gebhart/patrepeval huggingface dataset:
Monitoring of hemostasis in cardiac surgical patients: impact of point-of-care testing on blood loss and transfusion outcomes (1997)

Patients undergoing cardiac surgery with cardiopulmonary bypass (CPB) are at increased risk for excessive perioperative blood loss requiring transfusion of blood products. Strategies to optimize administration of heparin and protamine and the assessment of their effects on coagulation are evolving in cardiac surgical patients. Two recent evaluations have focused on the use of multiple point-of-care (POC) coagulation assays for patient-specific adjustment of heparin and protamine dosage. These studies indicate that blood loss and transfusion requirements in cardiac surgical patients may be reduced with more accurate control of heparin anticoagulation and its reversal. Blood component administration in patients with excessive post-CPB bleeding is generally empiric in part, related to turnaround times of laboratory-based tests. Methods are now available for rapid, POC assessment of coagulation to allow appropriate, targeted therapy for acquired hemostatic abnormalities. Recent studies indicate that a rapid evaluation of thrombocytopenia and coagulation factor deficiencies with POC tests can facilitate the optimal administration of pharmacologic and transfusion-based therapy in patients who exhibit excessive bleeding after CPB. POC tests that assess platelet function have been developed, and their use may facilitate identification of which patients at risk for excessive blood loss may respond to pharmacologic interventions such as desmopressin acetate or antifibrinolytic agents.
Interferon-Stimulated Response Element (ISRE)-Binding Protein Complex DRAF1 Is Activated in Sindbis Virus (HR)-Infected Cells (2001)

To elucidate the host cell defense mechanisms in response to Sindbis viral infection, we have started to characterize interferon (IFN)-stimulated response element (ISRE)-binding proteins activated in infected cells that are involved in the transcriptional induction of IFN type I-inducible genes. Using electromobility shift assays (EMSA), we detected several protein complexes with a human IFN-stimulated gene 15 (ISG15) ISRE in extracts from virus-infected L929 cells that were absent in extracts from uninfected cells. Comigration with Newcastle disease virus-activated ISRE-binding complexes, ISRE-binding specificity, supershift experiments, and conditions of formation indicate that the complexes activated by Sindbis viral infection in L929 cells correspond to DRAF1 and ISG factor 3 (ISGF3). Transfection of L929 cells with poly rI:rC induced only ISGF3. DRAF1 could be detected in Sindbis virus-infected mouse embryo fibroblasts derived from IFNR type I and type II KO mice. Viral RNA synthesis is required for activation of DRAF1.
Stressed Cells Survive Better with Light (2002)

ADVERTISEMENT RETURN TO ISSUEPREVPerspectivesStressed Cells Survive Better with LightAndrei P. Sommer, Uri Oron, E. Olavi Kajander, and Adam R. MesterView Author Information Department of Biomaterials, Central Institute of Biomedical Engineering, University of Ulm, 89081 Ulm, Germany, Department of Zoology, Faculty of Life Sciences, Tel-Aviv University, Ramat-Aviv, 69978 Tel-Aviv, Israel, Department of Biochemistry, University of Kuopio, 70211 Kuopio, Finland, and Department of Radiology and Oncotherapy, Semmelweis University of Medicine, 1082 Budapest, Hungary Cite this: Journal of Proteome Research 2002, 1, 5, 475Publication Date (Web):August 23, 2002Publication History Received16 June 2002Published online23 August 2002Published inissue 1 October 2002https://pubs.acs.org/doi/10.1021/pr0255396https://doi.org/10.1021/pr0255396review-articleACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views111Altmetric-Citations23LEARN 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:Cell imaging,Light,Optical imaging,Regenerative medicine,Stress Get e-Alerts
An introduction to computing with neural nets (1988)

Artificial neural net models have been studied for many years in the hope of achieving human-like performance in the fields of speech and image recognition. These models are composed of many nonlinear computational elements operating in parallel and arranged in patterns reminiscent of biological neural nets. Computational elements or nodes are connected via weights that are typically adapted during use to improve performance. There has been a recent resurgence in the field of artificial neural nets caused by new net topologies and a1gorithms, analog VLSI implementation techniques, and the belief that massive parallelism is essential for high performance speech and image recognition. This paper provides an introduction to the field of artificial neural nets by reviewing six important neural net models that can be used for pattern classification. These nets are highly parallel building blocks that illustrate neural- net components and design principles and can be used to construct more complex systems. In addition to describing these nets, a major emphasis is placed on exploring how some existing classification and clustering algorithms can be performed using simple neuron-like components. Single-layer nets can implement algorithms required by Gaussian maximum-likelihood classifiers and optimum minimum-error classifiers for binary patterns corrupted by noise. More generally, the decision regions required by any classification algorithm can be generated in a straightforward manner by three-layer feed-forward nets.
Crystal structures of λ exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity (2011)

The λ exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3' overhang. The crystal structure of λ exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of λ exonuclease in complex with DNA at 1.88-Å resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg(2+) ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5' phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of λ exonuclease operates not only at the level of the trimer, but also at the level of the monomer.
Polyhedrin initiator codon altered to AUU yields unexpected fusion protein from a baculovirus vector. (1991)

A recombinant baculovirus expression vector was constructed to express the core (capsid) protein of the hepatitis B virus. Along with the expected 21-kDa polypeptide, a second 24-kDa protein was observed. Immunoprecipitation and immunoblotting using a rabbit polyclonal anticore antiserum demonstrated that the two proteins were related. The core gene originally was cloned in-frame with the polyhedrin initiator codon that had been altered to AUU as a means of preventing fusion protein formation. A transient expression assay revealed expression of the 24-kDa protein was prevented if a frame-shift mutation was created upstream of the HBV core translation start site. These results suggest that the 24-kDa protein was the result of an unexpectedly high level of translation initiation at the AUU codon that gave rise to a polyhedrin-HBV core fusion protein. The 24-kDa core protein was shown to be a polyhedrin fusion protein by immunoblotting with an antipolyhedrin antiserum, and initiation at the AUU was demonstrated by amino terminal protein sequencing. Methods to prevent undesired fusion protein expression using this or similar vectors are discussed.
Pharmaceutical Development of (Investigational) Anticancer Agents for Parenteral Use-A Review (1996)

Due to the high mortality rate, the therapy of cancer has been and still is under vigorous investigation. Traditional approaches to new drug development have led to the discovery of several chemotherapeutic agents, which are now routinely used in the clinic. The objective of this review is to evaluate the current status of the pharmaceutical formulation of antineoplastic drugs from 1986 onwards. Among the aspects of the pharmaceutical development of antineoplastic drugs discussed are the following: formulation development process, solubilization techniques, the application of several colloidal systems, the use of prodrugs, and lyophilized (freeze-dried) formulations. Formulation procedures, the advantages and disadvantages of the different strategies, and the toxicity risk are described and illustrated with examples from the literature.
Inactivation of DNA Mismatch Repair by Variants of Uncertain Significance in the PMS2 Gene (2013)

Lynch syndrome (LS) is a common cancer predisposition caused by an inactivating mutation in one of four DNA mismatch repair (MMR) genes. Frequently a variant of uncertain significance (VUS), rather than an obviously pathogenic mutation, is identified in one of these genes. The inability to define pathogenicity of such variants precludes targeted healthcare. Here, we have modified a cell-free assay to test VUS in the MMR gene PMS2 for functional activity. We have analyzed nearly all VUS in PMS2 found thus far and describe loss of MMR activity for five, suggesting the applicability of the assay for diagnosis of LS.
Dynamic Bayesian networks for visual recognition of dynamic gestures (2002)

Dynamic Bayesian networks are a powerful representation to describe processes that vary over time inside a stochastic framework. This paper describes an online visual recognition system to recognize a set of five dynamic gestures executed with the user's right hand using dynamic Bayesian networks for recognition. Gestures are oriented to command mobile robots. The system employs a radial scan segmentation algorithm combined with a statistical-based skin detection method to find the candidate face of the user and to track his right-hand. It uses four simple features to describe the user's right-hand movement. Our system is able to recognize these five gestures in real-time with an average recognition rate of 84.01%, better result than using hidden Markov models for recognition.
In vitro assembly of the undecaprenylpyrophosphate-linked heptasaccharide for prokaryotic N-linked glycosylation (2005)

Campylobacter jejuni has a general N-linked glycosylation pathway (encoded by the pgl gene cluster), which culminates in the transfer of a heptasaccharide: GalNAc-alpha1,4-GalNAc-alpha1,4-(Glcbeta1,3)-GalNAc-alpha1,4-GalNAc-alpha1,4-GalNAc-alpha1,3-Bac [where Bac is bacillosamine (2,4-diacetamido-2,4,6-trideoxyglucose)] from a membrane-anchored undecaprenylpyrophosphate (Und-PP)-linked donor to the asparagine side chain of proteins at the Asn-X-Ser/Thr motif. Herein we report, the cloning, overexpression, and purification of four of the glycosyltransferases (PglA, PglH, PglI, and PglJ) responsible for the biosynthesis of the Und-PP-linked heptasaccharide. Starting with chemically synthesized Und-PP-linked Bac and various combinations of enzymes, we have deduced the precise functions of these glycosyltransferases. PglA and PglJ add the first two GalNAc residues on to the isoprenoid-linked Bac carrier, respectively. Elongation of the trisaccharide with PglH results in a hexasaccharide revealing the polymerase activity of PglH. The final branching glucose is then added by PglI, which prefers native lipids for optimal activity. The sequential activities of the glycosyl transferases in the pathway can be reconstituted in vitro. This pathway represents an ideal venue for investigating the integrated functions of a series of enzymatic processes that occur at a membrane interface.
Murine spinal fusion induced by engineered mesenchymal stem cells that conditionally express bone morphogenetic protein—2 (2005)

After their injection genetically engineered MSCs can efficiently form new bone in the paraspinal muscle of the mouse to obtain spinal fusion. The extent and quantity of this newly formed bone can be monitored by controlling the duration of rhBMP-2 gene expression.
PROTEIN TARGETING TO THE THYLAKOID MEMBRANE (1998)

The assembly of the photosynthetic apparatus at the thylakoid begins with the targeting of proteins from their site of synthesis in the cytoplasm or stroma to the thylakoid membrane. Plastid-encoded proteins are targeted directly to the thylakoid during or after synthesis on plastid ribosomes. Nuclear-encoded proteins undergo a two-step targeting process requiring posttranslational import into the organelle from the cytoplasm and subsequent targeting to the thylakoid membrane. Recent investigations have revealed a single general import machinery at the envelope that mediates the direct transport of preproteins from the cytoplasm to the stroma. In contrast, at least four distinct pathways exist for the targeting of proteins to the thylakoid membrane. At least two of these systems are homologous to translocation systems that operate in bacteria and at the endoplasmic reticulum, indicating that elements of the targeting mechanisms have been conserved from the original prokaryotic endosymbiont.
D-AMINO ACID OXIDASE IN LEUKOCYTES: A POSSIBLE D-AMINO-ACID-LINKED ANTIMICROBIAL SYSTEM (1969)

D-Amino acid oxidase has been identified within the granule fraction of human neutrophilic leukocytes. Leukocyte homogenates and purified kidney D-amino acid oxidase can utilize either isolated D-amino acids or some species of bacteria as substrates for the generation of hydrogen peroxide. When linked to leukocyte myeloperoxidase in vitro, purified D-amino acid oxidase constitutes a system lethal for certain bacteria. It is proposed that leukocyte D-amino acid oxidase and myeloperoxidase constitute a biochemically specific system for the recognition and killing of certain microorganisms.
Synthesis, Antimalarial Activity, and Molecular Modeling of Tebuquine Analogues (1997)

Tebuquine (5) is a 4-aminoquinoline that is significantly more active than amodiaquine (2) and chloroquine (1) both in vitro and in vivo. We have developed a novel more efficient synthetic route to tebuquine analogues which involves the use of a palladium-catalyzed Suzuki reaction to introduce the 4-chlorophenyl moiety into the 4-hydroxyaniline side chain. Using similar methodology, novel synthetic routes to fluorinated (7a, b) and a dehydroxylated (7c) analogue of tebuquine have also been developed. The novel analogues were subjected to testing against the chloroquine sensitive HB3 strain and the chloroquine resistant K1 strain of Plasmodium falciparum. Tebuquine was the most active compound tested against both strains of Plasmodia. Replacement of the 4-hydroxy function with either fluorine or hydrogen led to a decrease in antimalarial activity. Molecular modeling of the tebuquine analogues alongside amodiaquine and chloroquine reveals that the inter-nitrogen separation in this class of drugs ranges between 9.36 and 9.86 A in their isolated diprotonated form and between 7.52 and 10.21 A in the heme-drug complex. Further modeling studies on the interaction of 4-aminoquinolines with the proposed cellular receptor heme revealed favorable interaction energies for chloroquine, amodiaquine, and tebuquine analogues. Tebuquine, the most potent antimalarial in the series, had the most favorable interaction energy calculated in both the in vacuo and solvent-based simulation studies. Although fluorotebuquine (7a) had a similar interaction energy to tebuquine, this compound had significantly reduced potency when compared with (5). This disparity is possibly the result of the reduced cellular accumulation (CAR) of fluorotebuquine when compared with tebuquine within the parasite. Measurement of the cellular accumulation of the tebuquine analogues and seven related 4-aminoquinolines shows a significant relationship (r = 0.98) between the CAR of 4-aminoquinoline drugs and the reciprocal of drugs IC50.
A probabilistic graphical model for joint answer ranking in question answering (2007)

Graphical models have been applied to various information retrieval and natural language processing tasks in the recent literature. In this paper, we apply a probabilistic graphical model for answer ranking in question answering. This model estimates the joint probability of correctness of all answer candidates, from which the probability of correctness of an individual candidate can be inferred. The joint prediction model can estimate both the correctness of individual answers as well as their correlations, which enables a list of accurate and comprehensive answers. This model was compared with a logistic regression model which directly estimates the probability of correctness of each individual answer candidate. An extensive set of empirical results based on TREC questions demonstrates the effectiveness of the joint model for answer ranking. Furthermore, we combine the joint model with the logistic regression model to improve the efficiency and accuracy of answer ranking.
Vitamin D2Is Much Less Effective than Vitamin D3in Humans (2004)

Vitamins D(2) and D(3) are generally considered to be equivalent in humans. Nevertheless, physicians commonly report equivocal responses to seemingly large doses of the only high-dose calciferol (vitamin D(2)) available in the U.S. market. The relative potencies of vitamins D(2) and D(3) were evaluated by administering single doses of 50,000 IU of the respective calciferols to 20 healthy male volunteers, following the time course of serum vitamin D and 25-hydroxyvitamin D (25OHD) over a period of 28 d and measuring the area under the curve of the rise in 25OHD above baseline. The two calciferols produced similar rises in serum concentration of the administered vitamin, indicating equivalent absorption. Both produced similar initial rises in serum 25OHD over the first 3 d, but 25OHD continued to rise in the D(3)-treated subjects, peaking at 14 d, whereas serum 25OHD fell rapidly in the D(2)-treated subjects and was not different from baseline at 14 d. Area under the curve (AUC) to d 28 was 60.2 ng.d/ml (150.5 nmol.d/liter) for vitamin D(2) and 204.7 (511.8) for vitamin D(3) (P < 0.002). Calculated AUC(infinity) indicated an even greater differential, with the relative potencies for D(3):D(2) being 9.5:1. Vitamin D(2) potency is less than one third that of vitamin D(3). Physicians resorting to use of vitamin D(2) should be aware of its markedly lower potency and shorter duration of action relative to vitamin D(3).
Low-threshold al&lt;inf&gt;x&lt;/inf&gt;Ga&lt;inf&gt;1-x&lt;/inf&gt;As visible and IR-light-emitting diode lasers (1970)

The detailed properties of "close-confinement" LPE (AlGa)As junction lasers have been studied in the Al composition range where the alloy has a direct bandgap transition. It has been shown that the laser efficiency is essentially independent of wavelength at 300°K between 9000 and 8000 Å. This is important in applications where photocathodes are used to detect the laser radiation or where optical pumping of Nd:YAG laser is desired. Continuously operating red-emitting lasers at 77°K (6635 Å) have also been fabricated. At room temperature, the lowest threshold current density, 8300 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for low Al content, ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x \leq 0.1</tex> ) is only slightly higher than in GaAs, which is indicative of the excellent metallurgical properties possible in this alloy system. An external differential quantum efficiency of 43 percent at 300°K ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x \leq 0.1</tex> ) nearly equals the best GaAs laser value. Furthermore, the relatively low series resistance in these devices makes possible power conversion efficiencies of ∼10 percent at 300°K and ∼50 percent at 77°K. The variation of the laser threshold currents and efficiency with increasing Al content is very close to the theoretically predicted variation based on the change of the internal quantum efficiency, assuming a direct-to-indirect bandgap energy transition at 1.92 eV. This suggests that the best devices perform very nearly at their theoretically predicted maximum in relation to present similarly constructed GaAs lasers.
Innovations in Global Electronic Data Delivery (1999)

Abstract New techniques and technologies have been developed and assembled to create a global electronic data delivery framework that is robust, secure and efficient. This framework serves any data type throughout its life span—as it is acquired, processed and archived—and provides the means for it to be transmitted and intrinsically integrated into the end user's domain. Details of the data delivery framework and its overall scope will be given, followed by a number of geographically distinct, tailored applications of the technology. The advancing technology front has resulted in an explosion in data volume, of which an ever-increasing amount is digital. In the midst of this explosion, the need for the highest quality data to be efficiently and electronically delivered to its various destinations has remained a goal. The solution presented herein combines an enhanced mechanism for electronic data delivery with tools that improve data usability, storage and management. All the while the data adhere to the exploration and production (E&amp;P) standards. This framework is being applied today to formation evaluation data, such as wireline and logging-while-drilling data. However, it will soon expand to encompass all forms of data produced within the E&amp;P industry. As the industry rapidly assimilates advances in electronic communications to improve operations efficiency, its decision-makers are demanding drilling and formation evaluation data on their desktops in real time. This paper outlines significant contributions in the areas of data security and transmission reliability, capitalizing on established and expanding networks (Internet, intranet), data composition and management techniques, and the development of software applications to facilitate end-user data reception, handling and manipulation.