizabilities in the solid state, calculated with the measured nonlinear optical coefficient of the crystals. For both materials we show that the molecular nonlinearity in the solid state is considerably smaller than in solution. This lowering of the nonlinearity is attributed to the relatively strong Coulomb interactions in DAST and to the very strong hydrogen bonding in M2-MDB.