gebhart/patrepeval huggingface dataset:
Crystal Structure of Cas9 (2015)

Cas9 is an RNA-guided DNA endonuclease and is implicated in the bacterial CRISPR-Cas adaptive immune system. Cas9 binds dual guide RNAs or single-guide RNA, and the Cas9-RNA complex recognizes and cleaves target double-stranded DNA via RNA-DNA complementarity. To understand this unprecedented, RNA-guided DNA cleavage mechanism, we solved the crystal structure of Cas9 in complex with guide RNA and target DNA. The ternary complex structure provides insights into the RNA-guided DNA cleavage mechanism, and paves the way for the rational design of new, Cas9-based tools.
Synthesis and Characterization of Novel Unsymmetrical and Symmetrical 3-Halo- or 3-Methoxy-substituted 2-Dibenzoylamino-1,4-naphthoquinone Derivatives (2013)

Symmetrical and unsymmetrical 3-halo- or 3-methoxy- substituted 2-dibenzoylamino- 1,4-naphthoquinone analogs were synthesized with an average yield of 45% via sodium hydride promoted bis-acylation of 2-amino-3-chloro-1,4-naphthoquinone, 2-amino-3-bromo-1,4-naphthoquinone and 2-amino-3-methoxy-1,4-naphthoquinone.
Who Did What: Editor Role Identification in Wikipedia (2021)

Understanding the social roles played by contributors to online communities can facilitate the process of task routing. In this work, we develop new techniques to find roles in Wikipedia based on editors' low-level edit types and investigate how work contributed by people from different roles affect the article quality. To do this, we first built machine-learning models to automatically identify the edit categories associated with edits. We then applied a graphical model analogous to Latent Dirichlet Allocation to uncover the latent roles in editors' edit histories. Applying this technique revealed eight different roles editors play. Finally, we validated how our identified roles collaborate to improve the quality of articles. The results demonstrate that editors carrying on different roles contribute differently in terms of edit categories and articles in different quality stages need different types of editors. Implications for editor role identification and the validation of role contribution are discussed.
High-resolution structures of the IgM Fc domains reveal principles of its hexamer formation (2013)

IgM is the first antibody produced during the humoral immune response. Despite its fundamental role in the immune system, IgM is structurally only poorly described. In this work we used X-ray crystallography and NMR spectroscopy to determine the atomic structures of the constant IgM Fc domains (Cµ2, Cµ3, and Cµ4) and to address their roles in IgM oligomerization. Although the isolated domains share the typical Ig fold, they differ substantially in dimerization properties and quaternary contacts. Unexpectedly, the Cµ4 domain and its C-terminal tail piece are responsible and sufficient for the specific polymerization of Cµ4 dimers into covalently linked hexamers of dimers. Based on small angle X-ray scattering data, we present a model of the ring-shaped Cµ4 structure, which reveals the principles of IgM oligomerization.
Activation of olfactory and trigeminal cortical areas following stimulation of the nasal mucosa with low concentrations of S(−)‐nicotine vapor—An fMRI study on chemosensory perception (2008)

Applied to the nasal mucosa in low concentrations, nicotine vapor evokes odorous sensations (mediated by the olfactory system) whereas at higher concentrations nicotine vapor additionally produces burning and stinging sensations in the nose (mediated by the trigeminal system). The objective of this study was to determine whether intranasal stimulation with suprathreshold concentrations of S(-)-nicotine vapor causes brain activation in olfactory cortical areas or if trigeminal cortical areas are also activated. Individual olfactory detection thresholds for S(-)-nicotine were determined in 19 healthy occasional smokers using a computer-controlled air-dilution olfactometer. Functional magnetic resonance images were acquired using a 1.5T MR scanner with applications of nicotine in concentrations at or just above the individual's olfactory detection threshold. Subjects reliably perceived the stimuli as being odorous. Accordingly, activation of brain areas known to be involved in processing of olfactory stimuli was identified. Although most of the subjects never or only rarely observed a burning or painful sensation in the nose, brain areas associated with the processing of painful stimuli were activated in all subjects. This indicates that the olfactory and trigeminal systems are activated during perception of nicotine and it is not possible to completely separate olfactory from trigeminal effects by lowering the concentration of the applied nicotine. In conclusion, even at low concentrations that do not consistently lead to painful sensations, intranasally applied nicotine activates both the olfactory and the trigeminal system.
Quantitative morphology of the caudate nucleus in attention deficit hyperactivity disorder (1994)

Along with previous MRI findings of low volumes in corpus callosum regions, these results support developmental abnormalities of frontal-striatal circuits in ADHD.
Solar cell efficiency tables (version 22) (2003)

Abstract Consolidated tables showing an extensive listing of the highest independently confirmed efficiencies for solar cells and modules are presented. Guidelines for inclusion of results into these tables are outlined and new entries since January 2003 are reviewed. Copyright © 2003 John Wiley & Sons, Ltd.
Efficient multi-keyword search over p2p web (2008)

Current search mechanisms of DHT-based P2P systems can well handle a single keyword search problem. Other than single keyword search, multi-keyword search is quite popular and useful in many real applications. Simply using the solution for single keyword search will require distributed intersection/union operations in wide area networks, leading to unacceptable traffic cost. As it is well known that Bloom Filter (BF) is effective in reducing traffic, we would like to use BF encoding to handle multi-keyword search. Applying BF is not difficult, but how to get optimal results is not trivial. In this study we show, through mathematical proof, that the optimal setting of BF in terms of traffic cost is determined by the global statistical information of keywords, not the minimized false positive rate as claimed by previous methods. Through extensive experiments, we demonstrate how to obtain optimal settings. We further argue that the intersection order between sets is important for multi-keyword search. Thus, we design optimal order strategies based on BF for both "and" and "or" queries. To better evaluate the performance of this design, we conduct extensive simulations on TREC WT10G test collection and the query log of a commercial search engine. Results show that our design significantly reduces the search traffic of existing approach by 73%.
Homogénéisation à haute pression des dispersions alimentaires liquides (2010)

Les produits alimentaires liquides ou pâteux sont souvent des « dispersions », c'est-à-dire des produits composés d'une ou plusieurs phases dispersées (phases dites discontinues) au sein d'une phase dispersante (phase dite continue). L'homogénéisation à haute pression, qui consiste à projeter un produit liquide ou pâteux sous forte pression (30 à 1 000 bar), permet de stabiliser le résultat de la dispersion afin de limiter le phénomène de séparation. L'article présente en détail les principes de cette méthode, ainsi que les éléments constitutifs d'un homogénéisateur. D'autres aspects, comme les incidences du traitement sur la qualité du produit ou les technologies alternatives sont également abordés.
Generation of multiphoton quantum states on silicon (2019)

Multiphoton quantum states play a critical role in emerging quantum technologies and greatly improve our fundamental understanding of the quantum world. Integrated photonics is well recognized as an attractive technology offering great promise for the generation of photonic quantum states with high-brightness, tunability, stability, and scalability. Herein, we demonstrate the generation of multiphoton quantum states using a single-silicon nanophotonic waveguide. The detected four-photon rate reaches 0.34 Hz even with a low-pump power of 600 μW. This multiphoton quantum state is also qualified with multiphoton quantum interference, as well as quantum state tomography. For the generated four-photon states, the quantum interference visibilities are greater than 95%, and the fidelity is 0.78 ± 0.02. Furthermore, such a multiphoton quantum source is fully compatible with the on-chip processes of quantum manipulation, as well as quantum detection, which is helpful for the realization of large-scale quantum photonic integrated circuits (QPICs) and shows great potential for research in the area of multiphoton quantum science.
Highly phosphomannosylated enzyme replacement therapy for GM2 gangliosidosis (2010)

This lysosome-directed recombinant human enzyme drug derived from methylotrophic yeast has the high therapeutic potential to improve the motor dysfunction and quality of life of the lysosomal storage diseases (LSDs) patients with neurological manifestations. We emphasize the importance of neural cell surface M6P receptor as a delivery target of neural cell-directed enzyme replacement therapy (NCDERT) for neurodegenerative metabolic diseases.
Analysis of Periplasmic Enzymes in Intact Cultured Bacteria and Bacteroids of Bradyrhizobium japonicum and Rhizobium leguminosarum biovar phaseoli (1989)

Analysis of periplasmic enzymes of Bradyrhizobium japonicum or Rhizobium leguminosarum biovar phaseoli was hampered by the fact that only small amounts of marker enzyme activities were released from cells by osmotic shock or by lysozyme/EDTA treatment. However, up to 95 % of total activity of certain periplasmic marker enzymes could be measured in intact cells by including 003% Triton X-100 in enzyme assays. Less than 5% of the cytoplasmic marker enzyme -hydroxybutyrate dehydrogenase could be measured under these conditions, indicating that treatment with dilute detergent does not significantly perturb the cytoplasmic membrane. Various lines of evidence indicate that the dilute detergent treatment does not significantly alter wall structure but, instead, permits the assay of periplasmic enzymes by facilitating diffusion of substrates and products to and from the periplasmic space. For pyrophosphatase and phosphodiesterase, the proportion of total enzyme activity which could be measured in intact cells was higher in bacteroids than in bacteria at all Triton concentrations, suggesting that the outer membrane of bacteroids may be more permeable than the outer membrane of cultured bacteria. The effect of detergent on the hydrolysis of four disaccharides sucrose, α,α-trehalose, maltose and lactose was studied using intact cultured R. leguminosarum biovar phaseoli. The response of lactose hydrolysis to the addition of detergent was four-fold greater than the response of the other disaccharidase activities, indicating that a rhizobial lactase may be present in the periplasmic space.
Wetting properties of silicon surfaces (2002)

The wetting properties of silicon surfaces are believed to be important for the process of silicon-silicon direct bonding, and for the broader issue of biocompatibility. The authors have investigated 14 different surface treatments, including several etching and surface modifying agents, and the contact angles to water were measured for each surface treatment. It was shown that the contact angle could be controlled almost continuously between 5 degrees and 96 degrees by varying the surface treatment. Removing the native oxide layer in hydrofluoric acid results in a hydrophobic surface, whereas hydrophilic surfaces are obtained by inserting the wafer in, e.g. boiling NH/sub 3/:H/sub 2/O/sub 2/:H/sub 2/O. Protein compatibility was investigated by measuring the degree of interaction with insulin. The hydrophobic surfaces showed a relatively strong interaction, whereas hydrophilic surfaces are almost completely inert towards insulin.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Mechanisms Linking Social Ties and Support to Physical and Mental Health (2011)

Over the past 30 years investigators have called repeatedly for research on the mechanisms through which social relationships and social support improve physical and psychological well-being, both directly and as stress buffers. I describe seven possible mechanisms: social influence/social comparison, social control, role-based purpose and meaning (mattering), self-esteem, sense of control, belonging and companionship, and perceived support availability. Stress-buffering processes also involve these mechanisms. I argue that there are two broad types of support, emotional sustenance and active coping assistance, and two broad categories of supporters, significant others and experientially similar others, who specialize in supplying different types of support to distressed individuals. Emotionally sustaining behaviors and instrumental aid from significant others and empathy, active coping assistance, and role modeling from similar others should be most efficacious in alleviating the physical and emotional impacts of stressors.
Probing the single-wall carbon nanotube bundle: Raman scattering under high pressure (1999)

We report experimental and theoretical investigations on the pressure dependence of the Raman-active radial and tangential vibrational modes of single-wall carbon-nanotube bundles. Using 514.5-nm excitation, we find that the radial mode intensity disappears beyond 1.5 GPa, and the tangential mode intensity also drops considerably above this pressure. This observation is tentatively attributed to a loss in the electronic resonance in the Raman scattering cross section due to a hexagonal distortion in the cylindrical cross section of the tubes in the bundles under compression. Theoretical calculations were made as a function of pressure using a generalized tight-binding molecular dynamics scheme that included intertubule van der Waals coupling. Under certain model assumptions, the experimental pressure dependence of the radial mode is well described by the calculations, indicating that intertubule interactions strongly influence the ambient pressure frequency and the pressure behavior of the radial breathing mode.
A calorimetric characterization of the salt dependence of the stability of the GCN4 leucine zipper (1995)

The effects of different salts (LiCl, NaCl, ChoCl, KF, KCl, and KBr) on the structural stability of a 33-residue peptide corresponding to the leucine zipper region of GCN4 have been studied by high-sensitivity differential scanning calorimetry. These experiments have allowed an estimation of the salt dependence of the thermodynamic parameters that define the stability of the coiled coil. Independent of the nature of the salt, a destabilization of the coiled coil is always observed upon increasing salt concentration up to a maximum of approximately 0.5 M, depending on the specific cation or anion. At higher salt concentrations, this effect is reversed and a stabilization of the leucine zipper is observed. The effect of salt concentration is primarily entropic, judging from the lack of a significant salt dependence of the transition enthalpy. The salt dependence of the stability of the peptide is complex, suggesting the presence of specific salt effects at high salt concentrations in addition to the nonspecific electrostatic effects that are prevalent at lower salt concentrations. The data is consistent with the existence of specific interactions between anions and peptide with an affinity that follows a reverse size order (F- > Cl- > Br-). Under all conditions studied, the coiled coil undergoes reversible thermal unfolding that can be well represented by a reaction of the form N2<==>2U, indicating that the unfolding is a two-state process in which the helices are only stable when they are in the coiled coil conformation.
Genome‐scale expression profiling of Hutchinson–Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis (2004)

Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disease with widespread phenotypic features resembling premature aging. HGPS was recently shown to be caused by dominant mutations in the LMNA gene, resulting in the in-frame deletion of 50 amino acids near the carboxyl terminus of the encoded lamin A protein. Children with this disease typically succumb to myocardial infarction or stroke caused by severe atherosclerosis at an average age of 13 years. To elucidate further the molecular pathogenesis of this disease, we compared the gene expression patterns of three HGPS fibroblast cell strains heterozygous for the LMNA mutation with three normal, age-matched cell strains. We defined a set of 361 genes (1.1% of the approximately 33,000 genes analysed) that showed at least a 2-fold, statistically significant change. The most prominent categories encode transcription factors and extracellular matrix proteins, many of which are known to function in the tissues severely affected in HGPS. The most affected gene, MEOX2/GAX, is a homeobox transcription factor implicated as a negative regulator of mesodermal tissue proliferation. Thus, at the gene expression level, HGPS shows the hallmarks of a developmental disorder affecting mesodermal and mesenchymal cell lineages. The identification of a large number of genes implicated in atherosclerosis is especially valuable, because it provides clues to pathological processes that can now be investigated in HGPS patients or animal models.
Hoare Logic and Auxiliary Variables (1999)

Abstract. Auxiliary variables are essential for specifying programs in Hoare Logic. They are required to relate the value of variables in different states. However, the axioms and rules of Hoare Logic turn a blind eye to the role of auxiliary variables. We stipulate a new structural rule for adjusting auxiliary variables when strengthening preconditions and weakening postconditions. Courtesy of this new rule, Hoare Logic is adaptation complete, which benefits software re-use. This property is responsible for a number of improvements. Relative completeness follows uniformly from the Most General Formula property. Moreover, one can show that Hoare Logic subsumes Vienna Development Method's (VDM) operation decomposition rules in that every derivation in VDM can be naturally embedded in Hoare Logic. Furthermore, the new treatment leads to a significant simplification in the presentation for verification calculi dealing with more interesting features such as recursion.
Decentralized cooperative collision avoidance for acceleration constrained vehicles (2008)

Safety must be ensured in the deployment of multi-agent vehicle systems. This paper presents decentralized collision avoidance algorithms for systems with second order dynamics and acceleration constraints, using a switching control law. The technique augments existing multi-agent control laws with the capability to switch to provably safe collision avoidance maneuvers when required. Two algorithms with low computational cost are presented, one for two vehicles and one for more vehicles. In both methods, each vehicle computes avoid sets with respect to every other vehicle. When one or more vehicles are on the boundary of their avoid sets, collision avoidance action is taken. These algorithms are applied in simulation scenarios for which existing techniques either fail or are computationally expensive, and used for information theoretic control of a mobile sensor network to reduce the computational complexity. Finally, they are demonstrated in quadrotor helicopter flight experiments.
Visual Representations for Monitoring Project Performance: Developing Novel Prototypes for Improved Communication (2013)

Maintaining project control demands construction project managers navigate the discrepancies between target and actual performance—a specific challenge for large-scale construction projects that generate large amounts of ever-changing data. Project managers often use visual representations of data to make better-informed decisions; however, current approaches often fail to manifest the multifaceted considerations that render a successful project. Better visual representation tools would streamline communication and improve project efficiency. Applying a variety of research methods ranging from literature reviews to simulation and usability tests, this investigation’s six-step process developed four alternative visual representations prototypes for improved performance monitoring: Activity Icons, Map of Activities, Activity Wall, and Activity Gazer. This paper contributes to the body of knowledge by iteratively designing these four prototype visual representations in consultation with experienced project managers and by assessing industry’s receptivity. This paper also lays the foundation for long-term expansion of research into the most successful of the developed visual representation prototypes: Activity Gazer.
Matriptase activation and shedding with HAI-1 is induced by steroid sex hormones in human prostate cancer cells, but not in breast cancer cells (2006)

Matriptase and its cognate inhibitor, hepatocyte growth factor activator inhibitor-1 (HAI-1), have been implicated in carcinoma onset and malignant progression. However, the pathological mechanisms of matriptase activation are not defined. Steroid sex hormones play crucial roles in prostate and breast cancer. Therefore, we investigated the questions of whether and how steroid sex hormones regulate matriptase activation in these cancer cells. Treatment of cells with 17beta-estradiol had no effect on activation of matriptase in hormone-starved breast cancer cells, in part due to their high constitutive level of activated matriptase. In striking contrast, very low levels of activated matriptase were detected in hormone-starved lymph node prostatic adenocarcinoma (LNCaP) cells. Robust activation of matriptase was observed as early as 6 h after exposure of these cells to 5alpha-dihydrotestosterone (DHT). Activation of matriptase was closely followed by shedding of the activated matriptase with >90% of total activated matriptase present in the culture media 24 h after DHT treatment. Activated matriptase was shed in a complex with HAI-1 and may result from simultaneously proteolytic cleavages of both membrane-bound proteins. Latent matriptase and free HAI-1 were also shed into culture media. As a result of shedding, the cellular levels of matriptase and HAI-1 were significantly reduced 24 h after exposure to DHT. DHT-induced matriptase activation and shedding were significantly inhibited by the androgen antagonist bicalutamide, by the RNA transcription inhibitor actinomycin D, and by the protein synthesis inhibitor cycloheximide. These results suggest that in LNCaP cells, androgen induces matriptase activation via the androgen receptor, and requires transcription and protein synthesis.