gebhart/patrepeval huggingface dataset:
Ligand-induced internalization and increased cell calcium are mediated via distinct structural elements in the carboxyl terminus of the epidermal growth factor receptor. (1991)

Signals that can mediate ligand-induced receptor internalization and calcium regulation are present in a 48-amino acid "calcium-internalization" domain in the C' terminus of the epidermal growth factor (EGF) receptor. The basis of calcium and internalization regulation signalled by this 48-amino acid sequence was analyzed using deletion and substitution mutant receptors. Cells expressing truncated receptors containing either the NH2- or COOH-terminal portion of the 48-residue domain displayed high affinity EGF-dependent endocytosis and receptor down-regulation. These endocytosis-competent EGF receptor mutants that lacked any autophosphorylation site were unable to increase the concentration of intracellular calcium. To investigate the role of self-phosphorylation in EGF-induced calcium mobilization, phenylalanine was substituted for the single autophosphorylated tyrosine residue in this region of an internalization-competent truncated receptor. The receptor-mediated calcium response was abolished, while ligand-dependent receptor internalization was unimpaired. These results demonstrate that EGF-dependent receptor endocytosis and calcium mobilization are separate events. Tyrosine self-phosphorylation is required for increased [Ca2+]i, while structural features distinct from autophosphorylation are required for receptor internalization.
SIM-a system for semi-automatic indexing of multilingual documents (1999)

With the growing significance of digital libraries and the Internet, more and more electronic texts become accessible to a wide and geographically disperse public. This requires adequate tools to facilitate indexing, storage, and retrieval of documents written in different languages. We present a method for semi-automatic indexing of electronic documents and construction of a multilingual thesaurus, which can be used for query formulation and information retrieval. We use special dictionaries and user interaction in order to solve ambiguities and find adequate canonical terms in the language and an adequate abstract language-independent term. The abstract thesaurus is updated incrementally by new indexed documents and is used to search documents concerning terms in a query to the document base.
Streptomyces coelicolor Vesicles: Many Molecules To Be Delivered (2021)

Streptomycetes are widely distributed in nature and characterized by a complex life cycle that involves morphological differentiation. They are very relevant in industry because they produce about half of all clinically used antibiotics, as well as other important pharmaceutical products of natural origin. Streptomyces coelicolor is a model organism for the study of bacterial differentiation and bioactive molecule production. S. coelicolor produces extracellular vesicles which carry many molecules, such as proteins and metabolites, including antibiotics.
Recent Developments in Bio‐Based Materials for Controlled‐Release Fertilizers (2022)

The term “bio-based materials” has been used intensively for the development of recent materials. In agriculture as well, synthetic fertilizers that instantly dissolve in water may need bio-based polymer to detain fast nutrient leaching that causes environmental problems. The nutrients can release from coating and matrix models by diffusion through the insoluble part. Various controlled release systems are discussed, involving either a hydrophobic or hydrophilic barrier. The coating type is generally preferred since it precisely controls the release of plant nutrients. Not only are macronutrients like N, P, and K considered, but micronutrients (e.g. Fe, Zn, and B) have also been explored. Natural biopolymers such as polysaccharides and lignin are shown to have potential during intermediate development. Alkyd-based resins may require a further synthetic step to give advantages with improved properties. Bio-wastes treated with the right pyrolysis to give biochar and carbons can yield a slow-release rate for nutrients by water absorption.
Multi-layer Lattice Model for Real-Time Dynamic Character Deformation (2015)

Due to the recent advancement of computer graphics hardware and software algorithms, deformable characters have become more and more popular in real-time applications such as computer games. While there are mature techniques to generate primary deformation from skeletal movement, simulating realistic and stable secondary deformation such as jiggling of fats remains challenging. On one hand, traditional volumetric approaches such as the finite element method require higher computational cost and are infeasible for limited hardware such as game consoles. On the other hand, while shape matching based simulations can produce plausible deformation in real-time, they suffer from a stiffness problem in which particles either show unrealistic deformation due to high gains, or cannot catch up with the body movement. In this paper, we propose a unified multi-layer lattice model to simulate the primary and secondary deformation of skeleton-driven characters. The core idea is to voxelize the input character mesh into multiple anatomical layers including the bone, muscle, fat and skin. Primary deformation is applied on the bone voxels with lattice-based skinning. The movement of these voxels is propagated to other voxel layers using lattice shape matching simulation, creating a natural secondary deformation. Our multi-layer lattice framework can produce simulation quality comparable to those from other volumetric approaches with a significantly smaller computational cost. It is best to be applied in real-time applications such as console games or interactive animation creation.
Evaluation of Front-End Higher Energy Collision-Induced Dissociation on a Benchtop Dual-Pressure Linear Ion Trap Mass Spectrometer for Shotgun Proteomics (2011)

We report the implementation of front-end higher energy collision-induced dissociation (fHCD) on a benchtop dual-pressure linear ion trap. Software and hardware modifications were employed, described in detail vide-infra, to allow isolated ions to undergo collisions with ambient gas molecules in an intermediate multipole (q00) of the instrument. Results comparing the performance of fHCD and resonance excitation collision-induced dissociation (RE-CID) in terms of injection time, total number of scans, efficiency, mass measurement accuracy (MMA), unique peptide identifications, and spectral quality of labile modified peptides are presented. fHCD is approximately 23% as efficient as RE-CID, and depending on the search algorithm, it identifies 6.6% more or 15% less peptides (q < 0.01) from a soluble whole-cell lysate ( Caenorhabditis elegans ) than RE-CID using Mascot or Sequest search algorithms, respectively. fHCD offers a clear advantage for the analysis of phosphorylated and glycosylated (O-GlcNAc) peptides as the average cross-correlation score (XCorr) for spectra using fHCD was statistically greater (p < 0.05) than for spectra collected using RE-CID.
Shape Optimization of PZT Actuators and Laser Doppler Vibrometry Experimentation (2005)

It is well understood that, while piezoceramic bimorph actuators represent a viable option for the optimal control of two-dimensional flow fields, uniformly-electroded bimorphs typically induce undesirable threedimensional flow effects. In a series of papers, the authors have recently addressed the problem of shape optimization for electrodes used in piezoceramic actuators. In this work, shape optimization theory was applied to derive electrode shapes that minimize three-dimensional flow effects in both the static and dynamic cases. The resulting optimized electrodes performed well in numerical simulations, but the approach has a number of potential limitations. In particular, the actuator, which takes the form of a piezoelectric patch mounted to a small metal flap, is modeled using simple beam theory, employing kinematic assumptions that may not be valid in practice. Therefore, this paper is concerned with the experimental validation of the theoretical shape optimization results. In particular, this paper explores the use of a scanning laser Doppler vibrometer, which has been demonstrated to have unique capabilities for the sensing of micro-systems, to measure actuator deflections. Scanning laser Doppler vibrometry is described in detail and some preliminary experimental results are presented. These results represent the first step towards the ultimate goal of validating the response of the optimal electrode shapes obtained using the theoretical model.
Triggered message sequence charts (2002)

We propose an extension to Message Sequence Charts called Triggered Message Sequence Charts (TMSCs) that are intended to capture system specifications involving nondeterminism in the form of conditional scenarios. The visual syntax of TMSCs closely resembles that of MSCs; the semantics allows us to translate a TMSC specification into a framework that supports a notion of refinement based on Denicola's and Hennessy's must preorder. A simple but non-trivial example illustrates the utility of our extension to MSCs.
Computational problems related to quadratic residues (2005)

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Gas detection with quantum cascade lasers: An adapted photoacoustic sensor based on Helmholtz resonance (2002)

A photoacoustic gas sensor exploiting a quantum cascade laser as a radiation source is demonstrated. A detection limit of ∼1 ppm with 1 ms response time is found using a Peltier-cooled Fabry–Pérot InGaAs-based quantum cascade laser emitting at 9.4 μm, and a commercial microphone as a detector. The photoacoustic cell consists of a Helmholtz resonator preceeded by a low-pass acoustic filter. This geometry is well adapted to the shape of the laser beam and allows for an effective filtering of ambient acoustical noise. The relative simplicity of the system is particularly attractive for applications where sensitivity, robustness, and ease of fabrication are all fundamental requirements.
Double deficiency of toll-like receptors 2 and 4 alters long-term neurological sequelae in mice cured of pneumococcal meningitis (2019)

Toll-like receptor (TLR) 2 and 4 signalling pathways are central to the body's defence against invading pathogens during pneumococcal meningitis. Whereas several studies support their importance in innate immunity, thereby preventing host mortality, any role in protecting neurological function during meningeal infection is ill-understood. Here we investigated both the acute immunological reaction and the long-term neurobehavioural consequences of experimental pneumococcal meningitis in mice lacking both TLR2 and TLR4. The absence of these TLRs significantly impaired survival in mice inoculated intracerebroventricularly with Streptococcus pneumoniae. During the acute phase of infection, TLR2/4-deficient mice had lower cerebrospinal fluid concentrations of interleukin-1β, and higher interferon-γ, than their wild-type counterparts. After antibiotic cure, TLR2/4 double deficiency was associated with aggravation of behavioural impairment in mice, as shown by diurnal hypolocomotion throughout the adaptation phases in the Intellicage of TLR-deficient mice compared to their wild-type counterparts. While TLR2/4 double deficiency did not affect the cognitive ability of mice in a patrolling task, it aggravated the impairment of cognitive flexibility. We conclude that TLR2 and TLR4 are central to regulating the host inflammatory response in pneumococcal meningitis, which may mediate diverse compensatory mechanisms that protect the host not only against mortality but also long-term neurological complications.
The impact of hydrogen peroxide supply on LPMO activity and overall saccharification efficiency of a commercial cellulase cocktail (2018)

We report saccharification rates and yields for a model substrate (Avicel) and industrial lignocellulosic substrates that, at low H<sub>2</sub>O<sub>2</sub> feeding rates, are higher than those seen under standard aerobic conditions. In an industrial setting, controlling and supplying molecular oxygen and stoichiometric amounts of reductant are challenging. The present report shows that the use of small amounts of a liquid bulk chemical, H<sub>2</sub>O<sub>2</sub>, provides an alternative to the currently available processes, which likely is cheaper and more easy to control, while giving higher product yields.
Structure and Function of Alpha-Fetoprotein (1977)

This episode is based on a lecture by Barbara Casavecchia, who is a writer, curator, educator based in Milan, and currently mentor of the Ocean Fellowship at Ocean Space, Venice, for TBA21–Academy. She is advocating for an embodied and entangled art and politics as found in her recent experience working within a set of queer and trans-feminist archives and collectives in Milan. A written version of her lecture has been published on artsoftheworkingclass.org\n
Prostate cancer expression of runt‐domain transcription factor Runx2, a key regulator of osteoblast differentiation and function (2003)

Expression of Runx2 in CaP may be the molecular switch that is associated with expression of various bone-specific factors in CaP. In turn, expression of these factors can influence bone remodeling and possibly play a role in the growth and survival of CaP in bone.
P1-S4.19 Stochastic network models (2011)

Background We present a general modelling scheme particularly adapted for the epidemiology of sexually transmitted infections. Emphasis is placed on the complex interaction structure of the population and on the probabilistic nature of the dynamics. Methods We represent the interaction structure of the population with complex network models. Markov Stochastic Processes are used to consider the probabilistic time evolution of both the network structure and the epidemiological state of the population. Idealised epidemiological problems are considered: they are qualitatively inspired by real-world systems but no actual real-world data is fed to the models. All analytical results are systematically validated through Monte Carlo numerical simulations. Results By dedicating compartments to individuals with both similar epidemiological states and similar contact patterns, we observe great agreement between analytical results and Monte Carlo simulations see Abstract P1-S4.19 Figure 1. This is a special case of the general observation that compartmental models perform better when individuals within each compartment are very similar among themselves. Explicit examples are given for contact patterns changing through time as well as for the interactions of different infections in the same population. Abstract P1-S4.19 Figure 1 Epidemiology on networks. Conclusions By specifying the structure of the population through its local features, we successfully model the probabilistic evolution of complex epidemiological systems. Infection stages and/or behavioural groups are considered the same way they are in “classical” compartmental models. The generality of the approach facilitates its application to a vast array of epidemiological phenomena.
In Vitro Antiviral Activity of AG7088, a Potent Inhibitor of Human Rhinovirus 3C Protease (1999)

AG7088 is a potent, irreversible inhibitor of human rhinovirus (HRV) 3C protease (inactivation rate constant (k(obs)/[I]) = 1,470,000 +/- 440,000 M(-1) s(-1) for HRV 14) that was discovered by protein structure-based drug design methodologies. In H1-HeLa and MRC-5 cell protection assays, AG7088 inhibited the replication of all HRV serotypes (48 of 48) tested with a mean 50% effective concentration (EC(50)) of 0.023 microM (range, 0.003 to 0.081 microM) and a mean EC(90) of 0.082 microM (range, 0.018 to 0.261 microM) as well as that of related picornaviruses including coxsackieviruses A21 and B3, enterovirus 70, and echovirus 11. No significant reductions in the antiviral activity of AG7088 were observed when assays were performed in the presence of alpha(1)-acid glycoprotein or mucin, proteins present in nasal secretions. The 50% cytotoxic concentration of AG7088 was >1,000 microM, yielding a therapeutic index of >12,346 to >333,333. In a single-cycle, time-of-addition assay, AG7088 demonstrated antiviral activity when added up to 6 h after infection. In contrast, a compound targeting viral attachment and/or uncoating was effective only when added at the initiation of virus infection. Direct inhibition of 3C proteolytic activity in infected cells treated with AG7088 was demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of radiolabeled proteins, which showed a dose-dependent accumulation of viral precursor polyproteins and reduction of processed protein products. The broad spectrum of antiviral activity of AG7088, combined with its efficacy even when added late in the virus life cycle, highlights the advantages of 3C protease as a target and suggests that AG7088 will be a promising clinical candidate.
Strain-Specific Enhancement or Inhibition of Coumarin Hepatotoxicity in Mice Following Pretreatment with Two Different Liver Enzyme-Inducing Agents (1996)

Human exposure to coumarin continues despite controversy over its hepatotoxic potential. Greater understanding of human reactions to coumarin may be achieved by studying murine interstrain differences. The metabolic basis of coumarin hepatotoxicity and its modulation by liver enzyme inducers, β-naphthoflavone (βNF) and aroclor 1254 (ARO), were investigated in C3H/He and DBA/2 mice. Coumarin (200 mg/kg) was hepatotoxic to both strains, resulting in 2- to 15-fold plasma aminotransferase elevations, mild subcapsular linear hepatocyte necrosis after 24 hr, and, in some C3H/He mice, centrilobular necrosis. In this strain, /NF pretreatment caused a 2- to 3-fold further increase in plasma aminotransferases and produced periportal necrosis. In contrast, ARO-pretreated C3H/He mice tended to exhibit lower plasma aminotransferases and occasional midzonal damage. Neither pretreatment significantly altered coumarin hepatotoxicity in DBA/2 mice. In C3H/He mice, hepatic microsomal metabolism of [3-14C]-coumarin via the 3-hydroxylation pathway doubled following both βNF and ARO treatment The contrasting nonresponsiveness of DBA/2 mice suggested that this pathway is linked to the Ah locus, which is defective in this strain. ARO treatment caused a maximal 5-fold increase in coumarin 7-hydroxylation in C3H/He mice, whereas DBA/2 mice were 30% less responsive. Potentiation of coumarin hepatotoxicity corresponded to an increase in the 3-:7-coumarin hydroxylation ratio. Pretreatment-dependent shifts in the location of hepatocyte damage may be related to changes in the translobular ratio of enzymes involved in activation and detoxication of coumarin. These data highlight how genetic background, individual variation, and xenobiotic-induced alterations in enzyme profiles, factors all relevant to human risk assessment, can influence the consequence of coumarin exposure.
Urinary 28-kD Calbindin-D as a New Marker for Damage to Distal Renal Tubules Caused by Cisplatin-Based Chemotherapy (1996)

Calbindin-D, a vitamin D-dependent calcium-binding protein of 28 kD, is found predominantly in the distal tubules of the kidney and central nervous system tissues in humans. To evaluate damage to the renal tubules caused by cisplatin-based chemotherapy, levels of urinary and serum calbindin-D were determined in patients treated with cisplatin- or carboplatin-based chemotherapies using a highly sensitive enzyme immunoassay system developed in our laboratory. Levels of urinary 28-kD calbindin-D were also determined in patients with benign and malignant urological diseases. The mean urinary calbindin-D level was 2.44 + or - 0.31 (mean + or - SE) ng/mg creatinine in 40 healthy subjects. Urinary calbindin-D levels were elevated (>10 ng/mg creatinine) in 2 of 33 patients (6%) with benign and 1 of 50 (2%) with malignant urological diseases. Urinary calbindin-D levels were significantly increased after cisplatin-based chemotherapy in 14 patients, with peaks (71.8 + or - 13.5 ng/mg creatinine) being found 8 days after administration of cisplatin, and then a gradual return to the baseline. On the other hand, 7 patients receiving carboplatin-based chemotherapy demonstrated no significant elevation (highest level 7.7 + or - 2.5 ng/mg creatinine). In 7 patients treated with cisplatin-based chemotherapy the serum calbindin-D level was also raised after treatment, with a good correlation to urinary values. These findings suggest that urinary and serum calbindin-D may be kidney-derived and that 28-kDa calbindin-D is a useful marker for damage to the distal renal tubules associated with cisplatin-based chemotherapy.
Uberon, an integrative multi-species anatomy (2012)

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org