gebhart/patrepeval huggingface dataset:
Low Work Function Reduced Metal Complexes as Cathodes in Organic Electroluminescent Devices (2003)

Several electrochemically active polypyridine-metal complexes are isolated in the formally zero-charged state via reductive electrocrystallization, and are thermally evaporated to form conducting thin films with low work functions. Solution-phase cyclic voltammetry of the parent complexes is used to predict the work function of these materials. The reduced films are used as cathode materials in organic light-emitting devices, in place of the commonly used low work function metals such as calcium and aluminum. These reduced complexes represent a new class of materials available for use as electron-injecting contacts in organic electroluminescent devices.
PrP and β‐Amyloid Fragments Activate Different Neurotoxic Mechanisms in Cultured Mouse Cells (1997)

Alzheimer's disease and prion diseases such as Creutzfeldt-Jakob disease are caused by as yet undefined metabolic disturbances of normal cellular proteins, the amyloid precursor protein and the prion protein (PrP). Synthetic fragments of both proteins, beta-amyloid 25-35 (betaA25-35) and PrP106-126, have been shown to be toxic to neurons in culture. Cell death in both cases occurs by apoptosis. Here we show that there are considerable differences in the mechanisms involved. Thus, PrP106-126 is not toxic to cortical cell cultures of PrP knockout mouse neurons whereas betaA25-35 is. The toxicity of both peptides involves Ca2+ uptake through voltage-sensitive Ca2+ channels but only PrP106-126 toxicity involves the activity of NMDA receptors. The toxicity of betaA25-35, but not PrP106-126, is attenuated by the action of forskolin. These results indicate that PrP106-126 and PA25-35 induce neuronal apoptosis through different mechanisms.
Identification of the Staphylococcus aureus MSCRAMM clumping factor B (ClfB) binding site in the αC-domain of human fibrinogen (2008)

Clumping factor B (ClfB) of Staphylococcus aureus binds to cytokeratin 10 and to fibrinogen. In this study the binding site in human fibrinogen was localized to a short region within the C terminus of the Aalpha-chain. ClfB only bound to the Aalpha-chain of fibrinogen in a ligand-affinity blot and in solid-phase assays with purified recombinant fibrinogen chains. A variant of fibrinogen with wild-type Bbeta- and gamma-chains but with a deletion that lacked the C-terminal residues from 252-610 of the Aalpha-chain did not support adherence of S. aureus Newman expressing ClfB. A series of truncated mutants of the recombinant Aalpha-chain were tested for their ability to support adherence of S. aureus Newman ClfB(+), which allowed the binding site to be localized to a short segment of the unfolded flexible repeated sequence within the C terminus of the Aalpha-chain. This was confirmed by two amino acid substititions within repeat 5 of the recombinant Aalpha-chain which did not support adherence of Newman ClfB(+). Lactococcus lactis expressing ClfB mutants with amino acid substitutions (N256 and Q235) located in the putative ligand-binding trench between domains N2 and N3 of the A-domain were defective in adherence to immobilized fibrinogen and cytokeratin 10, suggesting that both ligands bind to the same or overlapping regions.
Purification and characterization of a new xylanase (xylanase B) produced by Streptomyces lividans 66 (1990)

A new extracellular xylanase produced by Streptomyces lividans 66 was isolated from a genetically engineered clone of that strain. This enzyme, named xylanase B, has an Mr of 31,000 and acts specifically on xylan as an endo-type xylanase producing short-chain xylo-oligosaccharides. The activity is optimal at pH 6.5 and at a temperature of 55 degrees C, which is similar to that of the previously characterized xylanase A. Xylanase B is glycosylated and has a pI of 8.4; its Km and Vmax. values are 3.71 mg/ml and 1.96 mmol/mg of enzyme respectively. Specific antibodies raised against xylanase A show no cross-reaction with xylanase B; however, the anti-(xylanase B) antibodies react slightly with xylanase A. A comparison of the hydrolysis products obtained from oat-spelts xylan with both enzymes show that xylanase A preferentially degrades short-chain oligo-xylosides, whereas xylanase B acts on the longer, water-insoluble, molecules.
Triplet-repeat oligonucleotide-mediated reversal of RNA toxicity in myotonic dystrophy (2009)

Myotonic dystrophy type 1 (DM1) is caused by toxicity of an expanded, noncoding (CUG)n tract in DM protein kinase (DMPK) transcripts. According to current evidence the long (CUG)n segment is involved in entrapment of muscleblind (Mbnl) proteins in ribonuclear aggregates and stabilized expression of CUG binding protein 1 (CUGBP1), causing aberrant premRNA splicing and associated pathogenesis in DM1 patients. Here, we report on the use of antisense oligonucleotides (AONs) in a therapeutic strategy for reversal of RNA-gain-of-function toxicity. Using a previously undescribed mouse DM1 myoblast-myotube cell model and DM1 patient cells as screening tools, we have identified a fully 2'-O-methyl-phosphorothioate-modified (CAG)7 AON that silences mutant DMPK RNA expression and reduces the number of ribonuclear aggregates in a selective and (CUG)n-length-dependent manner. Direct administration of this AON in muscle of DM1 mouse models in vivo caused a significant reduction in the level of toxic (CUG)n RNA and a normalizing effect on aberrant premRNA splicing. Our data demonstrate proof of principle for therapeutic use of simple sequence AONs in DM1 and potentially other unstable microsatellite diseases.
Identification of Fc α receptor (CD89) isoforms generated by alternative splicing that are differentially expressed between blood monocytes and alveolar macrophages (1996)

One of the hallmarks of mucosal-host defense is the clearance of inhaled Ags by alveolar macrophages (AM) through interactions of IgA Abs and IgA Fc receptors (Fc alpha R). AM constitutively expressed Fc alpha R at lower levels than freshly isolated and in vitro-differentiated monocytes as determined by immunofluorescence using four anti-Fc alpha R mAb. SDS-PAGE analysis of iodinated cell surface proteins revealed that Fc alpha R on AM has an Mr of 50 to 65 kDa, slightly lower than that on monocytes (55-75 kDa). Treatment of AM Fc alpha R by N-glycanase gave rise to a protein core of 28 KDa, smaller than the 32-kDa backbone of blood monocytes. AM Fc alpha R molecules were unaffected by phosphatidylinositol-phospholipase C treatment. Fc alpha R transcripts were analyzed by reverse transcription-PCR using primers in the 5' and 3' regions of a U937 Fc alpha R cDNA. Three transcripts were amplified, cloned, and sequenced from AM and/or monocyte mRNA, the full length Fc alpha R and two alternatively spliced products corresponding to deletions of 66 and 288 nucleotides in the portion coding for the extracellular domain; they were named Fc alpha R a.1, a.2, and a.3, respectively. These PCR products were transcribed and translated in vitro into three proteins (Mr 32, 30, and 22 kDa, respectively), in which the 32- and 30-kDa species were immunoprecipitated by an anti-Fc alpha R mAb. The predicted size of the protein encoded by the Fc alpha R a.2 transcript without the leader peptide is Mr approximately 27,400, a value that is consistent with the Mr of AM Fc alpha R backbone. These results indicate that AM express at their surfaces a protein product of an alternatively spliced Fc alpha R transcript, the Fc alpha R a.2 isoform, that might have physiologic relevance in IgA-mediated host defense at mucosal sites.
Neurocognitive complications after coronary artery bypass surgery (2005)

Both short- and long-term cognitive changes continue to occur after coronary artery bypass grafting (CABG), but the pathophysiology of these neurobehavioral changes remains incompletely understood. The persistence of mild postoperative neurocognitive changes despite multiple improvements in the cardiopulmonary bypass procedure may be partially because of surgical populations being older and having more prevalent comorbid disease. The cause of the early postoperative changes is most likely multifactorial and may include ischemic injury from microemboli, hypoperfusion, and other factors resulting from major surgery. Several lines of evidence suggest that the late cognitive decline between 1 and 5 years after surgery may be secondary to high rates of cerebrovascular disease among candidates for CABG. A history of hypertension and other risk factors for vascular disease is known to be associated with increased risk for long-term cognitive decline in community-dwelling elderly individuals. Cerebrovascular risk factors are also associated with silent magnetic resonance imaging abnormalities in patients undergoing CABG. Thus, whereas both short- and long-term postoperative cognitive changes have been associated with CABG, only the short-term, transient changes appear to be directly related to the use of cardiopulmonary bypass.
Modeling and simulation of an industrial‐scale parex process (2015)

The Parex unit for industrial‐scale purification of p‐xylene was studied through detailed simulation and the accuracy of the developed model tested against real industrial data. Starting from a comprehensive analysis of the construction and operation of the industrial unit, a simulation model was developed that incorporates the existing three major types of dead volumes: bed lines, which connect the beds to the rotary valve, circulation lines, which connect adjacent adsorbent chambers, and bed‐head dead volumes, which are located upstream of each bed due to the existence of internals. By gathering operation data and surveys in the pumparound line and in the extract stream, three case studies were defined and compared with simulation results. The model is capable of predicting the performance of the industrial unit. Further simulations were made and compared with plant data to assess the effect of adsorbent capacity loss on the long‐term performance of the unit. © 2015 American Institute of Chemical Engineers AIChE J , 61: 1345–1363, 2015
Band-Target Entropy Minimization (BTEM) Applied to Hyperspectral Raman Image Data (2003)

Band-target entropy minimization (BTEM) has been applied to extraction of component spectra from hyperspectral Raman images. In this method singular value decomposition is used to calculate the eigenvectors of the spectroscopic image data set. Bands in non-noise eigenvectors that would normally be used for recovery of spectra are examined for localized spectral features. For a targeted (identified) band, information entropy minimization or a closely related algorithm is used to recover the spectrum containing this feature from the non-noise eigenvectors, plus the next 5-30 eigenvectors, in which noise predominates. Tests for which eigenvectors to include are described. The method is demonstrated on one synthesized Raman image data set and two bone tissue specimens. By inclusion of small amounts of signal that would be unused in other methods, BTEM enables the extraction of a larger number of component spectra than are otherwise obtainable. An improvement in signal/noise ratio of the recovered spectra is also obtained.
Molecular Approaches to the Study of B Cell Epitopes (1991)

For some years, a major goal of immunochemistry has been to determine the molecular architecture of the antibody-combining site and its cognate surface on the antigen, the antigenic determinant or epitope, and to determine the molecular basis of specificity and affinity. In recent years, the crystal structures of several antigen-antibody complexes have been determined. In addition, recombinant DNA technology is beginning to play an increasingly important role in analysis of protein-protein interaction including the study of antigen structure and its interaction with antibody. The purpose of this review is to briefly present some of the major and common properties of the antigen-antibody interface as it is known today and to demonstrate, using a few selected studies, the efficacy of using site-directed mutagenesis to study the nature of the antigenic surface of protein molecules and its interaction with antibody.
Lattice Boltzmann model of immiscible fluids (1991)

We introduce a lattice Boltzmann model for simulating immiscible binary fluids in two dimensions. The model, based on the Boltzmann equation of lattice-gas hydrodynamics, incorporates features of a previously introduced discrete immiscible lattice-gas model. A theoretical value of the surface-tension coefficient is derived and found to be in excellent agreement with values obtained from simulations. The model serves as a numerical method for the simulation of immiscible two-phase flow; a preliminary application illustrates a simulation of flow in a two-dimensional microscopic model of a porous medium. Extension of the model to three dimensions appears straightforward.
Annotation and segmentation for multimedia indexing and retrieval (2002)

Describes a method for the indexing and retrieval of multimedia data based on annotation and segmentation. Our goal is the retrieval of segments of audio and video that are suitable for inclusion in multimedia documents. Annotation refers to the association of text data with particular time locations of the media. Segmentation is the partitioning of continuous media into homogenous regions. Retrieval is performed over segments of the media using the annotations associated with the segments. We present two scenarios that describe how these techniques might be applied. In the first, we describe how excerpts from a video-taped usage study of a new device are located for inclusion in a report on the utility of the device. In the second, we show how sound bites from a recorded meeting are obtained for use in authoring a summary of the meeting.
Multi-Agent Reinforcement Learning: A Survey (2006)

Multi-agent systems are rapidly finding applications in a variety of domains, including robotics, distributed control, telecommunications, economics. Many tasks arising in these domains require that the agents learn behaviors online. A significant part of the research on multi-agent learning concerns reinforcement learning techniques. However, due to different viewpoints on central issues, such as the formal statement of the learning goal, a large number of different methods and approaches have been introduced. In this paper we aim to present an integrated survey of the field. First, the issue of the multi-agent learning goal is discussed, after which a representative selection of algorithms is reviewed. Finally, open issues are identified and future research directions are outlined
Epidemiology of Clostridium difficile in Infants (1982)

The epidemiology of Clostridium difficile was studied prospectively in 451 newborn infants by daily screening of fecal samples. Colonization rates in three postnatal wards ranged from 2% to 52%. Many colonizations were sporadic, but on two wards there was evidence of clustering. On one of these occasions prospective environmental sampling yielded C. difficile organisms from a potential common source. Mothers were shown not to be the sources of their infants' organisms. Both toxin-producing and non-toxigenic strains were common; differentiation according to toxin type was epidemiologically useful. Cross contamination is the most likely explanation of the spread of C. difficile among hospitalized infants; the organism could spread among adults who are at risk of developing antibiotic-associated colitis in a similar manner.
Luminescent carbon quantum dots with high quantum yield as a single white converter for white light emitting diodes (2015)

Carbon quantum dots (CQDs) with high quantum yield (51.4%) were synthesized by a one-step hydrothermal method using thiosalicylic acid and ethylenediamine as precursor. The CQDs have the average diameter of 2.3 nm and possess excitation-independent emission wavelength in the range from 320 to 440 nm excitation. Under an ultraviolet (UV) excitation, the CQDs aqueous solutions emit bright blue fluorescence directly and exhibit broad emission with a high spectral component ratio of 67.4% (blue to red intensity to total intensity). We applied the CQDs as a single white-light converter for white light emitting diodes (WLEDs) using a UV-LED chip as the excitation light source. The resulted WLED shows superior performance with corresponding color temperature of 5227 K and the color coordinates of (0.34, 0.38) belonging to the white gamut.
CXCR2 Is Critical to Hyperoxia-Induced Lung Injury (2004)

Hyperoxia-induced lung injury is characterized by infiltration of activated neutrophils in conjunction with endothelial and epithelial cell injury, followed by fibrogenesis. Specific mechanisms recruiting neutrophils to the lung during hyperoxia-induced lung injury have not been fully elucidated. Because CXCL1 and CXCL2/3, acting through CXCR2, are potent neutrophil chemoattractants, we investigated their role in mediating hyperoxia-induced lung injury. Under variable concentrations of oxygen, murine survival during hyperoxia-induced lung injury was dose dependent. Eighty percent oxygen was associated with 50% mortality at 6 days, while greater oxygen concentrations were more lethal. Using 80% oxygen, we found that lungs harvested at day 6 demonstrated markedly increased neutrophil sequestration and lung injury. Expression of CXCR2 ligands paralleled neutrophil recruitment to the lung and CXCR2 mRNA expression. Inhibition of CXC chemokine ligands/CXCR2 interaction using CXCR2(-/-) mice exposed to hyperoxia significantly reduced neutrophil sequestration and lung injury, and led to a significant survival advantage as compared with CXCR2(+/+) mice. These findings demonstrate that CXC chemokine ligand/CXCR2 biological axis is critical during the pathogenesis of hyperoxia-induced lung injury.
Leukemia Inhibitory Factor Is Involved in Tubular Regeneration after Experimental Acute Renal Failure (2003)

Leukemia inhibitory factor (LIF) is known to play a crucial role in the conversion of mesenchyme into epithelium during nephrogenesis. This study was carried out to test the hypothesis that LIF and LIF receptor (LIFR) are involved in the renal epithelial regeneration after acute renal failure. First, the authors investigated the spatiotemporal expression of LIF and LIFR in fetal and adult rat kidney. In developing kidney, LIF was expressed in the ureteric buds and LIFR was located in nephrogenic mesenchyme and the ureteric buds; in adult kidney, LIF and LIFR expression was confined to the collecting ducts. Next, the authors examined the expression of LIF and LIFR during the recovery phase after ischemia-reperfusion injury. Real-time PCR analysis revealed that LIF mRNA expression was significantly increased from day 1 to day 7 after reperfusion and that LIFR mRNA was upregulated from day 4 to day 14. Histologic analysis demonstrated that the increased expression of LIF mRNA and protein was most marked in the outer medulla, especially in the S3 segment of the proximal tubules. To elucidate the mitogenic role of LIF in the regeneration process, cultured rat renal epithelial (NRK 52E) cells were subjected to ATP depletion (an in vitro model of acute renal failure), and LIF expression was found to be enhanced during recovery after ATP depletion. Blockade of endogenous LIF with a neutralizing antibody significantly reduced the cell number and DNA synthesis during the recovery period. These results suggest that LIF participates in the regeneration process after tubular injury.
XORs in the Air: Practical Wireless Network Coding (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> This paper proposes COPE, a new architecture for wireless mesh networks. In addition to forwarding packets, routers mix (i.e., code) packets from different sources to increase the information content of each transmission. We show that intelligently mixing packets increases network throughput. Our design is rooted in the theory of network coding. Prior work on network coding is mainly theoretical and focuses on multicast traffic. This paper aims to bridge theory with practice; it addresses the common case of unicast traffic, dynamic and potentially bursty flows, and practical issues facing the integration of network coding in the current network stack. We evaluate our design on a 20-node wireless network, and discuss the results of the first testbed deployment of wireless network coding. The results show that using COPE at the forwarding layer, without modifying routing and higher layers, increases network throughput. The gains vary from a few percent to several folds depending on the traffic pattern, congestion level, and transport protocol. </para>
Malpractice claims for permanent nerve injuries related to third molar removals (1998)

On the basis of the register of the Finnish Patient Insurance Association, the aim of this study was to examine malpractice claims for nerve injuries associated with third molar removals and determine whether they are concentrated among specialists, among less experienced dentists, or in certain geographic areas. During 1987-93 there were 139 claims for permanent sensory or motor disturbances related to removal of lower third molars in Finland. The lingual nerve was injured in 54% and the inferior alveolar nerve in 41% of the claims. In 91% of the cases the injury occurred in relation to surgical removal of the tooth and in 6% in relation to simple extraction. The claims were distributed among 123 dentists, of whom 78% were dental surgeons, 15% specialists in oral and maxillofacial surgery, and 7% other specialists. These figures represented 2% of the dental surgeons and 26% of the oral surgeons in Finland (P< 0.01). More than half the claims were associated with dentists with less than 10 years' experience. Claims originated more often from the eastern and northern (rural) areas of Finland than from urban areas (3.8 claims versus 2.4 claims per 100,000 inhabitants, P < 0.05). Compensation was paid to the patients in two-thirds of the cases, indicating that the dentists authorized to decide claims very often considered these injuries avoidable. Therefore, proper diagnosis, treatment planning, surgical techniques, and detailed patient information must be emphasized. In cases where risks are obvious, referral to an oral surgeon is recommended.
Cloning and characterization of a dextranase gene from Lipomyces starkeyi and its expression in Saccharomyces cerevisiae (2005)

A dextranase-encoding cDNA from L. starkeyi KSM22 was isolated and characterized. The 2052 bp cDNA fragment (lsd1) harbouring the dextranase gene exhibited one open reading frame (ORF) composed of 1824 bp flanked by a 41 bp 5'-UTR and a 184 bp 3'-UTR, including a 27 bp poly(A) tail. The lsd1 gene contains no introns. The open reading frame encodes a 608 amino acid polypeptide (LSD1) with a 67.6 kDa predicted molecular mass. There was a 77% deduced amino acid sequence identity between the LSD1 dextranase and the dextranase from Penicillium minioluteum. The primary structure of LSD1 dextranase exhibits distant similarity with the enzymes of the glycosyl hydrolase family 49 that comprises Penicillium dextranase. The optimum pH of LSD1 was 6.0 and the optimum temperature was 37 degrees C. LSD1 dextranase activity was substantially abolished by exposure to 1 mM Hg2+, Ag3+ and Mn2+. LSD1 exhibited high hydrolysing activity towards dextran (100%), soluble starch (22%) and mutan (8%).