gebhart/patrepeval huggingface dataset:
Evaluation and Field Validation of PCR Tests for Detection of Actinobacillus pleuropneumoniae in Subclinically Infected Pigs (2003)

Eight PCR tests were evaluated for their abilities to detect Actinobacillus pleuropneumoniae in swine tonsils. At first they were compared regarding their specificities by using A. pleuropneumoniae and related bacterial species and their analytical sensitivities by using tonsils experimentally infected in vitro. PCRs were carried out both directly with tonsil homogenates (direct PCR) and after culture of the sample (after-culture PCR). Most tests demonstrated good specificities; however, some tests gave false-positive results with some non-A. pleuropneumoniae species. High degrees of variation in the analytical sensitivities among the tests were observed for the direct PCRs (10(9) to 10(2) CFU/g of tonsil), whereas those of most of the after-culture PCRs were similar (10(2) CFU/g of tonsil). In a second phase, the effects of sample storage time and storage conditions were evaluated by using tonsils from experimentally infected animals. Storage at -20 degrees C allowed the detection of the organism for at least 4 months. Finally, the omlA PCR test described by Savoye et al. (C. Savoye et al., Vet. Microbiol. 73:337-347, 2000) and the commercially available Adiavet App PCR test were further validated with field samples. Their effectiveness was compared to those of standard and immunomagnetic separation-based methods of bacterial isolation. In addition, a comparison of tonsil biopsy specimens (from living animals) and whole tonsils (collected at the slaughterhouse) was also conducted. A. pleuropneumoniae was neither isolated nor detected by PCR from a herd serologically negative for A. pleuropneumoniae. PCR was more sensitive than the standard isolation method with whole tonsils from three infected herds. After-culture PCR offered the highest degree of sensitivity (93 and 83% for the omlA and Adiavet App PCRs, respectively). The PCR detection rate was higher with whole tonsils than with tonsil biopsy specimens. Good agreement (kappa = 0.65) was found between the presence of A. pleuropneumoniae in tonsils and the individual serological status of the animals.
Ultrasound-Assisted SWNTs Dispersion: Effects of Sonication Parameters and Solvent Properties (2010)

Ultrasonication is widely used for preparing Single-Walled Carbon Nanotube (SWNT) dispersions in different solvent media and it has been shown to play a critical role in dispersing and debundling SWNTs. The strong shear force that can exfoliate the SWNT bundles during sonication comes from cavitation, which entails a process of bubble formation, growth, and collapse. The efficiency of the cavitation process is closely correlated to many solvent parameters, including vapor pressure, viscosity, and surface tension, as well as the sonication frequency, intensity, and time. In this study, SWNTs were dispersed in a range of organic solvents assisted by tip sonication. The effects of sonication intensity and time were investigated in o-dichlorobenzene (o-DCB) and dimethylformamide (DMF). The aggregation fraction below the dispersion limit of SWNTs in the range of organic solvents was found to be influenced by the solvent parameters, particularly solvent vapor pressure and viscosity. It is demonstrated that the parameters associated with the sonication process rather than solvent solubility parameters govern the dispersion process. It is further confirmed that significant degradation of the SWNTs is affected during the dispersion process.
Application of reversible biotinylated label for directed immobilization of synthetic peptides and proteins: isolation of ligates from crude cell lysates. (1997)

Chaperonin 10 protein from Rattus norvegicus (Rat cpn 10) has been reported to bind chaperonin 60 from Escherichia coli (GroEL) in an ATP-dependent manner. Chemically synthesized Rat cpn10 was immobilized in a defined orientation to agarose-bound monomeric avidin using a reversible biotinylated affinity label (1), attached to the N alpha-terminal residue. The resulting affinity chromatographic matrix was then used to isolate binding proteins from a crude cell lysate. Following affinity separation the bound ligand and ligate was released by treatment with organic base. Rat cpn 10 was prepared using a highly effective synthetic protocol involving HBTU/HOBt activation and capping with N-(2-chlorobenzyloxycarbonyloxy) succinimide to terminate unreacted amino groups. The biotinylated Fmoc-based molecule (1) was introduced specifically onto the N alpha-terminal amino acid as the succinimidyl carbonate, before final cleavage and deprotection of side-chain protecting groups using a low-TFMSA/high-HF procedure. Crude biotinylated Rat cpn10 (Rat cpn10 + 1) was immobilized on monomeric avidin with a binding efficiency of approximately 75% and unlabelled truncated/capped impurities eluted off the column with buffer. The biotinylated Rat cpn10-avidin affinity matrix was then used to isolate GroEL from a crude cell lysate. The identity of the purified protein was confirmed by SDS-PAGE and binding to a specific anti-GroEL monoclonal antibody (MoAb). These results extend the applicability of the biotinylated label (1), providing a reversible non-covalent anchor for immobilization of peptide and protein ligands, thus simplifying isolation of ligates and enabling recovery of synthetic material under mild conditions.
Analytical Expression and PerformanceEvaluation of TCP Packet Loss Probability Over Geostationary Satellite (2004)

The letter contains the formulation of an analytical expression of the Transmission Control Protocol (TCP) packet loss probability over geostationary satellite channels on the basis of the state-of-the-art in the field. The expression obtained is function of the bandwidth available and is suited to be used in control mechanisms. It is compared with the results obtained through a satellite network emulator already validated in the literature.
A study to evaluate the use of handheld spirometry as an alternative to laboratory based volume-displacement spirometry in a low-risk population undergoing lung resection (2012)

Puri, Varun MD; Bell, Jennifer M. RN; Musick, Joanne F. RN; Crabtree, Traves D. MD; Krupnick, Alexander S. MD; Kreisel, Daniel MD, PhD; Patterson, Alexander G. MD; Meyers, Bryan F. MD, MPH Author Information
A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug dissociation from G protein-coupled receptors (2020)

Determining the drug-target residence time (RT) is of major interest in drug discovery given that this kinetic parameter often represents a better indicator of in vivo drug efficacy than binding affinity. However, obtaining drug-target unbinding rates poses significant challenges, both computationally and experimentally. This is particularly palpable for complex systems like G Protein-Coupled Receptors (GPCRs) whose ligand unbinding typically requires very long timescales oftentimes inaccessible by standard molecular dynamics simulations. Enhanced sampling methods offer a useful alternative, and their efficiency can be further improved by using machine learning tools to identify optimal reaction coordinates. Here, we test the combination of two machine learning techniques, automatic mutual information noise omission and reweighted autoencoded variational Bayes for enhanced sampling, with infrequent metadynamics to efficiently study the unbinding kinetics of two classical drugs with different RTs in a prototypic GPCR, the μ-opioid receptor. Dissociation rates derived from these computations are within one order of magnitude from experimental values. We also use the simulation data to uncover the dissociation mechanisms of these drugs, shedding light on the structures of rate-limiting transition states, which, alongside metastable poses, are difficult to obtain experimentally but important to visualize when designing drugs with a desired kinetic profile.
Catalytic Cracking of Acetic Acid to Acetic Anhydride (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalytic Cracking of Acetic Acid to Acetic AnhydrideNarayanan Padmanabhan, P. K. Deshpande, and N. R. KuloorCite this: Ind. Eng. Chem. Process Des. Dev. 1968, 7, 4, 511–516Publication Date (Print):October 1, 1968Publication History Published online1 May 2002Published inissue 1 October 1968https://pubs.acs.org/doi/10.1021/i260028a006https://doi.org/10.1021/i260028a006research-articleACS PublicationsRequest reuse permissionsArticle Views1175Altmetric-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 options Get e-Alerts
Identification of Genes Abnormally Expressed in Both Human and Murine MLL-ELL and/or MLL-ENL Leukemia. (2006)

Abstract Chromosome translocations are among the most common genetic abnormalities in human leukemia. Their abnormally expressed genes identify specific markers for their clinical diagnosis. Important biological properties are often conserved across species. However, although genetically engineered mouse leukemia models are well-established, few systematic studies have validated the genes that exhibit similar abnormal expression patterns in both human and mouse leukemia models. MLL-ELL and MLL-ENL fusion genes resulting from t(11;19)(q23;p13.1) and t(11;19)(q23;p13.3), respectively, are frequently involved in human acute leukemia, and in retrovirus-mediated mouse leukemia models. We used the SAGE technique to compare gene expression profiles between MLL-ELL or MLL-ENL myeloid leukemia progenitor cells and normal myeloid progenitor cells in both human and mouse. We analyzed four patient samples (two with each fusion) and two retrovirally-induced mouse leukemias containing either MLL-ELL or MLL-ENL fusions, and a leukemia cell line with an MLL-ELL fusion. 484,303 SAGE tags were identified from the nine samples, yielding 103,899 unique tags in human and 60,993 in mouse samples. We identified 40 candidate genes that appear to be abnormally expressed in both human and murine MLL-ELL leukemias (2 up- and 38 down-regulated), and 72 in both human and murine MLL-ENL leukemias (23 up and 49 down). 25 candidate genes are down-regulated in both types of leukemias, and many of them can bind with and/or regulate other candidate genes in the candidate list. For example, LCN2 can bind directly with and positively regulate MMP9; MMP9 and TMSB4X may positively regulate FOS; FOS and JUNB can bind directly and positively regulate each other. JUNB may inhibit proliferation and promote apoptosis, and it was reported that inactivation of JunB in LT-HSC leads to MPD while its inactivation in committed myeloid progenitors also predisposes to leukemia evolution. LCN2 may also positively regulate apoptosis. Meanwhile, some important candidate genes are observed only in one type of leukemia. For example, both PXN and ARHGEF1 are down-regulated only in MLL-ELL leukemias. PXN can bind directly with ARHGEF1, and the latter may inhibit proliferation. Similarly, MYB is significantly upregulated only in MLL-ENL leukemias, which was reported to play a role in MLL-ENL-mediated transformation. Taken together, some common pathways may exist in the development of both types of leukemias, whereas each may also have their own pathway. The deregulation of the important candidate genes may contribute to leukemogenesis through inhibiting apoptosis while promoting proliferation of hematopoietic cells. We have validated the expression patterns of the candidate genes, and are studying the functions and pathways of the validated candidate genes. Our studies will provide important insights into the complex functional pathways related to MLL rearrangements in the development of acute myeloid leukemia, which may lead to more effective therapy for these leukemias.
Outer s-shell ionization of neon, argon, and krypton by H$sub 2$$sup +$ and H$sup +$ impact (100 keV to 1000 keV) (1975)

The outer s-shell ionization of Ne, Ar and Kr by H$sub 2$$sup +$ and He$sup +$ impact has been studied in the energy range of 100 keV to 1,000 keV. The observed structures in the ionization functions are explainable by molecular processes and by direct Coulomb ionization. (orig.)
New Developments in Liposomal Drug Delivery (2015)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTNew Developments in Liposomal Drug DeliveryBhushan S. Pattni†, Vladimir V. Chupin‡, and Vladimir P. Torchilin*†§View Author Information† Department of Pharmaceutical Sciences, Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, Massachusetts 02115, United States‡ Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia§ Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia*Tel.: (617) 373-3206. E-mail: [email protected]Cite this: Chem. Rev. 2015, 115, 19, 10938–10966Publication Date (Web):May 26, 2015Publication History Received23 January 2015Published online26 May 2015Published inissue 14 October 2015https://pubs.acs.org/doi/10.1021/acs.chemrev.5b00046https://doi.org/10.1021/acs.chemrev.5b00046review-articleACS PublicationsCopyright © 2015 American Chemical SocietyRequest reuse permissionsArticle Views20991Altmetric-Citations1149LEARN 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 SUBJECTS:Cancer,Drug delivery,Encapsulation,Lipids,Vesicles Get e-Alerts
Shuaiba Transition Zone Reservoirs: From Modeling Studies to Field Development Challenges (2009)

Production data from several Shuaiba fields in the Sultanate of Oman demonstrate the oil recovery from capillary transition zones. This is underpinned by extensive detailed experimental and theoretical modeling studies describing favored oil mobility and residual oil saturation in transition zones in the Shuaiba formation reservoir. Nonetheless the economical development of capillary transition zone reservoirs, especially those with thin oil columns, remains an ongoing challenge and necessitates addressing uncertainties related to characterizing the lateral variations in initial oil saturation distribution, water flooding displacement, sweep efficiencies and accurate prediction of oil production. This paper discusses good practices for ongoing developments of transition zone fields and predicting their performance. The key enablers are: (1) properly characterized initial saturation height functions for long horizontal well planning, (2) implementation of consistent set of hysteresis saturation functions in the reservoir simulation models and (3) geosteering tools for accurate well placement and spacing. Examples of predicted well performances for a field compared to the actual production data will be shown. The results highlight the generic trends in transition zone oil production and the&lt;br&gt;recommended procedures for static and dynamic modeling during field development planning.
Vibrational dynamics of inclusion complexes by Raman scattering: an experimental and numerical study (2006)

Abstract\n Raman spectroscopy has been applied to the study of interactions&#13;\ninvolved in the formation of inclusion complexes between&#13;\ncyclodextrins and indomethacin. Raman spectra of free molecules&#13;\nand of their inclusion complexes have been recorded in the energy&#13;\nranges 10-50 and 100-3500 cm$^{-1}$, and significant energy&#13;\nshifts, intensity variations and broadening have been observed due&#13;\nto complexation. The experimental data have been interpreted by&#13;\ncomparison with the results of numerical simulation.
Optical properties of silver island films in the attenuated-total-reflection geometry (1986)

The absorptances of 633-nm photons by silver island films formed on room temperature substrates were measured in an attenuated-total-reflection geometry by the photoacoustic method as a function of the angle of photon incidence. From the data obtained for s-polarized light ∊″, the effective dielectric function for the direction parallel to the film and dopt, the effective optical thickness, were determined as a function of the mass thickness dm of the island films between 2 and 18 nm. The values of ∊″ and dopt were then used to calculate the absorptance for p-polarized light assuming that the films were optically isotropic. It was found that the calculated values agreed well with the experimental values indicating that the films were isotropic. The values of dopt agreed well with earlier results from an ellipsometric study in which the films were assumed to be isotropic.
ChemInform Abstract: Diastereodivergency in the Reactions of 3‐Metalated‐2‐methylbutanamide. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ENHANCEMENT OF SKIN ALLOGRAFT SURVIVAL BY SOLUBLE ALLOANTIGEN IS SERUM-MEDIATED (1976)

H-2d mice treated before skin grafting with either soluble alloantigen prepared from H-2b cells or with serum obtained from similarly sensitized mice showed a significantly prolonged survival of H-2b skin allografts. This in vivo enhancement was paralleled by a depression of cell-mediated cytotoxicity to [51Cr]H-2b target cells in vitro. Such in vitro and in vivo effects were abrogated when mice were repeatedly injected with soluble alloantigen before and after skin grafting, demonstrating that enhancing antibody present could be neutralized by this mode of antigen administration. The data suggest that serum factors present in mice pretreated with soluble alloantigen lead to specific blocking at the induction phase of the cell-mediated immune response and result in skin graft enhancement.
Isolation of Clostridium perfringens from foals. (1990)

Clostridium perfingens was isolated from four of 29 healthy foals and from all twelve foals with gastrointestinal diseases. The range of viable counts of C. perfringens in the faeces was 10(1)-10(5)/g and in the intestinal specimens 10(1)-10(7)/g. Of 41 isolates of C. perfringens, 37 were considered to be type A. Enterotoxin of the organism was demonstrated in the intestinal contents of five of eight foals with enteric diseases. These findings suggested that C. perfringens is a likely pathogen of foal intestinal diseases.
Diffusion tensor MRI: Preliminary anisotropy measures and mapping of breast tumors (2010)

Diffusion anisotropy is significantly lower in breast cancers than normal tissue, which may reflect alterations in tissue organization. Our preliminary results suggest that FA adds incremental value over ADC alone for discriminating malignant from normal tissue but does not help with distinguishing benign from malignant lesions.
Interleukin‐1β Uses Common and Distinct Signaling Pathways for Induction of the Interleukin‐6 and Tumor Necrosis Factor α Genes in the Human Astrocytoma Cell Line U373 (1996)

Cytokines are involved in the etiology of different disorders of the CNS. For a better understanding of their pathogenic role, we analyzed signal transduction pathways mediating the interleukin (IL)-1 beta-induced synthesis of IL-6 and tumor necrosis factor alpha (TNF alpha) in the human astrocytoma cell line U373 MG. Both protein kinase C and reactive oxygen intermediates (ROIs) were involved in IL-6 and TNF alpha gene expression by IL-1 beta. In contrast, protein tyrosine kinases were only necessary for expression of the IL-6 gene. Whereas activation of protein kinase A was able to induce expression of the IL-6 gene, it did not induce TNF alpha gene expression and was not involved in IL-1 beta-induced IL-6 and TNF alpha gene expression. Activation of the transcription factor nuclear factor-kappa B by IL-1 beta involved ROIs, whereas the IL-1 beta-induced activation of the transcription factor AP-1 was mediated via protein kinase C. Our findings provide the basis for the development of specific drugs for the treatment of disorders of the CNS in which cytokines play a pathogenic role.
A Nonverbal Behavior Approach to Identify Emergent Leaders in Small Groups (2011)

Identifying emergent leaders in organizations is a key issue in organizational behavioral research, and a new problem in social computing. This paper presents an analysis on how an emergent leader is perceived in newly formed, small groups, and then tackles the task of automatically inferring emergent leaders, using a variety of communicative nonverbal cues extracted from audio and video channels. The inference task uses rule-based and collective classification approaches with the combination of acoustic and visual features extracted from a new small group corpus specifically collected to analyze the emergent leadership phenomenon. Our results show that the emergent leader is perceived by his/her peers as an active and dominant person; that visual information augments acoustic information; and that adding relational information to the nonverbal cues improves the inference of each participant's leadership rankings in the group.
An Efficient Synthesis of Azetidine-2,3-diones from l-(+)-Diethyl Tartrate (2007)

A convenient route to enantiopure azetidine-2,3-diones is described. The chiral ketene generated from commercially available l-(+)-diethyl tartrate on Staudinger cycloaddition with different imines gave spiro-β-lactams in good yields. These spiro-β-lactams were transformed into azetidine-2,3-diones in excellent yields in a two-step process.