gebhart/patrepeval huggingface dataset:
Helix Orientation of the Functional Domains in Apolipoprotein E in Discoidal High Density Lipoprotein Particles (2004)

Human apolipoprotein E (apoE) mediates high affinity binding to the low density lipoprotein receptor when present on a lipidated complex. In the absence of lipid, however, apoE does not bind the receptor. Whereas the x-ray structure of lipid-free apoE3 N-terminal (NT) domain is known, the structural organization of its lipid-associated, receptor-active conformation is poorly understood. To study the organization of apoE amphipathic alpha-helices in a lipid-associated state, single tryptophan-containing apoE3 variants were employed in fluorescence quenching studies. The relative positions of the Trp residues with respect to the phospholipid component of apoE/lipid particles were established from the degree of quenching by phospholipids bearing nitroxide groups at various positions along their fatty acyl chains. Four apoE3-NT variants bearing Trp reporter groups at positions 141, 148, 155, or 162 within helix 4 and two apoE3 variants containing single Trp at positions 257 or 264 in the C-terminal (CT) domain, were reconstituted into phospholipid-containing discoidal complexes. Parallax analysis revealed that each engineered Trp residue in helix 4 of apoE3-NT, as well as those in the CT domain of apoE, localized approximately 5 A from the center of the bilayer. Circular dichroism studies revealed that lipid association induces additional helix formation in apoE. Protease protection assays suggest the flexible loop segment between the NT and CT domains may transition from unstructured to helix upon lipid association. Taken together, these data support a model wherein the alpha-helices in the receptor-binding region and the CT domain of apoE align perpendicular to the fatty acyl chains of the phospholipid bilayer. In this alignment, the residues of helix 4 are arrayed in a positively charged, curved helical segment for optimal receptor interaction.
Vaccines in Development to Prevent and Treat Atherosclerotic Disease (2008)

Coronary heart disease (CHD) remains the leading cause of death in the United States. Immune mechanisms have been recently proposed to play an important role in the development of atherosclerotic plaques in CHD. Heat shock proteins and oxidized low-density lipoprotein are proinflammatory substances that have been shown to have an important role in the pathogenesis of atherosclerosis, and are now targets for clinical vaccine development. In addition, a vaccine has been developed to inhibit cholesteryl ester transfer protein. It is now recognized that many medications used to combat plaque development and rupture have significant anti-inflammatory effects and these effects are critical for drug efficacy. The influenza vaccine is associated with an atheroprotective effect. In addition, a nicotine vaccine, an antiangiotensin vaccine, and an anti-obesity vaccine may play a therapeutic role in modifying known risk factors for the development of atherosclerosis and its complications. This article reviews these vaccines as possible additions to the armamentarium of atheroprotective treatment modalities.
Reaction Rates for the Partial Dehydration of Glucose to Organic Acids in Solid-Acid, Molecular-Sieving Catalyst Powders (1997)

Molecular-sieving catalysts have the potential to promote the production of oxygenated hydrocarbons from glucose. A kinetic model for the partial dehydration of glucose to organic acids by micro- and mesoporous aluminosilicate catalysts was developed. Kinetic parameters were estimated from glucose conversion and product yield versus time data at 150°C for HY-zeolite, aluminum-pillared montmorillonite, MCM-20 and MCM-41 catalyst powders of 0·5 mmol H+ g−1 solid-acid activity. Rate constants for the partial dehydration of glucose to 5-hydroxymethylfurfural (HMF) and the rehydration and cleavage of HMF to formic acid and 4-oxopentanoic acid were maximized at catalyst pore diameters of 10–30 Å. The final organic acid product yields were low, less than 60% of theoretical for formic acid and 10% of theoretical for 4-oxopentanoic acid, due to significant coke formation. © 1997 SCI.
Cyanolysis and Azidolysis of Epoxides by Haloalcohol Dehalogenase: Theoretical Study of the Reaction Mechanism and Origins of Regioselectivity (2008)

Haloalcohol dehalogenase HheC catalyzes the reversible dehalogenation of vicinal haloalcohols to form epoxides and free halides. In addition, HheC is able to catalyze the irreversible and highly regioselective ring-opening of epoxides with nonhalide nucleophiles, such as CN (-) and N 3 (-). For azidolysis of aromatic epoxides, the regioselectivity observed with HheC is opposite to the regioselectivity of the nonenzymatic epoxide-opening. This, together with a relatively broad substrate specificity, makes HheC a promising tool for biocatalytic applications. We have designed large quantum chemical models of the HheC active site and used density functional theory to study the reaction mechanism of the HheC-catalyzed ring-opening of ( R)-styrene oxide with the nucleophiles CN (-) and N 3 (-). Both the cyanolysis and the azidolysis reactions are shown to take place in a single concerted step. The results support the suggested role of the putative Ser132-Tyr145-Arg149 catalytic triad, where Tyr145 acts as a general acid, donating a proton to the substrate, and Arg149 interacts with Tyr145 and facilitates proton abstraction, while Ser132 positions the substrate and reduces the barrier for epoxide opening through interaction with the emerging oxyanion of the substrate. We have also studied the regioselectivity of ( R)-styrene oxide opening for both the cyanolysis and the azidolysis reactions. The employed active site model was shown to be able to reproduce the experimentally observed beta-regioselectivity of HheC. In silico mutations of various groups in the HheC active site model were performed to elucidate the important factors governing the regioselectivity.
Unraveling the Anxious Mind: Anxiety, Worry, and Frontal Engagement in Sustained Attention Versus Off-Task Processing (2013)

Much remains unknown regarding the relationship between anxiety, worry, sustained attention, and frontal function. Here, we addressed this using a sustained attention task adapted for functional magnetic resonance imaging. Participants responded to presentation of simple stimuli, withholding responses to an infrequent "No Go" stimulus. Dorsolateral prefrontal cortex (DLPFC) activity to "Go" trials, and dorsal anterior cingulate (dACC) activity to "No Go" trials were associated with faster error-free performance; consistent with DLPFC and dACC facilitating proactive and reactive control, respectively. Trait anxiety was linked to reduced recruitment of these regions, slower error-free performance, and decreased frontal-thalamo-striatal connectivity. This indicates an association between trait anxiety and impoverished frontal control of attention, even when external distractors are absent. In task blocks where commission errors were made, greater DLPFC-precuneus and DLPFC-posterior cingulate connectivity were associated with both trait anxiety and worry, indicative of increased off-task thought. Notably, unlike trait anxiety, worry was not linked to reduced frontal-striatal-thalamo connectivity, impoverished frontal recruitment, or slowed responding during blocks without commission errors, contrary to accounts proposing a direct causal link between worry and impoverished attentional control. This leads us to propose a new model of the relationship between anxiety, worry and frontal engagement in attentional control versus off-task thought.
Low-power heterogeneous reconfigurable digital signal processors with energy-efficient interconnect network (2004)

Future portable devices with rich multimedia functions ask for increasingly powerful digital signal processors that deliver high performance, ultra low power, low cost, and good flexibility. Flexibility is a necessity to achieve high system integration (to save the space and cost) in the presence of multiple standards, and to support the diverse and rapidly evolving multimedia applications. While ASICs or dedicated hardware can achieve the lowest power consumption and the highest performance for a specific application, they can't meet the flexibility requirement. At another end, general-purpose instruction-based microprocessors or DSPs either fall short of performance or are too power inefficient. Recently, reconflgurable architectures, which are characterized as both software programmable and post-fabrication hardware configurable, have emerged as key alternative solutions providing the performance, energy-efficiency and cost similar to ASIC while being flexible enough for the target wireless and embedded multimedia application domains. 
A heterogeneous reconfigurable digital signal processor consists of an array of coarse-grained computing units and memory units connected by reconfigurable local and global communications structures. The processor also contains distributed control units that dynamically analyze data operations and perform reconfiguration accordingly. The computing units can be independently configured to perform a variety of basic computational functions. 
This work thoroughly analyzes the algorithms of wireless speech coding and embedded multimedia processing such as video processing, and to identify the underlying computational kernels that account for a large fraction of execution time and energy. The main challenge of designing a reconfigurable processor is how to map these computational kernels effectively to the configurable computing units and to design a reconfigurable interconnect network that effectively combines these kernels into operational system. This thesis work describes the design methodology of an energy-efficient interconnect network, from both circuits and architecture perspective. Several novel low-swing interconnect schemes and hierarchical interconnect network architectures are proposed to achieve high energy efficiency. To verify the effectiveness of the proposed heterogeneous reconfigurable architecture, prototype chips were designed for wireless speech coding and embedded multimedia processing respectively. Measured results and benchmark studies demonstrate the effectiveness of the heterogenous reconfigurable architecture.
Near infrared thoracoscopy of tumoral protease activity for improved detection of peripheral lung cancer (2005)

Improvement in tumor detection using "smart" probes in combination with microcatheter fluorescence thoracoscopy was evaluated in a mouse model. These imaging probes increase in fluorescence intensity after protease activation; cathepsin B is a major activator of the probes used in this study. Lewis lung carcinoma cells were orthotopically implanted in the subpleural lung parenchyma. Two activatable near infrared (NIR) probes with different excitation and emission wavelength were administered intravenously to determine whether wavelength would modulate target to background ratio (TBR). Mice were selectively intubated and thoracoscopy performed. A 0.8 mm outer diameter imaging catheter was used to record simultaneous white-light (anatomic) and NIR (protease expression) images. At both wavelength pairs evaluated (680/700 and 750/780 nm excitation/emission), the intrinsic luminosity differences between tumors and normal lung in uninjected animals was low (p > 0.3 and p = 0.4, respectively and TBR near 1). In mice receiving protease probes IV, tumors were significantly more fluorescent than adjacent lung (p < 0.0005 for 680/700 and p < 0.006 for 750/780) and TBR increased to approximately 9-fold. Confirmatory fluorescence microscopy and immunohistochemistry were similar and revealed that normal lung had very low levels when compared to tumors of cathepsin B and probe fluorescence. In conclusion, protease sensitive imaging probes selective for cathepsin B, imaged with NIR microcatheters, significantly increase the TBR, making small peripheral lung tumors more readily apparent. Such an approach may be a useful adjunct in staging or restaging patients with lung cancer to find minimal disease in the pleural and subpleural space.
Epitope specificities of murine monoclonal and rabbit polyclonal antibodies against enterobacterial lipopolysaccharides of the Re chemotype (1989)

Murine monoclonal and rabbit polyclonal antibodies raised against the lipopolysaccharides (LPS) of Re mutants of Salmonella minnesota, Proteus mirabilis, and Escherichia coli were serologically characterized. Using natural Re LPS and natural and synthetic partial structures thereof, representing the 3-deoxy-D-manno-2-octulosonic acid (KDO) or lipid A region or both, the epitope specificities of four monoclonal antibodies were defined. Clones 20 (immunoglobulin M [IgM]) and 25 (IgG3) recognize a terminal alpha-pyranosidically linked KDO monosaccharide residue and the alpha-2,4-linked KDO disaccharide, respectively, as the immunodominant group. Therefore, these two antibodies are core antibodies which do not require the presence of lipid A constituents for binding. The minimal structure enabling binding of clone 17 (IgG2b) is a pseudotetrasaccharide of the sequence alpha-KDO-(2----4)-alpha-KDO-(2----6)-beta-glucosamine-(1----6)- glucosaminitol with two amide-linked 3-hydroxytetradecanoic acid residues. The smallest structure with which clone 22 (IgG3) reacted was de-O-acylated Re LPS. Therefore, clones 17 and 22 are LPS antibodies requiring both the lipid A and the KDO region for binding. Phosphoryl residues of the lipid A moiety in Re LPS are dispensable for the reaction with clone 17, whereas they are necessary for that with clone 22. These four different antibody types were also detected in polyclonal rabbit antisera and could be distinguished from each other by absorption experiments. It was found that type 20 and 25 antibodies either were not present or were present only in small amounts and that the majority of the antibodies were of types 17 and 22. From these data, we conclude that the immunodominant structures of Re LPS comprise both the KDO and lipid A domains.
Generalizations of the self-organizing map (2005)

It is pointed out in this paper that for the cells of a self-organizing map (SOM) one may select adaptive dynamic operators in stead of simple static units. Their updating may be made either by tuning their parameters, or in an evolutionary process. This kind of generic principle is supposed to define the category of SOM networks in a more general sense.
Ultra high-efficiency advanced triple-junction (ATJ) solar cell production at Emcore photovoltaics (2005)

Emcore Photovoltaics is in volume production of high-efficiency multijunction solar cells for spacecraft applications. Emcore's latest product is the advanced triple-junction (ATJ) InGaP/InGaAs/Ge solar cell. The ATJ cell exhibits a beginning-of-life (BOL) minimum average conversion efficiency of 27.5%, making it the highest efficiency flight cell available in the market to date. In this paper, the development and manufacturing aspects, as well as, space qualification results at the bare cell and coverglass-interconnected-cell (CIC) levels are presented.
Raney Ni-Sn Catalyst for H 2 Production from Biomass-Derived Hydrocarbons (2003)

Hydrogen (H2) was produced by aqueous-phase reforming of biomass-derived oxygenated hydrocarbons at temperatures near 500 kelvin over a tin-promoted Raney-nickel catalyst. The performance of this non-precious metal catalyst compares favorably with that of platinum-based catalysts for production of hydrogen from ethylene glycol, glycerol, and sorbitol. The addition of tin to nickel decreases the rate of methane formation from C-O bond cleavage while maintaining the high rates of C-C bond cleavage required for hydrogen formation.
Electrospinning: processing technique for tissue engineering scaffolding (2008)

Electrospinning has attracted tremendous interest in the research community as a simple and versatile technique to produce synthetic polymeric ultrafine fibres with diameters ranging from a few micrometres to tens of nanometres. Recently, some natural origin polymers have also been successfully electrospun. Owing to their very small diameter, polymeric nanofibres exhibit unusual properties such as high specific surface area, flexibility in surface functionalities and superior mechanical properties. In addition, electrospun non-woven meshes could physically mimic the extracellular matrix structure of native tissues. These remarkable properties render electrospun nanofibres useful for many applications, particularly those related to the field of biomedical engineering. The first part of this review is intended to provide a fundamental survey of the electrospinning process (apparatus, governing parameters) and of recent improvements of the technique, including associated structural modifications of polymeric nanofibre meshes. The prospective tissue engineering/biomedical applications of electrospun polymeric nanofibres are then reviewed, namely, wound dressings, medical prostheses, drug delivery systems, DNA release and tissue engineering scaffolds. The essential properties of scaffolds in terms of the structural features of electrospun nanofibre meshes are discussed. Finally, the future perspectives for applications of electrospun nanofibres, particularly in the field of tissue engineering, are considered.
Prostate Cancer Induces Bone Metastasis through Wnt-Induced Bone Morphogenetic Protein-Dependent and Independent Mechanisms (2008)

Prostate cancer (PCa) is frequently accompanied by osteosclerotic (i.e., excessive bone production) bone metastases. Although bone morphogenetic proteins (BMP) and Wnts are mediators of PCa-induced osteoblastic activity, the relation between them in PCa bone metastases is unknown. The goal of this study was to define this relationship. Wnt3a and Wnt5a administration or knockdown of DKK-1, a Wnt inhibitor, induced BMP-4 and 6 expression and promoter activation in PCa cells. DKK-1 blocked Wnt activation of the BMP promoters. Transfection of C4-2B cells with axin, an inhibitor of canonical Wnt signaling, blocked Wnt3a but not Wnt5a induction of the BMP promoters. In contrast, Jnk inhibitor I blocked Wnt5a but not Wnt3a induction of the BMP promoters. Wnt3a, Wnt5a, and conditioned medium (CM) from C4-2B or LuCaP23.1 cells induced osteoblast differentiation in vitro. The addition of DKK-1 and Noggin, a BMP inhibitor, to CM diminished PCa CM-induced osteoblast differentiation in a synergistic fashion. However, pretreatment of PCa cells with DKK-1 before collecting CM blocked osteoblast differentiation, whereas pretreatment with Noggin only partially reduced osteoblast differentiation, and pretreatment with both DKK-1 and Noggin had no greater effect than pretreatment with DKK-1 alone. Additionally, knockdown of BMP expression in C4-2B cells inhibited Wnt-induced osteoblastic activity. These results show that PCa promotes osteoblast differentiation through canonical and noncanonical Wnt signaling pathways that stimulate both BMP-dependent and BMP-independent osteoblast differentiation. These results show a clear link between Wnts and BMPs in PCa-induced osteoblast differentiation and provide novel targets, including the noncanonical Wnt pathway, for therapy of PCa.
Clinical Features of Acute Allergic Reactions to Peanut and Tree Nuts in Children (1998)

Acute allergic reactions to PN occur early in life. PN and TN allergic reactions coexist in one third of PN-allergic patients, frequently occur on first known exposure, and may be life-threatening, requiring emergency treatment. Accidental ingestions are common, occur frequently outside of the home, and often require emergency treatment. Consequently, early diagnosis followed by education on avoidance and treatment measures (including self-administered epinephrine) is imperative.
Peptide Cyclization and Cyclodimerization by CuI-Mediated Azide−Alkyne Cycloaddition (2009)

Head-to-tail cyclodimerization of resin-bound oligopeptides bearing azide and alkyne groups occurs readily by 1,3-dipolar cycloaddition upon treatment with Cu(I). The process was found to be independent of peptide sequence, sensitive to the proximity of the alkyne to the resin, sensitive to solvent composition, facile for alpha- and beta-peptides but not for gamma-peptides, and inhibited by the inclusion of tertiary amide linkages. Peptides shorter than hexamers were predominantly converted to cyclic monomers. Oligoglycine and oligo(beta-alanine) chains underwent oligomerization by 1,3-dipolar cycloaddition in the absence of a copper catalyst. These results suggest that cyclodimerization depends on the ability of the azido-alkyne peptide to form in-frame hydrogen bonds between chains in order to place the reacting groups in close proximity and lower the entropic penalty for dimerization. The properties of the resin and solvent are crucial, giving rise to a productive balance between swelling and interstrand H-bonding. These findings allow for the design of optimal substrates for triazole-forming ring closure and for the course of the reaction to be controlled by the choice of conditions.
PAK and other Rho-associated kinases – effectors with surprisingly diverse mechanisms of regulation (2005)

The Rho GTPases are a family of molecular switches that are critical regulators of signal transduction pathways in eukaryotic cells. They are known principally for their role in regulating the cytoskeleton, and do so by recruiting a variety of downstream effector proteins. Kinases form an important class of Rho effector, and part of the biological complexity brought about by switching on a single GTPase results from downstream phosphorylation cascades. Here we focus on our current understanding of the way in which different Rho-associated serine/threonine kinases, denoted PAK (p21-activated kinase), MLK (mixed-lineage kinase), ROK (Rho-kinase), MRCK (myotonin-related Cdc42-binding kinase), CRIK (citron kinase) and PKN (protein kinase novel), interact with and are regulated by their partner GTPases. All of these kinases have in common an ability to dimerize, and in most cases interact with a variety of other proteins that are important for their function. A diversity of known structures underpin the Rho GTPase-kinase interaction, but only in the case of PAK do we have a good molecular understanding of kinase regulation. The ability of Rho GTPases to co-ordinate spatial and temporal phosphorylation events explains in part their prominent role in eukaryotic cell biology.