gebhart/patrepeval huggingface dataset:
Adherence of group B streptococci to cultured epithelial cells: roles of environmental factors and bacterial surface components (1994)

Group B streptococci (GBS) are the major cause of neonatal pneumonia, sepsis, and meningitis. Steps considered to be important in the pathogenesis of this infection include colonization of the rectum and vagina of the mother, aspiration of GBS into the fetal lung during or just prior to delivery, and invasion of GBS into pulmonary epithelial cells. We have previously demonstrated that GBS can invade pulmonary epithelial cells both in vivo and in vitro. Adherence of GBS to epithelial cells may play an important role in colonization of the rectum and vagina and constitute a first step in invasion of pulmonary epithelial cells. Because GBS can both adhere to and invade epithelial cells, we have developed two assays for GBS adherence which measure cell surface and not intracellular bacteria. Using these assays, we were able to demonstrate specific adherence of GBS to pulmonary epithelial cells. Adherence levels were similar at 4 and 37 degrees C and for log- and stationary-phase bacteria. Physiologic conditions vary considerably between the rectum, vagina, and lung, and a range of conditions was therefore tested. Adherence was enhanced in hypotonic solutions, while magnesium and calcium had no effect on adherence at physiologic concentrations. In comparison with adherence at neutral pH, adherence was increased 6- to 20-fold at pH 4, which is the normal vaginal pH. Neither capsular polysaccharide nor lipoteichoic acid was important for adherence in these assays. Treatment of GBS with trypsin decreased their adherence by more than 75%, indicating that surface proteins play an important role.
Establishment of Higher Passage PER.C6 Cells for Adenovirus Manufacture (2007)

PER.C6 cells, an industrially relevant cell line for adenovirus manufacture, were extensively passaged in serum-free suspension cell culture to better adapt them to process conditions. The changes in cell physiology that occurred during this passaging were characterized by investigating cell growth, cell size, metabolism, and cultivation of replication-deficient adenovirus. The changes in cell physiology occurred gradually as the population doubling level, the number of times the cell population had doubled, increased. Higher passage PER.C6 (HP PER.C6) proliferated at a specific growth rate of 0.043 h(-1), 2-fold faster than lower passage PER.C6, and were capable of proliferation from lower inoculation cell densities. HP PER.C6 cell volume was 16% greater, and cellular yields on glucose, lactate, oxygen, and amino acids were greater as well. In batch cultures, HP PER.C6 cells volumetrically produced 3-fold more adenovirus, confirmed with three different constructs. The increase in productivity was also seen on a cell-specific basis. Although HP PER.C6 were more sensitive to the "cell density effect", requiring lower infection cell densities for optimal specific productivity, they proliferated more after infection than lower passage PER.C6, increasing the number of cells available for virus production. The extensive passaging established HP PER.C6 cells with several desirable attributes for adenovirus manufacture.
Fundamentals of bitumen coking processes analogous to granulations: A critical review (2002)

Abstract A number of coking processes use hot particles to heat liquid bitumen or petroleum residue to cause cracking reactions. These particles may be mineral or coke solids. Interactions of these particles, in fluid beds, moving beds and other types of contactors, are governed by the liquid films on the particle surfaces. This paper explores the analogy between granulation and coking, and suggests that the key relationships that will govern the behavior of wet particles in coking processes are the Stokes number of the particles, the thickness or the liquid films, and the diameter and surface roughness of the particles. The implications for distribution of liquid feed in the reactor, fouling, and defluidization or bogging are discussed. This analysis suggests experiments that can be performed under non‐reactive conditions with scaled variables in order to study phenomena that cannot be observed in situ in high‐temperature cracking processes.
Transport of Peptide-MHC Class II Complexes in Developing Dendritic Cells (2000)

Major histocompatibility complex class II (MHC II) molecules capture peptides within the endocytic pathway to generate T cell receptor (TCR) ligands. Immature dendritic cells (DCs) sequester intact antigens in lysosomes, processing and converting antigens into peptide-MHC II complexes upon induction of DC maturation. The complexes then accumulate in distinctive, nonlysosomal MHC II+ vesicles that appear to migrate to the cell surface. Although the vesicles exclude soluble lysosomal contents and antigen-processing machinery, many contain MHC I and B7 costimulatory molecules. After arrival at the cell surface, the MHC and costimulatory molecules remain clustered. Thus, transport of peptide-MHC II complexes by DCs not only accomplishes transfer from late endocytic compartments to the plasma membrane, but does so in a manner that selectively concentrates TCR ligands and costimulatory molecules for T cell contact.
Approximate inference for domain detection in spoken language understanding (2011)

This paper presents a semi-latent topic model for semantic domain detection in spoken language understanding systems. We use labeled utterance information to capture latent topics, which directly correspond to semantic domains. Additionally, we introduce an ’informative prior’ for Bayesian inference that can simultaneously segment utterances of known domains into classes and divide them from out-of-domain utterances. We show that our model generalizes well on the task of classifying spoken language utterances and compare its results to those of an unsupervised topic model, which does not use labeled information.
ChemInform Abstract: Complex‐Induced Proximity Effects: Stereoselective Carbon—Carbon Bond Formation in Chiral Auxiliary Mediated β‐Lithiation‐Substitution Sequences of β‐Substituted Secondary Carboxamides. (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.
Effects of resonance on low-frequency raman scattering from semiconductor nanocrystals (1995)

Abstract An investigation of Raman scattering in CdSe nanocrystals embedded in oxide glass matrix under resonant excitation has been accomplished. First we observe the dependence of both the longitudinal optical phonon and the low frequency scattering energies with the excitation wavelength which is explained in terms of size selective excitation. A peculiar attention is given to the behaviour of low-frequency spectra and selection rules due to resonance effects are reported. Most of the first harmonics of the different predicted vibration modes have been observed and a qualitative attempt has been made to link the observed modes with the excited electronic levels.
6,6-Dimethylpterins: stable quinoid dihydropterin substrate for dihydropteridine reductase and tetrahydropterin cofactor for phenylalanine hydroxylase (1983)

The tautomeric structure of the cofactor product of aromatic amino acid hydroxylases, quinoid dihydrobiopterin, is still unknown. Characterization of this molecule, which is also the substrate for dihydropteridine reductase (EC 1.6.99.7), has been hindered by the rapid rearrangement of quinoid dihydropterins to 7,8-dihydropterins. This tautomerization can be prevented by disubstitution at the 6-position. A procedure is presented for the synthesis of 6,6-disubstituted pterins from a vicinal diamine and 2-amino-6-chloro-4(3H)-pyrimidinone. The method is illustrated with the specific synthesis of 6,6-dimethyltetrahydropterin (6,6-Me2PH4). 6,6-Me2PH4 is a cofactor for rat liver phenylalanine hydroxylase (EC 1.14.16.1), with enzyme kinetic parameters similar to those of its positional isomer, 6,7-dimethyltetrahydropterin. The resulting quinoid 6,6-dimethyldihydropterin (q-6,6-Me2PH2) is stable; the half-life in 0.1 M Tris-HCl, pH 7.4, at 27 and 37 degrees C is 4 and 1.25 h, respectively. q-6,6-Me2PH2, produced either by phenylalanine hydroxylase or by chemical oxidation of 6,6-Me2PH4, is a substrate for dihydropteridine reductase, with a Km of 0.4 mM and a maximum velocity double that of the natural isomer of quinoid dihydrobiopterin. In concentrations up to 0.4 mM q-6,6-Me2PH2 is not an inhibitor of phenylalanine hydroxylase, in contrast to 6-methyl-7,8-dihydropterin and 7,8-dihydrobiopterin which inhibit competitively, with Ki's of 0.2 mM and 0.05 mM, respectively. The stability of q-6,6-Me2PH2 has facilitated definitive determination of chemical and physical properties of a quinoid dihydropterin.
The Immunolocalization of Basic Fibroblast Growth Factor in the Mouse Uterus During the Initial Stages of Embryo Implantation (1994)

Mammalian embryo implantation involves a series of complex interactions between maternal and embryonic cells. Uterine polypeptide growth factors may play critical roles in these cell interactions. Basic fibroblast growth factor (basic FGF) is a member of a family of growth factors. This growth factor may be potentially important for the process of embryo implantation because it (a) is stored within the extracellular matrix and is thus easily available during embryo invasion, (b) is a potent modulator of cell proliferation and differentiation and (c) stimulates angiogenesis. The immunolocalization of basic FGF in the uterus during the peri-implantation period of pregnancy is presented in this study. Uterine tissue samples were obtained on days 6-9 of pregnancy with day 1 of pregnancy being the day of a vaginal copulatory plug. Uterine samples were fixed in Bouin's fluid for no longer than 18 h. Following fixation and paraffin embedding, sections were exposed to primary antisera made in rabbits against either (a) human recombinant basic FGF or (b) 1-24 synthetic fragment of bovine basic FGF. The primary antibody was followed by biotinylated goat anti-rabbit IgG and a biotin-avidin-peroxidase complex. There were no differences in the immunolocalization of basic FGF using either source of primary antibody. Our results demonstrated both temporal and spatial changes in the localization of immunoreactive basic FGF within the implantation chamber during days 6-9 of pregnancy. Inter-implantation sites resembled the non-pregnant uterus with basic FGF present in extracellular matrices including basal laminae. On day 6 of pregnancy, decidual cells within the primary decidual zone lacked both intracellular and pericellular basic FGF while non-decidualized uterine stroma resembled inter-implantation sites. By days 7-8 of pregnancy, the secondary decidual zone had formed and was characterized by the distinct pericellular localization of basic FGF around individual decidual cells. By day 9 of pregnancy, the mesometrial region was forming and contained cords of decidual cells and a labyrinth of maternal blood vessels. The decidual cells contained diffuse intracellular basic FGF. Trophoblast cells were devoid of basic FGF at all times examined. These results indicate that basic FGF is present within the implantation chamber on days 6-9 of pregnancy and may be involved in the decidual cell response, trophoblast cell invasion and angiogenesis.
Diffusion Mechanism of Li Argyrodite Solid Electrolytes for Li-Ion Batteries and Prediction of Optimized Halogen Doping: The Effect of Li Vacancies, Halogens, and Halogen Disorder (2016)

Using density functional theory molecular dynamics simulations, the origin of the Li-ion conductivity in argyrodite solid electrolytes is investigated. The simulations show that besides Li-ion vacancies in Li6PS5Cl and Li6PS5Br, the influence of halogen atoms on their local surroundings also plays an important role in Li-ion diffusion. The difference in Li-ion conductivity between Li6PS5Cl and Li6PS5I, which is several orders of magnitude, is caused by the distribution of the halogen ions over the available crystallographic sites. This suggests that altering the halogen distribution in Li argyrodites during synthesis could increase the Li-ion conductivity of these materials. For Li6PS5Cl, the simulations predict an optimal Cl distribution of 1:3 over sites 4a and 4c, resulting in a Li-ion conductivity that is 2 times larger than that of the currently prepared materials. On the basis of these results, simulations were performed on Li5PS4X2 (X = Cl, Br, or I), which show Li-ion conductivities similar to those of Li6PS5Cl and Li6PS5Br, suggesting that the Li5PS4X2 compounds are interesting new compositions for solid state electrolytes.
Automated detection of vulnerabilities in privileged programs by execution monitoring (2002)

Presents a method for detecting exploitations of vulnerabilities in privileged programs by monitoring their execution using audit trails, where the monitoring is with respect to specifications of the security-relevant behavior of the programs. Our work is motivated by the intrusion detection paradigm, but is an attempt to avoid ad hoc approaches to codifying misuse behavior. Our approach is based on the observation that although privileged programs can be exploited (due to errors) to cause security compromises in systems because of the privileges accorded to them, the intended behavior of privileged programs is, of course, limited and benign. The key, then, is to specify the intended behavior (i.e. the program policy) and to detect any action by a privileged program that is outside the intended behavior and that imperils security. We describe a program policy specification language, which is based on simple predicate logic and regular expressions. In addition, we present specifications of privileged programs in Unix, and a prototype execution monitor for analyzing audit trails with respect to these specifications. The program policies are surprisingly concise and clear, and in addition, capable of detecting exploitations of known vulnerabilities in these programs. Although our work has been motivated by the known vulnerabilities in Unix, we believe that by tightly restricting the behavior of all privileged programs, exploitations of unknown vulnerabilities can be detected. As a check on the specifications, work is in progress on verifying them with respect to an abstract security policy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Red‐orange electroluminescence with new soluble and air‐stable poly(naphthalene‐vinylene)s* (1995)

The optical and electronic properties of new soluble derivatives of poly(naphthalene‐vinylene) (PNV) with different length alkyl side groups are reported. Quantum efficiencies of up to 10% and power efficiencies of up to 0.02% have been attained from polymer‐LEDs based on these materials, and the polymers themselves are found to have a well‐defined chemical structure and exhibit little main‐chain stiffness.
CAMP factor homologues in Propionibacterium acnes: a new protein family differentially expressed by types I and II (2005)

Analysis of the draft genome sequence of the opportunistic pathogen Propionibacterium acnes type strain NCTC 737 (=ATCC 6919) revealed five genes with sequence identity to the co-haemolytic Christie-Atkins-Munch-Peterson (CAMP) factor of Streptococcus agalactiae. The predicted molecular masses for the expressed proteins ranged from 28 to 30 kDa. The genes were present in each of the three recently identified recA-based phylogenetic groupings of P. acnes (IA, IB and II), as assessed by PCR amplification. Conserved differences in CAMP factor gene sequences between these three groups were also consistent with their previous phylogenetic designations. All type IA, IB and II isolates were positive for the co-haemolytic reaction on sheep blood agar. Immunoblotting and silver staining of SDS-PAGE gels, however, revealed differential protein expression of CAMP factors amongst the different groups. Type IB and II isolates produced an abundance of CAMP factor 1, detectable by specific antibody labelling and silver staining of SDS-PAGE gels. In contrast, abundant CAMP factor production was lacking in type IA isolates, although larger amounts of CAMP factor 2 were detectable by immunoblotting compared with type II isolates. While the potential role of the abundant CAMP factor 1 in host colonization or virulence remains to be determined, it should be noted that the type strain of P. acnes used in much of the published literature is a type IA isolate and is, therefore, lacking in this attribute.
The effects of piezoelectric poly-L-lactic acid films in promoting ossification in vivo. (1997)

Uniaxially drawn poly-L-lactic acid (PLLA) films with piezoelectric properties were inserted onto the periosteum of rabbit tibiae, and the effect of the films in promoting ossification was investigated. We also evaluated the optimum method for PLLA film insertion to promote ossification, by comparing three different types of PLLA films which differed from each other in terms of the direction of their molecular orientation. Furthermore, the course of ossification following the film insertion was observed histologically. Drawn PLLA films promoted ossification to a greater extent than undrawn PLLA film. The effect of drawn PLLA films in promoting ossification was greatest when a shearing stress was applied at 45 degrees to the axis of orientation. The newly formed osteoid was observed at 1 week, and matured over 6 to 8 weeks following insertion. The insertion of piezoelectric PLLA films can promote ossification through their piezoelectric effect, and this seems to be clinically applicable.
THE MECHANISIM OF FRUCTOSAN METABOLISM IN HIGHER PLANTS AS EXEMPLIFIED IN HELIANTHUS TUBEROSUS (1968)

S ummary The physiological behaviour of the fructose polymers, which are the sole carbohydrate reserve in Jerusalem artichoke tubers, is briefly described. It is suggested that certain enzymes which have been isolated from this tissue can account for these changes, and a theory of their integrated action is put forward: this involves the trisaccharide I F ‐fructosylsucrose, widely found in fructosan‐containing tissues, as a key intermediate, and the enzyme which produces it from sucrose as a controlling biochemical factor. Sucrose itself, both as a substrate and by its direct effect on the other enzymes, also acts as a major means of control. The hypothesis does not involve sugar phosphates or nucleotide sugars, and seems to be applicable to other plants which contain fructosans.
Diels–Alder reactivity of pyrano[4,3-b]indol-3-ones, indole 2,3-quinodimethane analogues (1990)

The pyrano[4,3-b]indol-3-ones (7) are stable indole-2,3-quinodimethane type dienes, which undergo Diels–Alder reaction with alkynes to give, after loss of carbon dioxide, carbazoles. The reactivity of the diene is increased by the presence of the electron-withdrawing t-butoxycarbonyl group on the indole nitrogen. The pyranoindolones (7) are less reactive, and exhibit the opposite regiochemistry in their Diels–Alder reactions than the isomeric pyrano[3,4-b]indol-3-ones (1). Factors which affect the regiochemistry of the Diels–Alder reaction are discussed.
Comprehensive analysis of current approaches to inhibit regulatory T cells in cancer (2012)

CD4(+)CD25(+)Foxp3(+) regulatory T cells (Treg) have emerged as a dominant T cell population inhibiting anti-tumor effector T cells. Initial strategies used for Treg-depletion (cyclophosphamide, anti-CD25 mAb…) also targeted activated T cells, as they share many phenotypic markers. Current, ameliorated approaches to inhibit Treg aim to either block their function or their migration to lymph nodes and the tumor microenvironment. Various drugs originally developed for other therapeutic indications (anti-angiogenic molecules, tyrosine kinase inhibitors,etc) have recently been discovered to inhibit Treg. These approaches are expected to be rapidly translated to clinical applications for therapeutic use in combination with immunomodulators.
Formal Total Synthesis of Oximidine II via a Suzuki-Type Cross-Coupling Macrocyclization Employing Potassium Organotrifluoroborates (2004)

A formal total synthesis of oximidine II has been achieved, employing a Suzuki-type coupling approach to construct the highly strained, polyunsaturated 12-membered macrolactone. To achieve this goal, benefit was derived from the stability of potassium alkenyltrifluoroborates to establish conditions for the macrocyclization. The stereocontrolled formation of the cis-1,2-diol subunit was accomplished using a diastereoselective, reagent controlled addition to a chiral aldehyde utilizing the Carreira protocol. Advantage was taken of the Snieckus hydroborating reagent to gain access to the key trifluoroborate needed for the macrocyclization.
CTLA4-Ig PLUS BONE MARROW INDUCES LONG-TERM ALLOGRAFT SURVIVAL AND DONOR-SPECIFIC UNRESPONSIVENESS IN THE MURINE MODEL (1996)

Allograft rejection is dependent on T cell activation, which requires both the engagement of the T cell receptor by antigen in the context of the MHC molecules and costimulatory signals delivered by cell surface molecules such as B7-CD28/CTLA4 pathway. CTLA4-Ig is a fusion protein that blocks this pathway and has previously been shown to prolong both allograft and xenograft survival. The current study demonstrates markedly prolonged murine cardiac allograft survival and specific prolongation of secondary skin grafts using a combination of CTLA4-Ig plus donor bone marrow. A role for hematopoietic chimerism in the establishment of CTLA4-Ig-induced transplantation tolerance was investigated using reverse transcriptase polymerase chain reaction analysis of recipient tissues. Expression of donor-specific MHC class II transcripts in both peripheral and lymphoid tissues was demonstrated at greater than 200 days after transplant. To investigate the functional significance of this observation, heart donors, and donor bone marrow were irradiated before transplantation in CTLA4-Ig-treated recipients. A reduction in allograft survival was associated with irradiation of both the donor heart and the bone marrow. These results suggest that there may be a donor-derived radiosensitive element that enhances allograft survival in this model. Reverse transcriptase polymerase chain reaction analysis of allografts of tolerant and control animals at days 5, 8, and 12 after transplantation failed to demonstrate a dramatic difference in the expression of interleukin (IL)-2, IL-4, IL-10, and interferon-gamma message. Cytotoxicity effector transcripts were largely intact in CTLA4-Ig + bone marrow-treated recipients as they showed no decrease in intragraft granzyme, perforin, Fas, or Fas ligand transcripts during thr first 8 days after transplant. These results imply that complex mechanisms may be important for the induction and maintenance of transplantation tolerance in the CTLA4-Ig plus bone marrow murine cardiac allograft model.