gebhart/patrepeval huggingface dataset:
Functional Mapping against Escherichia coli for the Broad-Spectrum Antimicrobial Peptide, Thanatin, Based on an In Vivo Monitoring Assay System (2000)

Previously, we established for the first time an in vivo monitoring assay system conjugated with random mutagenesis in order to study the structure-function relationship of the antimicrobial peptide, apidaecin [Taguchi et al. (1996) Appl. Environ. Microbiol. 62, 4652-4655]. In the present study, this methodology was used to carry out the functional mapping of a second target, thanatin, a 21-residue peptide that exhibits the broadest antimicrobial spectrum so far observed among insect defense peptides [Fehlbaum et al. (1996) Proc. Natl. Acad. Sci. USA 93, 1221-1225]. First, a synthetic gene encoding thanatin was expressed in a fused form with Streptomyces protease inhibitor protein, SSI, under the control of tac promoter in Escherichia coli JM109. Expression of the thanatin-fused protein was found to depend on the concentration of the transcriptional inducer, isopropyl-beta-D-thio-galactopyranoside (IPTG), and to parallel the degree of growth inhibition of the transformant cells. When a PCR random mutation was introduced into the structural gene for thanatin, diminished growth inhibition of the IPTG-induced transformed cells was mostly observed in variants as measured by colony size (plate assay) or optical density (liquid assay) in comparison with the wild-type peptide, possibly depending on the decreased antimicrobial activity of each variant. Next, wild-type thanatin and three variants screened by the in vivo assay, two singly mutated proteins (C11Y and M21R) and one doubly mutated protein (K17R/R20G), were stably overproduced with a fusion partner protein resulting in the efficient formation of inclusion bodies in E. coli BL21(DE3). The products were isolated in large amounts (yield 30%) from the fused protein by successive chemical and enzymatic digestions at the protein fusion linker site. Anti-E. coli JM109 activities, judged by minimum inhibitory concentration, of the purified peptides were in good agreement with those estimated semi-quantitatively by the in vivo assay. Based on the NMR solution structure and molecular dynamics, the structure-function relationship of thanatin is discussed by comparing the functional mapping data obtained here with the previous biochemical data. The functional mapping newly suggests the importance of a hydrogen bonding network formed within the C-terminal loop joining the beta-strands arranged antiparallel to one another that are supposed to be crutial for exhibiting anti-E. coli activity.
Functional Characterization of the Interaction between Bacterial Adhesin Multivalent Adhesion Molecule 7 (MAM7) Protein and Its Host Cell Ligands (2011)

The ability of a pathogen to rapidly form a stable interaction with the host cell surface is key to its success. Bacterial pathogens use a repertoire of virulence factors, but their efficient use relies on close contact between the host and the pathogen. We have recently identified a constitutively expressed MAM7 (multivalent adhesion molecule 7), which is widely distributed in gram-negative pathogens and enables them to establish initial contact with the host cell. Here, we describe the dissection of the MAM7 interaction with the host cell surface into two distinct binding events, involving the host protein fibronectin and the membrane phospholipid phosphatidic acid. We analyzed which domains within MAM7 and fibronectin are necessary for complex formation. We further studied phosphatidic acid binding by MAM7 using site-directed mutagenesis and liposome association assays and demonstrated that a specific distribution of basic charge on MAM7 is required for high affinity binding. Finally, we showed that fibronectin and phosphatidic acid binding to MAM7 are not mutually exclusive and that the three molecules likely assemble into a tripartite complex on the host cell surface.
Replication Protein A (RPA): The Eukaryotic SSB (1999)

Replication protein A (RPA) is a heterotrimeric single-stranded DNA-binding protein that is highly conserved in eukaryotes. RPA plays essential roles in many aspects of nucleic acid metabolism, including DNA replication, nucleotide excision repair, and homologous recombination. In this review, we provide a comprehensive overview of RPA structure and function and highlight the more recent developments in these areas. The last few years have seen major advances in our understanding of the mechanism of RPA binding to DNA, including the structural characterization of the primary DNA-binding domains (DBD) and the identification of two secondary DBDs. Moreover, evidence indicates that RPA utilizes a multistep pathway to bind single-stranded DNA involving a particular molecular polarity of RPA, a mechanism that is apparently used to facilitate origin denaturation. In addition to its mechanistic roles, RPA interacts with many key factors in nucleic acid metabolism, and we discuss the critical nature of many of these interactions to DNA metabolism. RPA is a phosphorylation target for DNA-dependent protein kinase (DNA-PK) and likely the ataxia telangiectasia-mutated gene (ATM) protein kinase, and recent observations are described that suggest that RPA phosphorylation plays a significant modulatory role in the cellular response to DNA damage.
In vitro drug sensitivity of M. avium-intracellulare complex in the presence and absence of dimethyl sulphoxide. (1982)

In vitro growth inhibition of 27 drug resistant isolates of M. avium-intracellulare was compared following continuous culture in the presence of single drugs alone and in combination with 2.5% dimethyl sulphoxide. In the absence of DMSO, 63% of the isolates were inhibited by rifampin and streptomycin, 19% by isoniazid and ethambutol and 4% by ethionamide. Addition of DMSO increased the number of isolates demonstrating growth inhibition by 26-30% for all drugs except ethionamide (11%). The growth inhibitory effect of each drug, whether assayed alone or in combination with DMSO, varied considerably for each strain. Three isolates were inhibited only in the presence of DMSO plus a drug, six isolates demonstrated growth inhibition without any enhanced effect due to DMSO, while the remaining eighteen isolates were sensitive to at least one drug in the presence of DMSO and to different drugs in the absence of DMSO.
A Preliminary Study to Delineate Irreversible Electroporation From Thermal Damage Using the Arrhenius Equation (2009)

Intense but short electrical fields can increase the permeability of the cell membrane in a process referred to as electroporation. Reversible electroporation has become an important tool in biotechnology and medicine. The various applications of reversible electroporation require cells to survive the procedure, and therefore the occurrence of irreversible electroporation (IRE), following which cells die, is obviously undesirable. However, for the past few years, IRE has begun to emerge as an important minimally invasive nonthermal ablation technique in its own right as a method to treat tumors and arrhythmogenic regions in the heart. IRE had been studied primarily to define the upper limit of electrical parameters that induce reversible electroporation. Thus, the delineation of IRE from thermal damage due to Joule heating has not been thoroughly investigated. The goal of this study was to express the upper bound of IRE (onset of thermal damage) theoretically as a function of physical properties and electrical pulse parameters. Electrical pulses were applied to THP-1 human monocyte cells, and the percentage of irreversibly electroporated (dead) cells in the sample was quantified. We also determined the upper bound of IRE (onset of thermal damage) through a theoretical calculation that takes into account the physical properties of the sample and the electric pulse characteristics. Our experimental results were achieved below the theoretical curve for the onset of thermal damage. These results confirm that the region to induce IRE without thermal damage is substantial. We believe that our new theoretical analysis will allow researchers to optimize IRE parameters without inducing deleterious thermal effects.
Stimulation of fracture repair by recombinant human basic fibroblast growth factor in normal and streptozotocin-diabetic rats. (1994)

The effect of local application of recombinant human basic fibroblast growth factor (rhbFGF) on fracture repair was examined using normal rats and streptozotocin-diabetic rats with impaired repairing ability. Immediately after fracturing the fibula, rhbFGF was applied by a single injection to the fracture site. Application of rhbFGF increased the volume and mineral content of callus in a dose-dependent manner in both normal and diabetic rats, and callus formation of diabetic rats was stimulated to levels similar to those in nontreated normal rats. The marked effect of rhbFGF on fracture repair was associated with an improvement in the mechanical properties of the healing fibula in both normal and diabetic rats. Immunohistochemical staining showed that endogenous bFGF was widely distributed in normal rats 1 and 3 weeks after fracture, especially in the soft callus and periosteum, whereas much less bFGF was detected in diabetic rats. Insulin treatment of diabetic rats restored the immunostaining for bFGF. These results demonstrate that bFGF is expressed during the early stage of fracture repair, and that the impaired fracture-repairing ability in diabetic rats is associated with reduced expression of bFGF at the fracture site. A single application of bFGF immediately after fracture not only facilitates the repair process in normal rats, but also recovers the impaired repairing ability in diabetic rats. These results suggest that local application of bFGF may facilitate bone union in patients with impaired as well as normal repairing ability.
A functional description of the Lincoln TX-2 computer (1957)

The TX-2 is a large scale digital computer designed and built at the Massachusetts Institute of Technology Lincoln Laboratory utilizing new memory and circuit components and some new logical design concepts. The computer will be applied as a research tool in scientific computations, and in data-handling and real-time problems. The design of the computer reflects not only the characteristics of the components available, but also the nature of the intended applications. This paper explains the functional and organizational aspects of the computer which are important from the user's point of view.
LDAHash: Improved Matching with Smaller Descriptors (2011)

SIFT-like local feature descriptors are ubiquitously employed in computer vision applications such as content-based retrieval, video analysis, copy detection, object recognition, photo tourism, and 3D reconstruction. Feature descriptors can be designed to be invariant to certain classes of photometric and geometric transformations, in particular, affine and intensity scale transformations. However, real transformations that an image can undergo can only be approximately modeled in this way, and thus most descriptors are only approximately invariant in practice. Second, descriptors are usually high dimensional (e.g., SIFT is represented as a 128-dimensional vector). In large-scale retrieval and matching problems, this can pose challenges in storing and retrieving descriptor data. We map the descriptor vectors into the Hamming space in which the Hamming metric is used to compare the resulting representations. This way, we reduce the size of the descriptors by representing them as short binary strings and learn descriptor invariance from examples. We show extensive experimental validation, demonstrating the advantage of the proposed approach.
KLF11-mediated Repression Antagonizes Sp1/Sterol-responsive Element-binding protein-induced Transcriptional Activation of Caveolin-1 in Response to Cholesterol Signaling (2004)

Cholesterol is a potent regulator of gene expression via a canonical pathway co-regulated by SREBP and Sp1. Here we establish the caveolin-1 gene promoter as a cell type-specific model for SREBP/Sp1 regulation whereby lipoprotein cholesterol depletion activates caveolin-1 transcription in endothelial type cells, but not in fibroblasts, both in vitro and in vivo. By extending this model, we describe a novel pathway distinct from the prototypical SREBP/Sp1 regulatory loop involving the Sp1-like protein, KLF11. Through a combination of RNA interference, chromatin immunoprecipitation assays, electrophoretic mobility shift assays, and reporter assays, we demonstrate that in the presence of cholesterol, KLF11 acts as a dominant repressor of the caveolin-1 gene. Mechanistically, cholesterol depletion results in displacement of KLF11 from an Sp1 site flanking an SRE, indicating that activation by SREBP/Sp1 requires antagonism of KLF11 repression. The displacement of KLF11 results from both a down-regulation of its expression and competition by Sp1 for DNA binding. Therefore, these studies identify a novel pathway whereby KLF11 repression is coordinated with Sp1/SREBP activation of cholesterol-dependent gene expression in a cell type-specific manner and outline the mechanisms by which these functions are achieved.
The mae1 gene of Schizosaccharomyces pombe encodes a permease for malate and other C4 dicarboxylic acids (1995)

The mae1 gene of the yeast Schizosaccharomyces pombe was identified on the basis of its ability to complement a mutant defective in the transport of malic acid. Analysis of the DNA sequence revealed an open reading frame of 1314 base pairs, encoding a polypeptide of 438 amino acids with a predicted molecular weight of 49 kDa. A hydropathy profile of the predicted amino acid sequence revealed a protein with ten membrane-spanning or associated domains and hydrophilic N- and C- termini. The predicted secondary structure of the protein in similar to models proposed for other integral membrane proteins from both prokaryotes and eukaryotes. The S. pombe mae1 gene encodes a single mRNA of 1.5 kb. The mea1 gene is expressed constitutively and is not subject to catabolite repression as was previously reported for the malate permease systems of Candida utilis and Hansenula anomala. The mae1 gene was mapped 2842 bp 5' to the MFml gene on chromosome I. Transport assays revealed that the mae1 gene encodes a permease involved in the uptake of L-malate, succinate and malonic acid.
Pharmacological regulation of hepatic glucose production. (2003)

The discovery of antidiabetic agents that inhibit hepatic glucose production is a popular and potentially fruitful research area for the pharmaceutical research community. Metformin, a marketed agent with this mechanism of action, is widely used for the treatment of type 2 diabetes, however, more efficacious agents are sought. A number of promising proteins are being targeted for modulation by new compounds, including the glucagon receptor, glycogen phosphorylase, glucocorticoid receptor, 11 beta-hydroxysteroid dehydrogenase-1, fructose-1,6-bisphosphatase, carnitine palmitoyltransferase-1, glycogen synthase kinase-3, glucose-6-phosphate T1 translocase and the A2B receptor. Compounds designed to work against these targets are at the early clinical or preclinical phase of study. Glucagon receptor antagonists, glycogen phosphorylase inhibitors, 11 beta-hydroxysteroid dehydrogenase-1 inhibitors, carnitine palmitoyltransferase-1 inhibitors and fructose-1,6-bisphosphatase inhibitors are, or have been, clinically evaluated. Preclinical studies against the other targets have yielded compounds that demonstrate efficacy in diabetic animal models and clinical activity will continue.
High refractive index transparent nanocomposites prepared by in situ polymerization (2014)

High refractive index transparent nanocomposites have been developed by in situ polymerization of a precursor that contains functional monomers and surface modified anatase TiO2 nanoparticles for optoelectronic applications. The monomers are in the liquid form, so environmentally friendly solventless precursors can be prepared. The precursor can be processed into various shapes or thick films (>50 microns) of the nanocomposite. The relationships of the chemical structure of the organic matrix, nanoparticle content and dispersity with the refractive index, transparency, mechanical and thermal properties are systematically investigated. The refractive index, and mechanical and thermal properties of the nanocomposite are increased with increasing TiO2 content and aromatic structure in the organic matrix due to their rigid characteristics. The transparency of the nanocomposite is increased with increasing TiO2 content and dispersity. At the same loading of nanoparticles, the higher dispersity and the better transparency are due to the less extent of Rayleigh scattering. At 18 vol% (60 wt%) of TiO2, the acetic acid modified TiO2/poly(4-vinyl benzyl alcohol) nanocomposite has a refractive index of 1.73 and excellent transparency (>85% from 500 nm to 800 nm). The refractive index of the nanocomposite can be further increased to 1.77 by replacing aliphatic acetic acid modified TiO2 with aromatic phenyl acetic acid modified TiO2. The results of this work provide new knowledge and a new pathway to design a polymer based high refractive index material.
The triple helix ⇌ coil conversion of collagen‐like polytripeptides in aqueous and nonaqueous solvents. Comparison of the thermodynamic parameters and the binding of water to (L‐Pro‐L‐Pro‐Gly)n and (L‐Pro‐L‐Hyp‐Gly)n (1977)

Abstract The collagen‐like peptides ( L ‐Pro‐ L ‐Pro‐Gly) n and ( L ‐Pro‐ L ‐Hyp‐Gly) n with n = 5 and 10, were examined in terms of their triple helix ⇌ coil transitions in aqueous and nonaqueous solvents. The peptides were soluble in 1,2‐propanediol containing 3% acetic acid and they were found to form triple‐helical structures in this solvent system. The water content of the solvent system and the amount of water bound to the peptides were assayed by equilibrating the solvent with molecular sieves and carrying out Karl Fischer titrations on the solvent phase. After the solvent was dehydrated, much less than one molecule of water per tripeptide unit was bound to the peptides. Since the peptides remained in a triple‐helical conformation, the results indicated that water was not an essential component of the triple‐helical structure. Comparison of peptides with the same chain length demonstrated that the presence of hydroxyproline increased the thermal stability of the triple helix even under anhydrous conditions. The results, therefore, did not support recent hypotheses that hydroxyproline stabilizes the triple helix of collagen and collagen‐like peptides by a specific interaction with water molecules. Analysis of the thermal transition curves in several solvent systems showed that although the peptides containing hydroxyproline had t m values which were 18.6° to 32.7°C higher, the effect of hydroxyproline on Δ G was only 0.1 to 0.3 kcal per tripeptide unit at 25°C. The results suggested, therefore, that the influence of hydroxyproline on helical stability may be explained by intrinsic effects such as dipole–dipole interactions or by changes in the solvation of the peptides by alcohol, acetic acid, and water. A direct calorimetric measurement of the transition enthalpy for ( L ‐Pro‐ L ‐Pro‐Gly) n in 3% or 10% acetic acid gave a value of −1.84 kcal per tripeptide unit for the coil‐to‐helix transition. From the value for enthalpy and from data on the effects of different chain lengths on the thermal transition, it was calculated that the apparent free energy for nucleation was +5 kcal/mol at 25°C (apparent nucleation parameter = 2 × 10 −4 M −2 ). The value was dependent on solvent and on chemical modification of end groups.
Unraveling the role of fungal symbionts in plant abiotic stress tolerance (2011)

Fungal symbionts have been found associated with every plant studied in natural ecosystem, where they colonize and reside entirely in the internal tissues of their host plant or partially. Fungal endophytes can express/form a range of different lifestyle/relationships with different host including symbiotic, mutualistic, commensalistic and parasitic in response to host genotype and environmental factors. In mutualistic association fungal endophyte can enhance growth, increase reproductive success and confer biotic and abiotic stress tolerance to its host plant. Since abiotic stress such as, drought, high soil salinity, heat, cold, oxidative stress, heavy metal toxicity is the common adverse environmental conditions that affect and limit crop productivity worldwide. It may be a promising alternative strategy to exploit fungal endophytes to overcome the limitations to crop production brought by abiotic stress. There is increasing interest in developing the potential biotechnological applications of fungal endophytes for improving plant stress tolerance and sustainable production of food crops. Here we have described the fungal symbioses, fungal symbionts and their role in abiotic stress tolerance. A putative mechanism of stress tolerance by symbionts has also been covered.
Toxicity Assessment and Decomposition Characteristics of Triclosan in an E-beam Irradiation Process (2012)

The abjective of this study was to study the degradation behavior and acute toxicity assessment of Triclosan and acute toxicity under E-beam irradiation. The experiments were conducted to investigate the efficts of the degradation efficiency in the initial concentration of Triclosan and the irradiation capacity of E-beam and the degree of mineralization based on a change of scavenger gas. The biological toxicity test by using on green algae, Pseudokirchneriella Subcapitata was conducted to lead the reducing toxicity. Degradation efficiency of Triclosan was improved when E-beam irradiation intensity was higher. Additionally, the % of TOC removal in each Radical scavenger gas was increased as the follows orders: > > , The toxicity test showed that the toxicity effect after 4 days(96hrs) was decreased by increase of E-beam irradiation intensity.
Peptide Cross‐Linking at Ambient Surfaces by Reactions of Nanosprayed Molecular Cations (2012)

Chemical synthesis with ambient ions: Peptide cross-linking is achieved nearly instantaneously and quantitatively by delivering solvated peptide cations in microdroplets to a cross-linker present on a glass surface (see picture) or vice versa. The reaction can be carried out in an open laboratory environment.
Adaptive DCT for image‐data compression (1992)

Abstract This paper deals with the development of a coding system for image data compression based on the Discrete Cosine Transform (DCT). The aim is to integrate several methods into a single approach in order to obtain an adaptive coder characterized by higher performances. In particular, a variable blocksize scheme is used, which is based on quadtree segmentation driven by edge information. To improve data compression, DCT coefficients are then coded by a vector quantizer. Experiments have shown that the values of compression factors can be notably increased, while maintaining a good reconstruction quality.
Mesocortical Dopaminergic Function and Human Cognition (1988)

In summary, we have reviewed rCBF data in humans that suggest that mesoprefrontal dopaminergic activity is involved in human cognition. In patients with Parkinson's disease and possibly in patients with schizophrenia, prefrontal physiological activation during a cognitive task that appears to depend on prefrontal neural systems correlates positively with cognitive performance on the task and with clinical signs of dopaminergic function. It may be possible in the future to examine prefrontal dopamine metabolism directly during prefrontal cognition using positron emission tomography and tracers such as F-18 DOPA.