gebhart/patrepeval huggingface dataset:
Three novel mammalian toll-like receptors: gene structure, expression, and evolution. (2000)

We describe three novel genes, encoding members of the Toll-like receptor (Tlr) family (TLR7, TLR8, and TLR9). These Tlr family members, unlike others reported to date, were identified within a genomic database. TLR7 and TLR8 each have three exons, two of which have coding function, and lie in close proximity to one another at Xp22, alongside a pseudogene. The remaining gene (TLR9) resides at 3p21.3 (in linkage with the MyD88 gene), and is expressed in at least two splice forms, one of which is monoexonic and one of which is biexonic, the latter encoding a protein with 57 additional amino acids at the N-terminus. The novel Tlrs comprise a cluster as nearest phylogenetic neighbors. Combining all sequence data related to Toll-like receptors, we have drawn several inferences concerning the phylogeny of vertebrate and invertebrate Tlrs. According to our best estimates, mammalian TLRs 1 and 6 diverged from a common mammalian ancestral gene 95 million years ago. TLR4, which encodes the endotoxin sensor in present-day mammals, emerged as a distinct entity 180 million years ago. TLRs 3 and 5 diverged from a common ancestral gene approximately 150 million years ago, as did Tlr7 and Tlr8. Very likely, fewer Tlrs existed during early vertebrate evolution: at most three or four were transmitted with the primordial vertebrate line. Phylogenetic data that we have adduced in the course of this work also suggest the existence of a Drosophila equivalent of MyD88, and indicate that the plasma membrane protein SIGIRR is close functional relative of MyD88 in mammals. Finally, a single present-day representative of the Toll-like proteins in Drosophila has striking cytoplasmic domain homology to mammalian Tlrs within the cluster that embraces TLRs 1, 2, 4, and 6. This would suggest that an ancestral (pre-vertebrate) Tlr may have adopted a pro-inflammatory function 500 million years ago.
Kinetics of small molecule interactions with membrane proteins in single cells measured with mechanical amplification (2015)

Measuring small molecule interactions with membrane proteins in single cells is critical for understanding many cellular processes and for screening drugs. However, developing such a capability has been a difficult challenge. We show that molecular interactions with membrane proteins induce a mechanical deformation in the cellular membrane, and real-time monitoring of the deformation with subnanometer resolution allows quantitative analysis of small molecule-membrane protein interaction kinetics in single cells. This new strategy provides mechanical amplification of small binding signals, making it possible to detect small molecule interactions with membrane proteins. This capability, together with spatial resolution, also allows the study of the heterogeneous nature of cells by analyzing the interaction kinetics variability between different cells and between different regions of a single cell.
Titan: a toolset that connects software architecture with quality analysis (2014)

In this tool demo, we will illustrate our tool---Titan---that supports a new architecture model: design rule spaces (DRSpaces). We will show how Titan can capture both architecture and evolutionary structure and help to bridge the gap between architecture and defect prediction. We will demo how to use our toolset to capture hundreds of buggy files into just a few architecturally related groups, and to reveal architecture issues that contribute to the error-proneness and change-proneness of these groups. Our tool has been used to analyze dozens of large-scale industrial projects, and has demonstrated its ability to provide valuable direction on which parts of the architecture are problematic, and on why, when, and how to refactor. The video demo of Titan can be found at https://art.cs.drexel.edu/~lx52/titan.mp4
Binding analysis of peptides that recognize preferentially cis‐azobenzene groups of synthetic polymers (2010)

Peptides identified by the PD method against a film surface composed of azobenzene-containing synthetic polymers were characterized by QCM measurements. Among the four peptides analyzed, the c16 peptide with the sequence Trp-His-Thr-Leu-Pro-Asn-Ala showed the highest binding affinity to the films rich in cis-azobenzene groups. SPR served to determine the association/dissociation constants of the c16 peptide against the trans- and cis-azobenzene groups. The binding constants were estimated to be 1.3 × 10(5) and 1.4 × 10(6) /M, respectively, indicating a high specificity of the c16 peptide for cis-azobenzene conformer. Then mutants of the c16 peptide were synthesized and characterized to gain information on the structural requirements for the cis-form specificity. An Ala-scan clearly revealed that all the amino acid residues of the c16 peptide were essential for the specificity. More importantly, the results with peptides of inverted sequence and containing Gly insertions confirmed that the specificity is strictly derived from the primary sequence of the c16 peptide.
Design of a New Class of Amphipathic Helical Peptides for the Plasma Apolipoproteins That Promote Cellular Cholesterol Efflux But Do Not Activate LCAT (1997)

Amphipathic helical peptides represent the lipid-binding units of the soluble plasma apolipoproteins. Several synthetic peptide analogues have been designed to mimic such structures and have been used to unravel some of the mechanisms involved in the physiological function of the apolipoproteins, including lipid binding, LCAT activation, and enhancement of cholesterol efflux from lipid-laden cells. A series of novel synthetic peptides, named ID peptides, was modeled on the basis of the structural properties common to the amphipathic helices of apolipoprotein (apo) A-I. In these new peptides, however, the segregation between hydrophobic and hydrophilic faces of the helices is more pronounced than in apoA-I, so that the surface of the hydrophobic and hydrophilic faces of the amphipathic helices is equal. Moreover, there are fewer negatively charged residues in the center of the hydrophilic face of the helical peptides. Most charged amino acids are located along the edge of the helix and are susceptible to forming salt bridges with residues of an antiparallel helix, such as around a discoidal phospholipid/peptide complex. The physicochemical characteristics of these peptides and their complexes with phospholipids were compared with those of the 18A peptide and its lipid/peptide complex. All ID peptides bind dimyristoylphosphatidylcholine vesicles more rapidly than the 18A peptide to yield discoidal peptide/phospholipid complexes of comparable size. The alpha-helical content of the lipid-free ID peptides is close to that of the 18A peptide and increases slightly on lipid binding. The stability of the ID and 18A peptides and of the phospholipid/peptide complexes against guanidinium hydrochloride denaturation is higher than that of lipid-free and lipid-bound apoA-I. LCAT activation by the 18A/phospholipid/cholesterol complexes equals that of apoA-I/ phospholipid/cholesterol complexes, whereas none of the ID peptides tested is able to activate LCAT to a significant extent. Incubation of the peptide/phospholipid complexes with lipid-laden macrophages induces cellular cholesterol efflux and incorporation of cholesterol into the complexes. The cholesterol efflux capacity of the peptide/phospholipid complexes is comparable among the peptides and higher than that of apoprotein/phospholipid complexes. In conclusion, although the amphipathicity of the new peptides is higher than that of the 18A model peptide, the lack of LCAT activation by the ID peptides suggests that an enhanced segregation of the hydrophobic and hydrophilic residues, equal magnitude of hydrophobic and hydrophilic faces of the helix, and the absence of negatively charged residues in the central part of the hydrophilic face might account for the lack of LCAT activity of these peptides. These parameters do not affect the capacity of the peptide/phospholipid complexes to promote cellular cholesterol efflux.
Synthesis of alumina-pillared clay with desired pillar population using Na-montmorillonite having controlled cation exchage capacity (1989)

Alumina-pillared montmorillonite with the desired pillar population was prepared by the ion-exchange of Na-montmorillonite, controlling the cation exchange capacity, with aluminium chlorohydroxy oligomers.
Autonomic Computing - a means of achieving dependability? (2004)

Autonomic computing is emerging as a significant new approach to the design of computing systems. Its goal is the development of systems that are self-configuring, self-healing, self-protecting and self-optimizing. Dependability is a long-standing desirable property of all computer-based systems. The purpose of the paper is to consider how autonomic computing can provide a framework for dependability.
Surface Interactions of C2 and C3 Polyols with γ-Al2O3 and the Role of Coadsorbed Water (2012)

The formation of surface species from two- and three-carbon polyols on γ-Al(2)O(3) in the presence and absence of coadsorbed water is investigated. Aqueous-phase adsorption isotherms indicate that competitive adsorption between water and polyol inhibits the uptake of the polyol molecules on γ-Al(2)O(3) and that the polyol with the most hydroxyl groups, glycerol, experienced the greatest uptake. Deuterium solid echo pulse NMR measurements support the fact that glycerol strongly interacts with γ-Al(2)O(3) in the presence of physisorbed water and that ethylene glycol interacts with γ-Al(2)O(3) only after the physisorbed water has been removed. In situ high-vacuum FT-IR analysis combined with DFT simulations demonstrate that glycerol readily forms a multidentate alkoxy species through its primary hydroxyl groups with coordinatively unsaturated Al atoms of γ-Al(2)O(3) in the presence of physisorbed water. This surface species exhibits a bridging alkoxy bond from one of its primary hydroxyl groups and a strong interaction with the remaining primary hydroxyl group. FT-IR analysis of 1,3-propanediol on γ-Al(2)O(3) also demonstrates the formation of a multidentate alkoxy species in the presence of coadsorbed water. In contrast, polyols with hydroxyl groups only on the one- and two-carbon atoms, ethylene glycol, and 1,2-propanediol do not form alkoxy bonds with the γ-Al(2)O(3) surface when coadsorbed water is present. These polyols will form alkoxy bonds to γ-Al(2)O(3) when coadsorbed water is removed, and these alkoxy species are removed when water is readsorbed on the sample. The formation of strongly bound, stable multidentate alkoxy species by ethylene glycol and 1,2-propanediol on γ-Al(2)O(3) is prevented by steric limitations of vicinal alcohol groups.
n -type carbon nanotube field-effect transistors fabricated by using Ca contact electrodes (2005)

We have fabricated n-type carbon nanotube field effect transistors by choosing the contact metal. Single-walled carbon nanotubes were grown directly on a SiO2∕Si substrate by chemical vapor deposition using patterned metal catalysts. Following the nanotube growth, Ca contacts with a small work function were formed by evaporating and lifting off the metal. The devices showed n-type transfer characteristics without any doping into the nanotube channel. In contrast, the devices with Pd contacts showed p-type conduction. These results can be explained by taking into account the work functions of the contact metals.
Riluzole enhances expression of brain‐derived neurotrophic factor with consequent proliferation of granule precursor cells in the rat hippocampus (2002)

The dentate gyrus of the hippocampus, generating new cells throughout life, is essential for normal recognition memory performance. Reduction of brain-derived neurotrophic factor (BDNF) in this structure impairs its functions. To elucidate the association between BDNF levels and hippocampal neurogenesis, we first conducted a search for compounds that stimulate endogenous BDNF production in hippocampal granule neurons. Among ion channel modulators tested, riluzole, a neuroprotective agent with anticonvulsant properties that is approved for treatment of amyotrophic lateral sclerosis, was highly effective as a single dose by an intraperitoneal injection, causing a rise in BDNF localized in dentate granule neurons, the hilus, and the stratum radiatum of the CA3 region. Repeated, but not single, injections resulted in prolonged elevation of hippocampal BDNF and were associated with increased numbers of newly generated cells in the granule cell layer. This appeared due to promoted proliferation rather than survival of precursor cells, many of which differentiated into neurons. Intraventricular administration of BDNF-specific antibodies blocked such riluzole effects, suggesting that BDNF increase is necessary for the promotion of precursor proliferation. Our results suggest the basis for a new strategy for treatment of memory dysfunction.
Remodeling the mammalian heart using transgenesis. (1995)

Our objective was to test the hypothesis that, via transgenesis, one can modify the contractile protein complement of the mouse heart. Using a promoter derived from the mouse myosin heavy chain gene (alpha-MyHC), we attempted to remodel the mouse myocardium by ectopically expressing a ventricular form of the myosin light chain 2 (MLC2v) in the atrium. The ability of the heart to maintain contractile isoform stoichiometry was tested by overexpressing the cDNA in both the atria and ventricle. The promoter drove high levels of transgene expression in both cardiac compartments and was controlled in an appropriate manner during development. The data show that ectopic overexpression of a contractile protein isoform can lead to compartment specific replacement. However, if the transgene encodes the isoform that is normally present (e.g., MLC2v expressed in the ventricle), the protein levels remain unaffected, although the transgenic transcript accumulates to very high levels. The basic function and the physiologic or pathophysiologic significance of differential MLC2 isoform content was examined. Using the whole working heart preparation, we show that an MLC2a --> MLC2v shift in the atrium severely affects contractile function and performance.
2-Alkylmalonic Acid: Amphiphilic Chelator and a Potent Inhibitor of Metalloenzyme (2010)

The present investigation demonstrates the potential of 2-alkylmalonic acid amphiphile as inhibitor of metalloenzymes like Taq DNA polymerase and alpha-amylase. A dose-dependent inhibition of Taq DNA polymerase was observed when a polymerase chain reaction (PCR) was performed in the presence of amphiphiles while in the case of alpha-amylase the inhibition was found to be independent of the inhibitor concentration. Control experiments revealed that both the chelating as well as the amphiphilic nature of the inhibitor was essential for enzyme inhibition. The fluorescence intensity and lifetime of alpha-amylase were also found to decrease in the presence of the amphiphiles. Steady-state fluorescence quenching studies suggested that removal of the metal ion from the enzyme leads to a decrease in the solvent accessibility of tryptophans, indicating change in the tertiary structure of the protein. It is proposed that removal of metal ion from the active sites of the enzyme by the amphiphilic compound possibly leads to disruption of the native conformation of the enzyme which is responsible for loss of its activity.
Characterization of dairy farm environments and their effect on cow lifespan (2007)

Environmental sensitivity exists when an environmental difference has more effect on some genotypes than on others (Falconer and Mackay, 1996). Quantifying the degree of environmental sensitivity shown by individual sires allows us to identify sires as specialists (those which rank highly in certain environments) or generalists (those which rank similarly across environments). Dairy farm environments vary enormously and this affects the production and health of the cows. The aims of this study were (1) to relate detailed survey information on farm management systems to information available at the national level to provide a definition of farm environment, and (2) to assess the effect of environment on lifespan.
Design and Synthesis of the First Generation of Novel Potent, Selective, and in Vivo Active (Benzothiazol-2-yl)acetonitrile Inhibitors of the c-Jun N-Terminal Kinase (2005)

Several lines of evidence support the hypothesis that c-Jun N-terminal kinase (JNKs) plays a critical role in a wide range of diseases including cell death (apoptosis)-related disorders (neurodegenerative diseases, brain, heart, and renal ischemia, epilepsy) and inflammatory disorders (multiple sclerosis, rheumatoid arthritis, inflammatory bowel diseases). Screening of our internal compound collection for inhibitors of JNK3 led to the identification of (benzothiazol-2-yl)acetonitrile derivatives as potent and selective JNK1, -2, -3 inhibitors. Starting from initial hit 1 (AS007149), the chemistry and initial structure-activity relationship (SAR) of this novel and unique kinase inhibitor template were explored. Investigation of the SAR rapidly revealed that the benzothiazol-2-ylacetonitrile pyrimidine core was crucial to retain a good level of potency on rat JNK3. Therefore, compound 6 was further optimized by exploring a number of distal combinations in place of the chlorine atom. This led to the observation that the presence of an aromatic group, two carbons away from the aminopyrimidine moiety and bearing substituents conferring hydrogen bond acceptor (HBA) properties, could improve the potency. Further improvements to the biological and biopharmaceutical profile of the most promising compounds were performed, resulting in the discovery of compound 59 (AS601245). The in vitro and in vivo anti-inflammatory potential of this new JNK inhibitor was investigated and found to demonstrate efficacy per oral route in an experimental model of rheumatoid arthritis (RA).
FPGA PUF using programmable delay lines (2010)

This paper proposes a novel approach for efficient implementation of a real-valued arbiter-based physical unclon-able function (PUF) on FPGA. We introduce a high resolution programmable delay logic (PDL) implemented by lookup table (LUT) internal structure. Using the PDL, we perform fine tuning to cancel out delay skews caused by asymmetries in routing and systematic variations. We devise a symmetric switch structure that can be easily implemented on FPGA. To mitigate the arbiter metastability problem, we present and analyze methods for majority voting of responses. Lastly, a method to classify and group challenges into different robustness sets is introduced, to further increase the corresponding responses' stability in the face of environmental variations. Experimental evaluations show that the responses to robust challenges have an average error rate of less than 2% under temperature variations from -10°C to 75°C.
Prediction of the Coding Sequences of Unidentified Human Genes.XV. The Complete Sequences of 100 New cDNA Clones from Brain Which Code for Large Proteins in vitro (1999)

In order to obtain information on the coding sequences of unidentified human genes, we newly determined the sequences of 100 cDNA clones of unknown human genes, which we named KIAA1193 to KIAA1292, from two sets of size-fractionated human adult and fetal brain cDNA libraries. The results of our particular strategy to select cDNA clones which have the potentiality of coding for large proteins in vitro revealed that the average sizes of the inserts and the corresponding open reading frames reached 5.2 kb and 2.8 kb (933 amino acid residues), respectively. By the computational analysis of the predicted amino acid sequences against the OWL and Pfam databases, 58 predicted gene products were classified into the following five functional categories: cell signaling/communication, cell structure/motility, nucleic acid management, protein management and metabolism. It was also found that 30 gene products had homologues in the public databases which were similar in sequence throughout almost their entire regions to the newly identified genes. The chromosomal loci of the genes were assigned by using human-rodent hybrid panels unless their mapping data were already available in the public databases. The expression profiles of the genes were studied in 10 human tissues, 8 brain regions, spinal cord, fetal brain and fetal liver by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.
Neuroendocrine Response to Fenfluramine Challenge in Boys (1997)

In young boys, aggressive behavior and social circumstances that are conducive to the development of aggressive behavior are positively correlated with a marker of central serotonergic activity.
Lambda Chains and Genes in Inbred Mice (1985)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
The role of corticosteroids in muscular dystrophy: A critical appraisal (2007)

Over the years various steroid trials have been conducted in Duchenne muscular dystrophy (DMD). In children who are still able to walk as well as in those who are wheelchair-bound, corticosteroids have been found to stabilize muscle strength for a period of time. Controlled clinical observations have shown that some boys remain ambulatory for years longer than reported in natural history data. The two main steroids used are prednisone/prednisolone and deflazacort. They are probably equally effective in stabilizing muscle strength but may have different side-effect profiles; for instance, deflazacort causes less weight gain. The exact mechanism by which steroids slow the dystrophic process is under investigation. DMD children treated long term also seem to develop other complications of the condition less frequently. For instance, they develop respiratory insufficiency later and have fewer cardiac symptoms. The therapeutic value of corticosteroids is limited, but these drugs represent the best treatment option currently available.
Synthesis of Potent Leukotriene A4 Hydrolase Inhibitors. Identification of 3-[Methyl[3-[4-(phenylmethyl)phenoxy]propyl]amino]propanoic Acid (2002)

Leukotriene B4 (LTB4) is a potent, proinflammatory mediator involved in the pathogenesis of a number of diseases including inflammatory bowel disease, psoriasis, rheumatoid arthritis, and asthma. The enzyme LTA4 hydrolase represents an attractive target for pharmacological intervention in these disease states, since the action of this enzyme is the rate-limiting step in the production of LTB4. Our previous efforts focused on the exploration of a series of analogues related to screening hit SC-22716 (1, 1-[2-(4-phenylphenoxy)ethyl]pyrrolidine) and resulted in the identification of potent, orally active inhibitors such as 2. Additional structure−activity relationship studies around this structural class resulted in the identification of a series of α-, β-, and γ-amino acid analogues that are potent inhibitors of the LTA4 hydrolase enzyme and demonstrated good oral activity in a mouse ex vivo whole blood LTB4 production assay. The efforts leading to the identification of clinical candidate SC-57461A (8d, 3-[methyl[3-[4-(phenylmethyl)phenoxy]propyl]amino]propanoic acid) are described.