gebhart/patrepeval huggingface dataset:
Identification of Rab6 as an N-ethylmaleimide-sensitive fusion protein-binding protein (2000)

In this study we show the interaction of N-ethylmaleimide-sensitive fusion protein (NSF) with a small GTP-binding protein, Rab6. NSF is an ATPase involved in the vesicular transport within eukaryotic cells. Using the yeast two-hybrid system, we have isolated new NSF-binding proteins from the rat lung cDNA library. One of them was Rab6, which is involved in the vesicular transport within the Golgi and trans-Golgi network as a Ras-like GTPase. We demonstrated that the N-terminal domain of NSF interacted with the C-terminal domain of Rab6, and these proteins were co-immunoprecipitated from the rat brain extract. This interaction was maintained preferentially in the presence of hydrolysable ATP. Recombinant NSF-His(6) can also bind to C-terminal Rab6-glutathione S-transferase under the conditions to allow the ATP hydrolysis. Surprisingly, Rab6 stimulates the ATPase activity of NSF by approx. 2-fold as does alpha-soluble NSF attachment protein receptor. Anti-Rab6 polyclonal antibodies significantly inhibited the Rab6-stimulated ATPase activity of NSF. Furthermore, we found that Rab3 and Rab4 can also associate with NSF and stimulate its ATPase activity. Taken together, we propose a model in which Rab can form an ATP hydrolysis-regulated complex with NSF, and function as a signalling molecule to deliver the signal of vesicle fusion through the interaction with NSF.
Approximate lifted inference with probabilistic databases (2015)

This paper proposes a new approach for approximate evaluation of #P-hard queries with probabilistic databases. In our approach, every query is evaluated entirely in the database engine by evaluating a fixed number of query plans, each providing an upper bound on the true probability, then taking their minimum. We provide an algorithm that takes into account important schema information to enumerate only the minimal necessary plans among all possible plans. Importantly, this algorithm is a strict generalization of all known results of PTIME self-join-free conjunctive queries: A query is safe if and only if our algorithm returns one single plan. We also apply three relational query optimization techniques to evaluate all minimal safe plans very fast. We give a detailed experimental evaluation of our approach and, in the process, provide a new way of thinking about the value of probabilistic methods over non-probabilistic methods for ranking query answers.
A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease (2023)

Kidney stone disease causes significant morbidity and increases health care utilization. In this work, we decipher the cellular and molecular niche of the human renal papilla in patients with calcium oxalate (CaOx) stone disease and healthy subjects. In addition to identifying cell types important in papillary physiology, we characterize collecting duct cell subtypes and an undifferentiated epithelial cell type that was more prevalent in stone patients. Despite the focal nature of mineral deposition in nephrolithiasis, we uncover a global injury signature characterized by immune activation, oxidative stress and extracellular matrix remodeling. We also identify the association of MMP7 and MMP9 expression with stone disease and mineral deposition, respectively. MMP7 and MMP9 are significantly increased in the urine of patients with CaOx stone disease, and their levels correlate with disease activity. Our results define the spatial molecular landscape and specific pathways contributing to stone-mediated injury in the human papilla and identify associated urinary biomarkers.
Hybrid Observer Combining Measurements of Different Fidelities**This work was supported by the Research Council of Norway through the Centres of Excellence funding scheme, project number 23254 - NTNU AMOS, and in part by NSF grant number ECCS-1508757 and AFOSR grant number FA9550-15-1-0155. (2016)

A signal-based hybrid observer combining measurements of different fidelities is proposed for position and velocity estimation of marine vessels. The concept assumes that noisy position measurements are available only sporadically at a non-constant sampling rate. Predictions of position between the samples are provided by integrating acceleration measurements, which are available at a high rate (approximated to be continuous sampling). Estimates with smaller variance are computed by averaging multiple observer copies of the position. This work is a continuation of the observer proposed in Brodtkorb et al. (2015). The main contributions of this paper is extending the observer to the more realistic scenario where linear velocity and angular acceleration measurements are not available. A simulation study showed that the observer performed well in closed loop with a controller conducting dynamic positioning operations of a marine vessel.
Do Invariances in Deep Neural Networks Align with Human Perception? (2023)

An evaluation criterion for safe and trustworthy deep learning is how well the invariances captured by representations of deep neural networks (DNNs) are shared with humans. We identify challenges in measuring these invariances. Prior works used gradient-based methods to generate identically represented inputs (IRIs), ie, inputs which have identical representations (on a given layer) of a neural network, and thus capture invariances of a given network. One necessary criterion for a network's invariances to align with human perception is for its IRIs look 'similar' to humans. Prior works, however, have mixed takeaways; some argue that later layers of DNNs do not learn human-like invariances yet others seem to indicate otherwise. We argue that the loss function used to generate IRIs can heavily affect takeaways about invariances of the network and is the primary reason for these conflicting findings. We propose an adversarial regularizer on the IRI generation loss that finds IRIs that make any model appear to have very little shared invariance with humans. Based on this evidence, we argue that there is scope for improving models to have human-like invariances, and further, to have meaningful comparisons between models one should use IRIs generated using the regularizer-free loss. We then conduct an in-depth investigation of how different components (eg architectures, training losses, data augmentations) of the deep learning pipeline contribute to learning models that have good alignment with humans. We find that architectures with residual connections trained using a (self-supervised) contrastive loss with l_p ball adversarial data augmentation tend to learn invariances that are most aligned with humans. Code: github.com/nvedant07/Human-NN-Alignment
Synthesis and Biological Evaluation of Lactimidomycin and Its Analogues (2015)

The studies culminating in the total synthesis of the glutarimide-containing eukaryote translation elongation inhibitor lactimidomycin are described. The optimized synthetic route features a Zn(II)-mediated intramolecular Horner-Wadsworth-Emmons (HWE) reaction resulting in a highly stereoselective formation of the strained 12-membered macrolactone of lactimidomycin on a 423 mg scale. The presence of the E,Z-diene functionality was found to be key for effective macrocyclizations as a complete removal of these unsaturation units resulted in exclusive formation of the dimer rather than monocyclic enoate. The synthetic route features a late-stage installation of the glutarimide functionality via an asymmetric catalytic Mukaiyama aldol reaction, which allows for a quick generation of lactimidomycin homolog 55 containing two additional carbons in the glutarimide side chain. Similar to lactimidomycin, this analog was found to possess cytotoxicity against MDA-MB-231 breast cancer cells (GI50 =1-3 μM) using in vitro 2D and 3D assays. Although lactimidomycin was found to be the most potent compound in terms of anticancer activity, 55 as well as truncated analogues 50-52 lacking the glutarimide side-chain were found to be significantly less toxic against human mammary epithelial cells.
3D Analytical Modelling of Sink Heat Distribution for Fast Optimisation of Power Converters (2019)

With the development of embedded systems, it is crucial to reduce weight of equipments. In power converter, heat sink is a heavy part that often can be reduced in volume and weight. There are several models and methods to calculate a heat sink thermal resistance. However the more precise these methods are, the more time consuming they are and thus they can be hardly integrated in a weight optimization routine. Using analytical models to calculate heat sink thermal resistance is a good compromise between execution time and precision of results.&#13;\nThey are usually one-dimensional models which are simple but do not take into account heat spreading effects, which is important when power electronic heat sources are small compared to their heat sink. This paper describes a three-dimensional analytical model of forced convection plate fin heat sink, which will be compared with numerical simulation. A maximum difference of 2.5% has been observed between models. This analytical model will be used in an optimization routine to reduce the weight of an existing heat sink in order to show that fast and precise optimization of cooling system is possible with analytical models.
Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens (2023)

Most variants associated with complex traits and diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown effects. Using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR screens, and single-cell transcriptomic and proteomic sequencing, we discovered 124 <i>cis</i>-target genes of 91 noncoding blood trait GWAS loci. Using precise variant insertion through base editing, we connected specific variants with gene expression changes. We also identified <i>trans</i>-effect networks of noncoding loci when <i>cis</i> target genes encoded transcription factors or microRNAs. Networks were themselves enriched for GWAS variants and demonstrated polygenic contributions to complex traits. This platform enables massively parallel characterization of the target genes and mechanisms of human noncoding variants in both <i>cis</i> and <i>trans</i>.
Fireworks, and: The Basset (2004)

Behind Dick Leckband's house that afternoon we blew up toy entrenchments, bushes, crabgrass, whole strings dissolving, drifting down in flakes, cans rocketing through the air over cannoncrackers, rattling windows until a cruiser idled by, its red light flashing like a Roman candle.
Cutaneous sodium lauryl sulphate irritation potential: age and regional variability (1990)

To investigate differences in response to irritation according to age and site seven young-adult and eight elderly females were exposed to 0.25% sodium lauryl sulphate (SLS) under patch-test occlusion for 24 h. Ten anatomical regions were tested: forehead, upper arm, volar and dorsal forearm, postauricular, palm, abdomen, upper back, thigh, and ankle. The skin responses were evaluated 24 h post-patch removal by visual scoring and by transepidermal water loss measurements (TEWL). Non-treated symmetrical anatomical regions served as controls. SLS induced a mild erythematous reaction on most anatomical regions except the palm and TEWL was significantly increased as compared with controls. The elderly group demonstrated significantly less susceptibility to SLS-induced irritation for most regions of the body as indicated by visual scores and TEWL measurements. In addition, evaluation of the stratum corneum water content following SLS irritation demonstrated lower responses in the old age group for most regions. The thigh had the highest reactivity and the palm the lowest, in both age groups. These data suggest that young adult skin is more sensitive to SLS than old skin and that SLS irritation varies considerably with respect to region. Moreover, objective TEWL measurements seem to be a better indicator of irritant susceptibility, especially in the elderly, than clinical evaluation by visual scoring.
The Puzzle of Santamaria's Politicization of Catholic Movements (2005)

In 1954–55 the Australian Labor Party suffered a devastating split which shaped politics in this country for a generation. A traumatic event in the lives of many Australians, the Split not only tore apart former political allies and trade unionists but divided Catholic from Catholic, and friend from friend, and even rent individual families. 
Fifty years on, this chapter examines the perspective of the role played by B. A. Santamaria.
Synthesis of Germanium Oxide Nanoparticles in Low-Pressure Premixed Flames (2004)

Germanium oxide (GeOx) nanoparticles in the size range from 1 nm to 5 nm were synthesized in a low-pressure premixed H2/O2/Ar flat flame of 30 mbar. The premixed flame was doped with different amounts of tetramethyl germanium (Ge(CH3)4) ranging from 250 ppm to 2000 ppm. The influence of process parameters such as the amount of oxygen in the reaction gas, the condensation and reaction time, standoff, and precursor concentration with respect to growth of germanium oxide particles were investigated. The particles formed were analyzed in situ according to their mass and charge with a particle mass spectrometer. The specific surface area was determined ex situ by the BET method. The crystal form and chemical composition of produced nanopowders were characterized by EDX analysis and X-ray diffraction measurements.
Detection of Pesticide Residues on Individual Particles (2002)

An aerosol time-of-flight mass spectrometer (ATOFMS) is used to analyze the size and composition of individual particles containing pesticides. Pesticide residues are found in the atmosphere as a result of spray drift, volatilization, and suspension of coated soils. The ability of the ATOFMS to identify the presence of these contaminants on individual particles is assessed for particles created from pure solutions of several commonly used pesticides, as well as pesticides mixed with an organic matrix, and coated on soils. The common names of the pesticides studied are 2,4-D, atrazine, chlorpyrifos, malathion, permethrin, and propoxur. Analysis of the mass spectra produced by single- and two-step laser desorption/ionization of pesticide-containing particles allows for identification of peaks that can be used for detection of pesticide residues in the ambient aerosol. The identified marker peaks are used to approximate detection limits for the pesticides applied to soils, which are on the order of a fraction of a monolayer for individual particles. Results suggest that this technique may be useful for studying the real-time partitioning and distribution of pesticides in the atmosphere immediately following application in agricultural regions.
Supplemental Table S3 from Activity of PXD101, a histone deacetylase inhibitor, in preclinical ovarian cancer studies (2023)

Supplemental Table S3 from Activity of PXD101, a histone deacetylase inhibitor, in preclinical ovarian cancer studies
3,3‘-Bis(trisarylsilyl)-Substituted Binaphtholate Rare Earth Metal Catalysts for Asymmetric Hydroamination (2006)

Chiral 3,3'-bis(trisarylsilyl)-substituted binaphtholate rare earth metal complexes (R)-[Ln{Binol-SiAr3}(o-C6H4CH2NMe2)(Me2NCH2Ph)] (Ln = Sc, Lu, Y; Binol-SiAr3 = 3,3'-bis(trisarylsilyl)-2,2'-dihydroxy-1,1'-binaphthyl; Ar = Ph (2-Ln), 3,5-xylyl (3-Ln)) and (R)-[La{Binol-Si(3,5-xylyl)3}{E(SiMe3)2}(THF)2] (E = CH (4a), N (4b)) are accessible via facile arene, alkane, and amine elimination. They are efficient catalysts for the asymmetric hydroamination/cyclization of aminoalkenes, giving TOF of up to 840 h(-1) at 25 degrees C for 2,2-diphenyl-pent-4-enylamine (5c) using (R)-2-Y. Enantioselectivities of up to 95% ee were achieved in the cyclization of 5c with (R)-2-Sc. The reactions show apparently zero-order rate dependence on substrate concentration and first-order rate dependence on catalyst concentration, but rates depend on total amine concentrations. Activation parameters for the cyclization of pent-4-enylamine using (R)-2-Y (deltaH(S)(double dagger) = 57.4(0.8) kJ mol(-1) and deltaS(S)(double dagger) = -102(3) J K(-1) mol(-1); deltaH(R)(double dagger) = 61.5(0.7) kJ mol(-1) and deltaS(R)(double dagger) = -103(3) J K(-1) mol(-1)) indicate a highly organized transition state. The binaphtholate catalysts were also applied to the kinetic resolution of chiral alpha-substituted aminoalkenes with resolution factors f of up to 19. The 2,5-disubstituted aminopentenes were formed in 7:1 to > or = 50:1 trans diastereoselectivity, depending on the size of the alpha-substituent of the aminoalkene. Rate studies with (S)-1-phenyl-pent-4-enylamine ((S)-15e) gave the activation parameters for the matching (deltaH(double dagger) = 52.2(2.8) kJ mol(-1), deltaS(double dagger) = -127(8) J K(-1) mol(-1) using (S)-2-Y) and mismatching (deltaH(double dagger) = 57.7(1.3) kJ mol(-1), deltaS(double dagger) = -126(4) J K(-1) mol(-1) using (R)-2-Y) substrate/catalyst combination. The absolute configuration of the Mosher amide of (2S)-2-methyl-4,4-diphenyl-pyrrolidine and (2R)-methyl-(5S)-phenyl-pyrrolidinium chloride, prepared from (S)-15e, were determined by crystallographic analysis. Catalyst (R)-4a showed activity in the anti-Markovnikov addition of n-propylamine to styrene.
Simplified sigmoidal curve fitting for a 6 MV FFF photon beam of Halcyon to determine the field size for beam commissioning and quality assurance (2020)

Abstract Background : An O-ring gantry-type linear accelerator (Linac) with a 6 MV flattening filter-free (FFF) photon beam, Halcyon, includes a reference beam containing the representative information regarding the percent depth dose, profile, output factor, etc. for commissioning and quality assurance. However, because it does not provide the information of the field size, we proposed a method to determine all field sizes according to all depths for radiation therapy using simplified sigmoidal curve fitting (SCF). Methods : After a mathematical definition of the SCF using four coefficients, the defined curves were fitted to both the reference and measured data. For a high agreement between the fitting curve and the profiles in each data set, the field sizes were determined by identifying the maximum point along the third derivative of the fitting curve. The curve fitting included the field sizes for beam profiles of 2 × 2, 4 × 4, 6 × 6, 8 × 8, 10 × 10, 20 × 20 and 28 × 28 cm 2 as a function of depth (at 1.3, 5, 10, 20 cm). The results of the field size from the reference data were compared with the results in the measured data using the same condition. Results : All fitting curves show values of goodness of fit, R 2 , better than 0.99. The differences in the field size between the reference data and the measured data were within the range of 0 to 0.2 cm. The lowest difference in the field sizes at a depth of 10 cm, which is a surface-to-axis distance, was reported. Conclusion : The application of the SCF has been proven to accurately obtain the field size of the preconfigured reference and of the measured FFF photon beam data for the Halcyon system. The current work can be useful for beam commissioning as a counte-rcheck methodology to determine the field size from the reference data in the treatment planning system of a newly installed Halcyon system and for the routine quality assurance to ascertain the correctness of field sizes clinically used with the Halcyon system.
ChemInform Abstract: Sulfonation of Perfluorovinylamines: Synthesis of the First Examples of Nitrogen‐Substituted β‐Fluorosultones. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
New Dopamine D3-Selective Receptor Ligands Containing a 6-Methoxy-1,2,3,4-tetrahydroisoquinolin-7-ol Motif (2018)

A series of analogues featuring a 6-methoxy-1,2,3,4-tetrahydroisoquinolin-7-ol unit as the arylamine "head" group of a classical D3 antagonist core structure were synthesized and evaluated for affinity at dopamine D1, D2, and D3 receptors (D1R, D2R, D3R). The compounds generally displayed strong affinity for D3R with very good D3R selectivity. Docking studies at D2R and D3R crystal structures revealed that the molecules are oriented such that their arylamine units are positioned in the orthosteric binding pocket of D3R, with the arylamide "tail" units residing in the secondary binding pocket. Hydrogen bonding between Ser 182 and Tyr 365 at D3R stabilize extracellular loop 2 (ECL2), which in turn contributes to ligand binding by interacting with the "tail" units of the ligands in the secondary binding pocket. Similar interactions between ECL2 and the "tail" units were absent at D2R due to different positioning of the D2R loop region. The presence of multiple H-bonds with the phenol moiety of the headgroup of <b>7</b> and Ser192 accounts for its stronger D3R affinity as compared to the 6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline-containing analogue <b>8</b>.