gebhart/patrepeval huggingface dataset:
Temporal synthesis of proteins and RNAs during human astrovirus infection of cultured cells (1991)

Astroviruses are nonenveloped particles with a distinctive star-shaped surface structure that have been detected by electron microscopy in stool samples from humans and animals with gastroenteritis. We examined the patterns of macromolecular synthesis in astrovirus-infected cells with a goal of establishing a molecular basis for taxonomic classification. Trypsin is required for continuous replication of astrovirus in cultured cells; however, during a single cycle of infection, astrovirus antigen was synthesized earlier and at higher levels when serum, rather than trypsin, was included in the growth medium. This enhanced production of antigen, as measured by enzyme immunoassay, was accompanied by the appearance of aggregates of virus particles in the cytoplasm of infected cells. During astrovirus replication in cells cultured in the presence of serum, we detected a single infection-specific protein (90 kDa) beginning at 12 h postinfection. This protein was recognized by antiastrovirus rabbit serum and was sensitive to trypsin digestion in vitro, with the concomitant appearance of three smaller immunoreactive proteins (31, 29, and 20 kDa). We also detected two dactinomycin-resistant RNAs (7.2 and 2.8 kb), both of which were polyadenylated, in the cytoplasm of astrovirus-infected cells. The larger of these two RNAs is presumably the viral genome, whereas the smaller species may be a subgenomic messenger. Comparison of the proteins and RNAs synthesized in astrovirus-infected cells with those of the recognized families of nonenveloped single-stranded RNA animal viruses suggests that astroviruses should not be classified as members of either Caliciviridae or Picornaviridae.
Reorganizing web sites based on user access patterns (2001)

In this paper, an approach for reorganizing Web sites based on user access patterns is proposed. The approach consists of three steps: preprocessing, page classification, and site reorganization. In preprocessing, pages on a Web site are processed to create an internal representation of the site, and page access information of its users is extracted from its server log. In page classification, the Web pages on the site are classified into two categories, index pages and content pages, based on the page access information. After the pages are classified, in site reorganization, the Web site is examined to find better ways to organize and arrange the pages on the site. Our experiments on a large real data set show that the approach is efficient and practical for adaptive Web sites.
Structure Stability of Lytic Peptides During Their Interactions With Lipid Bilayers (2001)

In this work, molecular dynamics simulations were used to examine the consequences of a variety of analogs of cecropin A on lipid bilayers. Analog sequences were constructed by replacing either the N- or C-terminal helix with the other helix in native or reverse sequence order, by making palindromic peptides based on both the N- and C-terminal helices, and by deleting the hinge region. The structure of the peptides was monitored throughout the simulation. The hinge region appeared not to assist in maintaining helical structure but help in motion flexibility. In general, the N-terminal helix of peptides was less stable than the C-terminal one during the interaction with anionic lipid bilayers. Sequences with hydrophobic helices tended to regain helical structure after an initial loss while sequences with amphipathic helices were less able to do this. The results suggests that hydrophobic design peptides have a high structural stability in an anionic membrane and are the candidates for experimental investigation.
<i>glmS</i> of <i>Thermus thermophilus</i> HB8: an essential gene for cell‐wall synthesis identified immediately upstream of the S‐layer gene (1995)

A 30 kbp chromosomal region containing the S-layer gene (slpA) from Thermus thermophilus HB8 was cloned from a lambda phage gene library. DNA sequence analysis of the region upstream to the slpA gene revealed the presence of an open reading frame (ORF) which coded for a 604-amino-acid protein highly homologous to the glucosamine-6-P synthases (EC 2.6.1.16) of both prokaryotic and eukaryotic origin. The identification of this ORF as the glucosamine-6-P synthase gene from T. thermophilus (glmSth) has been carried out using three different strategies: (i) complementation of an Escherichia coli glmS mutant; (ii) in vivo insertional inactivation of the gene; and (iii) in vitro synthesis of glucosamine-6-P at 60 degrees C by a cytoplasmic extract of an overproducing E. coli strain. The glmSth gene is transcribed divergently from slpA in a 2.0 kb mRNA which probably also includes a tryptophan tRNA gene (trpTth) identified at its 3' extreme. As the products of both the glmSth and the slpA genes are main components of the cell envelope of T. thermophilus, their unusual clustering in the chromosome could be related to the existence of specific mechanisms for their coordinate expression.
Titanium Dioxide Nanoparticles Trigger Loss of Function and Perturbation of Mitochondrial Dynamics in Primary Hepatocytes (2015)

Titanium dioxide (TiO2) nanoparticles are one of the most highly manufactured and employed nanomaterials in the world with applications in copious industrial and consumer products. The liver is a major accumulation site for many nanoparticles, including TiO2, directly through intentional exposure or indirectly through unintentional ingestion via water, food or animals and increased environmental contamination. Growing concerns over the current usage of TiO2 coupled with the lack of mechanistic understanding of its potential health risk is the motivation for this study. Here we determined the toxic effect of three different TiO2 nanoparticles (commercially available rutile, anatase and P25) on primary rat hepatocytes. Specifically, we evaluated events related to hepatocyte functions and mitochondrial dynamics: (1) urea and albumin synthesis using colorimetric and ELISA assays, respectively; (2) redox signaling mechanisms by measuring reactive oxygen species (ROS) production, manganese superoxide dismutase (MnSOD) activity and mitochondrial membrane potential (MMP); (3) OPA1 and Mfn-1 expression that mediates the mitochondrial dynamics by PCR; and (4) mitochondrial morphology by MitoTracker Green FM staining. All three TiO2 nanoparticles induced a significant loss (p < 0.05) in hepatocyte functions even at concentrations as low as 50 ppm with commercially used P25 causing maximum damage. TiO2 nanoparticles induced a strong oxidative stress in primary hepatocytes. TiO2 nanoparticles exposure also resulted in morphological changes in mitochondria and substantial loss in the fusion process, thus impairing the mitochondrial dynamics. Although this study demonstrated that TiO2 nanoparticles exposure resulted in substantial damage to primary hepatocytes, more in vitro and in vivo studies are required to determine the complete toxicological mechanism in primary hepatocytes and subsequently liver function.
A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases (1995)

The superimposable dinucleotide fold domains of MetRS, GlnRS and TyrRS define structurally equivalent amino acids which have been used to constrain the sequence alignments of the 10 class I aminoacyl-tRNA synthetases (aaRS). The conservation of those residues which have been shown to be critical in some aaRS enables to predict their location and function in the other synthetases, particularly: i) a conserved negatively-charged residue which binds the alpha-amino group of the amino acid substrate; ii) conserved residues within the inserted domain bridging the two halves of the dinucleotide-binding fold; and iii) conserved residues in the second half of the fold which bind the amino acid and ATP substrate. The alignments also indicate that the class I synthetases may be partitioned into two subgroups: a) MetRS, IleRS, LeuRS, ValRS, CysRS and ArgRS; b) GlnRS, GluRS, TyrRS and TrpRS.
Microbiological monitoring in the biodegradation of sewage sludge and food waste (2004)

Aim: To study the microbiology of intensive, in-vessel biodegradation of a mixture of sewage sludge and vegetable food waste. Methods and Results: The biodegradation was performed in a closed reactor with the addition of a starter culture of Bacillus thermoamylovorans SW25 under conditions of controlled aeration, stirring, pH and temperature (60°C). The content of viable bacterial cells, determined by flow cytometry, increased from 5 × 108 g−1 of dry matter to 61 × 108 g−1 for 6 days of the process and then dropped to the initial value at the end of the process. The reductions of organic matter, 16S rRNA of methanogens and coenzyme F420 fluorescence during 10 days of the treatment were 67, 54 and 87% of the initial values, respectively. The biodegradability of the organic matter decreased during the 10 days of the treatment from 3·8 to 1·3 mg CO2 g−1 of organic matter per day. The treatment of sewage sludge and food waste at 60°C did not remove enterobacteria, which are the agents of intestinal infections, from the material. The percentage of viable enterobacterial cells, determined by fluorescent in situ hybridization (FISH) with Enterobacteriaceae-specific oligonucleotide probe and flow cytometry, varied from 1 to 14% of the viable bacterial cells. Conclusions: The mixture of sewage sludge and food waste can be degraded by the aerobic thermophilic bacteria; the starter culture of Bacillus thermoamylovorans SW25 can be used to perform this process; and enterobacteria can survive under treatment of sewage sludge and food waste at 60°C for 13 days. Significance and Impact of the Study: The results show that FISH with an oligonucleotide probe can be used to study not only the growth but also the degradation of biomass. Obtained results could be used to design the bioconversion of sewage sludge and food waste into organic fertilizer.
Multi-camera based human tracking with non-Overlapping fields of view (2009)

This paper presents approach for an automated surveillance system which performs human detection and tracking across multiple non-overlapping cameras. At single camera level, motion based segmentation is achieved using an accurate optical flow estimation technique. Feature matching and region-based shape descriptors are used for object tracking and classification. The proposed approach extends these features across fields of view (FOV) of multiple non-overlapping cameras in order to obtain correct inter-camera correspondences. Performance evaluation of the system was done in different scenarios which verify that the proposed method can efficiently tackle the complexity of video motion tracking with high processing speed.
Block phase-precoding for blind multiuser detection of BPSK/DS-CDMA signals (2003)

A new approach for blind multiuser detection of BPSK/DS-CDMA signals is proposed. This approach is based on precoding the phase of the transmitted data, uniquely for each user, over a block of data, to enable separation and detection of a desired user's signal in an unknown multipath channel. Detection does not involve channel estimation, and does not even need knowledge of the desired user's code. The method does not involve any sacrifice in data rate or system bandwidth. With some additional complexity, the method can be made to deal with the case of carrier frequency offsets. Computer simulations show good performance compared to some existing methods.
Hybrid Dissymmetrical Colloidal Particles (2005)

Colloidal particles with a controlled morphology combining both organic and inorganic parts were synthesized through a seeded emulsion polymerization process. Silica seed particles from 50 to 150 nm were first surface-modified by adsorption of an oxyethylene-based macromonomer or covalent grafting of a trialkoxysilane derivative. Then, emulsion polymerization of styrene was carried out in the presence of these particles, the formation of polystyrene nodules being highly favored at the silica surface in such conditions. While varying different experimental parameters, we have demonstrated that the ratio between the number of silica seeds and the number of growing nodules is a key parameter in controlling the morphology of the final hybrid nanoparticles. For instance, in the particular case when this ratio was close to 1, dumbbell-like or snowman-like particles were obtained. Further selective surface modification of their silica moiety was also tested successfully, indicating a potential application of these hybrid particles as original building blocks toward supraparticulate assemblies.
The World Bank GEF energy efficiency projects, post-implementation impact assessment : synthesis report (2006)

Four energy efficiency/demand-side (DSM) management projects were assessed in 2004-5 to determine their long-term impacts and to draw out lessons that could be applied in the development of future World Bank/ Global Environment Facility (GEF) projects. The projects were: o Poland Efficient Lighting Project (PELP) o Mexico High Efficiency Lighting Project (ILUMEX) o Thailand Promotion of Electrical Energy Efficiency Project (TPEEE) o Jamaica Demand-Side Management Demonstration Project (JDSMDP). All four projects had the objectives of developing DSM capacity, reducing electricity consumption and greenhouse gas (GHG) emissions, and developing technical and financial program models that could be replicated. Some of the lessons learned are: a) Impact assessments are greatly facilitated when information is collected throughout the project life cycle and an appropriate evaluation framework is established from the beginning. b) There is substantial confusion (particularly in recipient countries) about the various forms of audits, completion reports, assessments, and evaluations. c) Project information and ongoing monitoring information can be easily lost during staff changes at the World Bank or in the implementing entity. d) Difficulty in obtaining information on actual events (such as time-series data on sales) in some countries, let alone data for counter-factual scenarios. e) Identifying and gaining access to key informants is essential. This can be difficult, however, particularly without a local contact. f) Field missions are essential opportunities to collect opinions as well as documentation that are hard to obtain otherwise. However, it is easy for missions to be diverted from core objectives. g) Lack of certain data makes it difficult to develop credible estimates of impact. h) Understanding the context of the changes is very important to drawing conclusions on attribution. i) In addition to understanding the project and country context, it is important that the analysis be grounded in a thorough understanding of the evolution of the World Bank's own approaches. Finally, j) The significance and value of the analysis is greatly enhanced by a comparative study of several projects.
Antigen receptor-induced cell cycle arrest in WEHI-231 B lymphoma cells depends on the duration of signaling before the G1 phase restriction point. (1990)

Stimulation of antigen receptors on WEHI-231 B lymphoma cells with anti-receptor antibodies (anti-immunoglobulin M [IgM]) causes irreversible growth arrest. This may be a model for antigen-induced tolerance to self components in the immune system. Antigen receptor stimulation also causes inositol phospholipid hydrolysis, producing diacylglycerol, which activates protein kinase C, and inositol 1,4,5-trisphosphate, which causes release of calcium from intracellular stores. To better understand the nature of the antigen receptor-induced growth arrest of WEHI-231 cells, we have examined the basis for it. WEHI-231 cells in various phases of the cell cycle were isolated by centrifugal elutriation, and their response was evaluated following treatment with either anti-IgM or pharmacologic agents that raise intracellular free calcium levels and activate protein kinase C. Treatment with anti-IgM or the pharmacologic agents did not lengthen the cell cycle. Instead, growth inhibition was solely the result of arrest in the G1 phase. The efficiency of G1 arrest increased with the length of time during which the cells received signaling before reaching the G1 phase arrest point. Maximum efficiency of arrest was achieved after approximately one cell cycle of receptor signaling. These results imply that anti-IgM causes G1 arrest of WEHI-231 cells by slowly affecting components required for S phase progression, rather than by rapidly inhibiting such components or by rapidly activating a suicide mechanism. Antigen receptor stimulation was twice as effective as stimulation via the mimicking reagents phorbol dibutyrate and ionomycin. Thus, although the phosphoinositide second messengers diacylglycerol and calcium probably play roles in mediating the effects of anti-IgM on WEHI-231 cells, other second messengers may also be involved.
Fractography (2001)

Abstract This article illustrates typical fractographic features for a number of different composite materials. It describes the differences in fracture characteristics due to different loading, material processing, and environmental conditions. The article presents fractographic data obtained from epoxy matrix materials. Minimal fractographic data from other brittle thermoset resin systems are also presented. The article discusses the interlaminar fracture of composites with ductile thermoplastic matrices. It also provides information on the translaminar fracture features of the composite materials.
Enhanced magnetoelectric effects in laminate composites of Terfenol-D/Pb(Zr,Ti)O3 under resonant drive (2003)

We have found that laminate composites consisting of longitudinally magnetized magnetostrictive Terfenol-D and longitudinally poled piezoelectric Pb(Zr,Ti)O3 layers have dramatically enhanced magnetoelectric effects when driven near resonance. The maximum induced magnetoelectric voltage at resonance was ∼10 Vp/Oe, which is ∼102 times higher than previous reports at subresonant frequencies.
Ciclesonide for the treatment of asthma. (2006)

Ciclesonide is a nonhalogenated corticosteroid that is converted to its clinically active metabolite, desisobutyryl-ciclesonide, by esterases in the airways. Pharmacodynamic studies have shown that inhaled ciclesonide has potent antiinflammatory activity in patients with asthma, and does not appear to have clinically relevant systemic effects, even at high doses. It is highly protein-bound and rapidly metabolized by the liver, and thus has a low oral bioavailability. Ciclesonide is formulated as a solution for inhalation using a hydrofluoroalkane pressurized metered-dose inhaler. This formulation delivers a high fraction of respirable particles that yield high lung deposition with even distribution throughout the lungs and minimal oropharyngeal deposition. Results from numerous 12-week trials in patients (including children) with varying degrees of asthma show that morning or evening dosing with ciclesonide is more effective than placebo, and at least equivalent to other inhaled corticosteroids such as budesonide and fluticasone, with regard to improved spirometry, symptom scores, and less need for rescue medication. Results with once-daily ciclesonide are similar to those with twice-daily budesonide or fluticasone. At the dosages used in clinical trials, ciclesonide did not exert any untoward adverse effects and did not affect cortisol production. The favorable pharmacological properties of ciclesonide help explain the low incidence of adverse events, which are mostly mild to moderate in nature. Once-daily ciclesonide offers an efficacious treatment option for stepwise asthma management when inhaled corticosteroids are required.
Memory CD8 T cells mediate severe immunopathology following respiratory syncytial virus infection (2018)

Memory CD8 T cells can provide protection from re-infection by respiratory viruses such as influenza and SARS. However, the relative contribution of memory CD8 T cells in providing protection against respiratory syncytial virus (RSV) infection is currently unclear. To address this knowledge gap, we utilized a prime-boost immunization approach to induce robust memory CD8 T cell responses in the absence of RSV-specific CD4 T cells and antibodies. Unexpectedly, RSV infection of mice with pre-existing CD8 T cell memory led to exacerbated weight loss, pulmonary disease, and lethal immunopathology. The exacerbated disease in immunized mice was not epitope-dependent and occurred despite a significant reduction in RSV viral titers. In addition, the lethal immunopathology was unique to the context of an RSV infection as mice were protected from a normally lethal challenge with a recombinant influenza virus expressing an RSV epitope. Memory CD8 T cells rapidly produced IFN-γ following RSV infection resulting in elevated protein levels in the lung and periphery. Neutralization of IFN-γ in the respiratory tract reduced morbidity and prevented mortality. These results demonstrate that in contrast to other respiratory viruses, RSV-specific memory CD8 T cells can induce lethal immunopathology despite mediating enhanced viral clearance.
IS91 transposase is related to the rolling-circle-type replication proteins of the pUB110 family of plasmids (1992)

Journal Article IS91 transposase is related to the rolling-circle-type replication proteins of the pUB110 family of plasmids Get access M.Victoria Mendiola, M.Victoria Mendiola Departamento de Biologia Molecular, Universidad de Cantabna, C. Herrera Oria s/n, 39011 Santander, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar Fernando de la Cruz Fernando de la Cruz * Departamento de Biologia Molecular, Universidad de Cantabna, C. Herrera Oria s/n, 39011 Santander, Spain * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 20, Issue 13, 11 July 1992, Page 3521, https://doi.org/10.1093/nar/20.13.3521 Published: 11 July 1992 Article history Received: 22 April 1992 Published: 11 July 1992
Summary of a 15-Month Biology Articulation Program through Drake University (1972)

During the summer of 1970, a five-day workshop was held at Drake to begin our 15-month articulation program. Discussion of textbooks and their merits and identification of lab manuals used was our first consideration. Many sessions were held on the criteria for evaluation of biology programs and facilities, with a rating scale for our use developed after discussions on ideal conditions.
Advanced Glycation End Products in Diabetes‐Associated Atherosclerosis and Renal Disease: Interventional Studies (2005)

There is increasing evidence that advanced glycation end products (AGEs) and their interactions with various receptors (in particular, the receptor RAGE) play a pivotal role in the development and progression of diabetic macro- and microvascular complications. Several approaches have been used to inhibit tissue accumulation of AGEs in diabetes, including inhibitors of AGE formation such as aminoguanidine, ALT 946, and pyridoxamine-or putative cross-link breakers such as ALT 711. Alternative interventions have also included the administration of a soluble receptor for RAGE, sRAGE, thus capturing circulating AGEs and preventing them from binding to the cell-bound full-length receptor RAGE, thereby inhibiting the proinflammatory and profibrotic response following AGE-RAGE binding. In this review we summarize the evidence for such antiglycation therapies in retarding or delaying the development and progression of diabetes-associated atherosclerosis and renal disease while focusing on interventional strategies inhibiting AGE accumulation. In summary, all approaches have been shown to confer some degree of antiatherosclerotic and renoprotective effects, albeit to different degrees and by different mechanisms.