gebhart/patrepeval huggingface dataset:
Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN (2018)

The small molecules thalidomide, lenalidomide, and pomalidomide induce the ubiquitination and proteasomal degradation of the transcription factors Ikaros (IKZF1) and Aiolos (IKZF3) by recruiting a Cys<sub>2</sub>-His<sub>2</sub> (C2H2) zinc finger domain to Cereblon (CRBN), the substrate receptor of the CRL4<sup>CRBN</sup> E3 ubiquitin ligase. We screened the human C2H2 zinc finger proteome for degradation in the presence of thalidomide analogs, identifying 11 zinc finger degrons. Structural and functional characterization of the C2H2 zinc finger degrons demonstrates how diverse zinc finger domains bind the permissive drug-CRBN interface. Computational zinc finger docking and biochemical analysis predict that more than 150 zinc fingers bind the drug-CRBN complex in vitro, and we show that selective zinc finger degradation can be achieved through compound modifications. Our results provide a rationale for therapeutically targeting transcription factors that were previously considered undruggable.
Kernel Methods and Multi-layer Perceptrons Learn Linear Models in High Dimensions (2022)

Empirical observation of high dimensional phenomena, such as the double descent behaviour, has attracted a lot of interest in understanding classical techniques such as kernel methods, and their implications to explain generalization properties of neural networks. Many recent works analyze such models in a certain high-dimensional regime where the covariates are independent and the number of samples and the number of covariates grow at a fixed ratio (i.e. proportional asymptotics). In this work we show that for a large class of kernels, including the neural tangent kernel of fully connected networks, kernel methods can only perform as well as linear models in this regime. More surprisingly, when the data is generated by a kernel model where the relationship between input and the response could be very nonlinear, we show that linear models are in fact optimal, i.e. linear models achieve the minimum risk among all models, linear or nonlinear. These results suggest that more complex models for the data other than independent features are needed for high-dimensional analysis.
Intratumoral administration of a 1,2‐dimyristyloxypropyl‐3‐ dimethylhydroxyethyl ammonium bromide/dioleoylphosphatidylethanolamine formulation of the human interleukin‐2 gene in the treatment of metastatic renal cell carcinoma (2004)

Immunotherapy with intratumorally administered Leuvectin is safe and can lead to durable objective responses in patients with metastatic renal cell carcinoma.
Casper : a Cached Architecture Supporting Persistence (1992)

Persistent object systems greatly simplify programming tasks since they hide the traditional distinction between short-term and long-term storage from the applications programmer. As a result, the programmer can operate at a level of abstraction in which short-term and long-term data are treated uniformly. It is important that such a persistent system be capable of being used concurrently; such concurrent usage may arise because of parallel process facilities in the programming language concerned, or because of multiple users of the same persistent store. Concurrent access has not been satisfactorily supported in existing persistent store implementations and a number of significant research issues remain to be investigated. This paper describes an architecture that supports concurrent access to a shared persistent object store. The persistent distributed architecture represented by our system exploits a number of the facilities provided by the Mach distributed operating system 1. Intro...
Motion Estimation Using a Spherical Camera (2004)

Motion estimation using a spherical camera Robotic navigation algorithms increasingly make use of the panoramic field of view provided by omnidirectional images to assist with localization tasks. Since the images taken by a particular class of omnidirectional sensors can be mapped to the sphere, the problem of attitude estimation arising from 3D motions of the camera can be treated as a problem of estimating the camera motion between spherical images. This problem has traditionally been solved by tracking points or features between images. However, there are many natural scenes where the features cannot be tracked with confidence. We present an algorithm that uses image features to estimate ego-motion without explicitly searching for correspondences. We formulate the problem as a correlation of functions defined on the product of spheres S2 × S2 which are acted upon by elements of the direct product group SO(3) × SO(3). We efficiently compute this correlation and obtain our solution using the spectral information of functions in S2 × S2.
Geometrical and Electronic Structure of the Pt7 Cluster: A Density Functional Study. (2004)

We present a study on the structural and electronic properties of the Pt&lt;sub&gt;7&lt;/sub&gt; cluster by using density functional\ntheory within the generalized gradient approximation for the exchange and correlation. The structures, relative\nstabilities, and vibrational frequencies of various isomers are calculated and compared with the well-studied\nAu&lt;sub&gt;7&lt;/sub&gt; cluster. The ground state of the Pt&lt;sub&gt;7&lt;/sub&gt; cluster favors a three-dimensional geometrytwo-dimensional local\nminima are not locatedwhereas for its neighbor, gold heptamer, a two-dimensional geometry is favored.\nThe most stable isomer of Au&lt;sub&gt;7&lt;/sub&gt; is found to be an edge-capped rhombus structure and an edge-capped tetrahedron\nstructure is found to be the most stable three-dimensional local minimum. The ground state of the Pt&lt;sub&gt;7&lt;/sub&gt; cluster\nis found to be a coupled tetragonal pyramid structure with the quintet state in contrast to a pentagonal bipyramid\nstructure obtained by semiempirical molecular dynamics calculation. The natural orbital analysis shows that\nthe overall charge transfer is from 6s to 5d orbitals in the Pt&lt;sub&gt;7&lt;/sub&gt; cluster, whereas in Au&lt;sub&gt;7&lt;/sub&gt; cluster it is from 5d to\n6s. The molecular orbital picture shows that the bonding orbitals are due to the hybridization between 5d and\n6s molecular orbitals in Pt&lt;sub&gt;7&lt;/sub&gt; cluster, and the nonbonding and antibonding orbitals lie close to the highest\noccupied molecular orbital. This may be compared with the Au&lt;sub&gt;7&lt;/sub&gt; electronic structure, where the nonbonding\nand antibonding orbitals mainly consists of 5d6s hybridized molecular orbitals.
The Women's EMPOWER Survey: Women's Knowledge and Awareness of Treatment Options for Vulvar and Vaginal Atrophy Remains Inadequate (2017)

The Women's EMPOWER survey demonstrates and reinforces that even with multimedia marketing and educational strategies in the years after other major VVA surveys, minimal progress has been made toward increasing women's awareness of, knowledge about, or understanding of VVA. Based on these data, a focus on initiating discussions and education with postmenopausal women so that they better comprehend VVA as a chronic progressive medical condition (not just aging), the symptoms associated with VVA, and the benefit-risk profile regarding treatment options is warranted. Krychman M, Graham S, Bernick B, et al. The Women's EMPOWER Survey: Women's Knowledge and Awareness of Treatment Options for Vulvar and Vaginal Atrophy Remains Inadequate. J Sex Med 2017;14:425-433.
Cholinesterase Inhibitory Constituents from Onosma hispida. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
“Unmasking” of Human Lymphoid Cell Heteroantigens by Neuraminidase Treatment (1972)

Treatment of human lymphoid tissue-culture cells and fresh human lymphocytes with Vibrio cholerae neuraminidase (NASE) under conditions that removed 65% of the cell-surface sialic acid uncovered surface structures capable of reacting with substances, probably antibodies, in normal rabbit serum. Three to five times more of these surface components were detectable on NASE-treated cultured lymphoid cells than on untreated cells. The antibody in normal rabbit serum could be removed by absorption with NASE-treated lymphoid cells in the presence of ethylene-diamine tetraethylacetate without lowering complement levels.
Ontwikkeling van analogen van calcitriol met opgedrongen zijketenoriëntatie. (2008)

Calcitriol (1,25-dihydroxy-vitamine D3) is het hormonaal actieve metaboliet van vitamine D3. Naast het regelen van het calciummetabolisme, stimuleert ze ook differentiatie en inhibeert ze de proliferatie van verscheidene celtypes. Deze laatste eigenschappen leidden tot een verhoogde interesse in vitamine D3 met betrekking tot haar potentieel om gebruikt te worden in de behandeling tegen welbepaalde carcinomen, huidziekten, etc. . De vereiste dosis geeft echter aanleiding tot verstoring van de calciumhomeostase. Om deze nevenwerkingen te minimaliseren is er een zoektocht ontstaan naar de ontwikkeling van analogen. Bij dit onderzoek is de kennis omtrent de structuur-functierelatie van groot belang. Dit doctoraatsonderzoek trachtte de invloed van de oriëntatie van de zijketen op de biologische activiteit van de analogen op te helderen. Hiertoe worden CD-ring gemodificeerde analogen ontwikkeld. Door dit bicyclisch CD-ringsysteem in calcitriol te vervangen door één 6-ring en door aanbrenging van twee strategische methylgroepen, wordt aan de zijketen een bepaalde oriëntatie opgedrongen. Deze conformationele beperking maakt de ontrafeling van de structuur-functierelatie mogelijk. De beoogde analogen kunnen in drie reeksen opgedeeld worden naar gelang de positie van de twee aangebrachte methylgroepen. In onze onderzoeksgroep werd één van deze reeksen reeds onderzocht, nl. de C13,C16-dimethyl-gesubstitueerde analogen. In het kader van dit doctoraatswerk was het de bedoeling deze familie te vervolledigen met de overige twee reeksen: C13,C20 –en C16,C20 dimethyl-gesubstitueerde analogen. In verband met de biologische testen werd samengewerkt met Prof. dr. R. Bouillon en Prof. dr. A. Verstuyf van het laboratorium voor experimentele geneeskunde & endocrinologie te Leuven (Katholieke Universiteit Leuven). Deze resultaten zijn van het grootste belang in verband met het achterhalen van de structuur-functierelatie. Door deze goede samenwerking was het mogelijk de vooropgestelde hypothese te bevestigen en zo extra informatie over de structuur-activiteitsrelatie te bekomen.
Crystalline poly (3‐methyl butene‐1) obtained by cationic polymerisation (1962)

Abstract The polymerization of 3‐methyl butene‐1 was studied using AlCl 3 solutions at low working temperatures. A crystalline high polymer was obtained at −130°C. Physical characterization of this product is reported. The X‐ray diffraction pattern of this new crystalline polymer is different from that of isotactic poly(3‐methyl butene‐1) obtained with metal alkyl coordination catalyst. A tentative structure is discussed.
Transportable hyperpolarized metabolites (2017)

Nuclear spin hyperpolarization of <sup>13</sup>C-labelled metabolites by dissolution dynamic nuclear polarization can enhance the NMR signals of metabolites by several orders of magnitude, which has enabled in vivo metabolic imaging by MRI. However, because of the short lifetime of the hyperpolarized magnetization (typically <1 min), the polarization process must be carried out close to the point of use. Here we introduce a concept that markedly extends hyperpolarization lifetimes and enables the transportation of hyperpolarized metabolites. The hyperpolarized sample can thus be removed from the polarizer and stored or transported for use at remote MRI or NMR sites. We show that hyperpolarization in alanine and glycine survives 16 h storage and transport, maintaining overall polarization enhancements of up to three orders of magnitude.
Prioritized access arbitration to shared resources on integrated software systems in multicore environments (2012)

In the past few decades the extent of automotive software based functionalities has grown continuously. More recently this has applied in particular to automotive infotainment systems, which are available for all classifications of cars nowadays. A change in that process of growth is not foreseeable. Concurrently, formerly distributed functionalities are now integrated into a common hardware platform. The demand for the computational power of future infotainment systems will be countered with multicore hardware platforms. These allow the parallel computation of a rising number of independently developed software components. This constitutes both new opportunities and challenges. One of the latter is to integrate software components with different temporal requirements on a common hardware platform, which compete for shared system resources. In the following an approach is presented, that supports the development and integration process by use of static priorities to manage the access to shared resources from in-parallel executed components. The applicability is demonstrated through the use of a prototypical implementation.
Novel Functions of Prototype Foamy Virus Gag Glycine- Arginine-Rich Boxes in Reverse Transcription and Particle Morphogenesis (2010)

Prototype foamy virus (PFV) Gag lacks the characteristic orthoretroviral Cys-His motifs that are essential for various steps of the orthoretroviral replication cycle, such as RNA packaging, reverse transcription, infectivity, integration, and viral assembly. Instead, it contains three glycine-arginine-rich boxes (GR boxes) in its C terminus that putatively represent a functional equivalent. We used a four-plasmid replication-deficient PFV vector system, with uncoupled RNA genome packaging and structural protein translation, to analyze the effects of deletion and various substitution mutations within each GR box on particle release, particle-associated protein composition, RNA packaging, DNA content, infectivity, particle morphology, and intracellular localization. The degree of viral particle release by all mutants was similar to that of the wild type. Only minimal effects on Pol encapsidation, exogenous reverse transcriptase (RT) activity, and genomic viral RNA packaging were observed. In contrast, particle-associated DNA content and infectivity were drastically reduced for all deletion mutants and were undetectable for all alanine substitution mutants. Furthermore, GR box I mutants had significant changes in particle morphology, and GR box II mutants lacked the typical nuclear localization pattern of PFV Gag. Finally, it could be shown that GR boxes I and III, but not GR box II, can functionally complement each other. It therefore appears that, similar to the orthoretroviral Cys-His motifs, the PFV Gag GR boxes are important for RNA encapsidation, genome reverse transcription, and virion infectivity as well as for particle morphogenesis.
BCG vaccination improves DTaP immune responses in mice and is associated with lower pertussis incidence in ecological epidemiological studies (2021)

This work was supported by the Ministry of "Economía y Competitividad"; European Commission H2020 program, "Gobierno de Aragón"; CIBERES; "Fundação Butantan"; Instituto de Salud Carlos III and "Fondo FEDER".
New Selective Metal‐Free Oxidations of Primary Alcohols by HNO3 or HNO3 and O2, Catalyzed by Br2. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Sintering (2019)

Sintering or densification is an irreversible thermodynamic phenomenon to convert unstable packed powder having excess free energy to stable sintered agglomerates. The sintering phenomenon involves the fusion of particles, volume reduction, decrease in porosity, and increase in grain size. Sintering kinetics have been studied by many investigators from both experimental and theoretical points of view. Crystalline particles usually contain dislocations at the surface, created while they were produced. These dislocations are moved or recovered at an initial stage of sintering to form a neck at the contact point of particles. The principal mass transfer depends on the composition of the material, sintering conditions, and the sintering step. Sintering mechanisms of amorphous materials such as glass and resine are usually controlled by plastic flow. Sintering is an important process to determine the size distribution of nanoparticles synthesized via building-up process. The sintering process of mixed materials depends primarily on wettability between particles of different types.
Techno-economic Feasibility of a STATCOM with Battery Energy Storage for the Offshore Wind Power Plants (2019)

An integrated power converter and battery energy storage system (BESS) has been proposed to meet multi-functional requirements for active and reactive power control and harmonic filtering in large wind power plants (WPPs).<br/>In this paper, first a high-voltage, high MVA static synchronous compensator (STATCOM) based on modular multilevel converters (MMCs) with an integrated BESS system is analyzed from the techno-economic feasibility point of view. Economic benefits of the additional functionalities are quantified based on available market data (and trends) for ancillary services or the least cost option for the mandatory compliance with the relevant Grid Code. Afterwards, its efficacy in achieving different ancillary services to the WPP and to the grid is qualitatively discussed. Their significance to the operation and control of offshore WPPs and their relevance for the market and the grid are evaluated.
Synthesis of Spherical Graphitized Carbon Powder with Homolytic Crystals by a Dry Granulation Process (2014)

太陽光発電用シリコンウエハーの製造に用いるるつぼ材などの特殊炭素材料やリチウム電池用の負極材料など，さまざまな分野で使用されている炭素材料は，強度や導電性が優れており，2,000°Cを超える非酸化性雰囲気での強度部材として，唯一選択しうる材料である．また，特殊炭素材料の分野では，成形体にしたときの各特性の方向依存がない，等方性の特徴を持つ炭素材が求められている．本研究では，石油系の生コークス原料に着目し，乾式造粒技術を用いることで炭素材料の球形化について検討した．その結果，高温での黒鉛化処理を行っても球形粒子形状を維持し，等方性結晶の特性を持つ球形黒鉛粉末が得られた．
Expression of placental leucine aminopeptidase/oxytocinase in neuronal cells and its action on neuronal peptides (2001)

The placental leucine aminopeptidase (P-LAP)/oxytocinase whose serum level increases with gestation is thought to contribute to the maintenance of normal pregnancy. P-LAP mRNAs are expressed in various tissues other than the placenta. In this study, we identified P-LAP protein in the brain. In contrast with the placenta where a significant portion of P-LAP is released, the enzyme was localized in the membrane fraction in brain and PC12 cells and no soluble form of the enzyme was detected. When PC12 cells were differentiated into neuronal cells by nerve growth factor (NGF), a significant increase in the expression level of P-LAP in the cell was observed. As in the case of insulin treatment of 3T3-L1 adipocytes, treatment of PC12 cells with forskolin caused the translocation of the enzyme from intracellular vesicle to the cell surface plasma membrane. In addition, P-LAP was shown to degrade several bioactive neuropeptides such as Met-enkephalin and dynorphin A (1-8). These results suggest that P-LAP plays an important role in the regulation of neuronal cell function in the brain.
Prediction of carboxyhemoglobin concentration from transient carbon monoxide exposure. (1977)

The mathematical model of Coburn, Forster, and Kane (2) was investigated for use in estimating carboxyhemoglobin concentrations resulting from transient carbon monoxide exposures. The model proved useful in estimating the probable pattern of carbon monoxide exposures in two fatal cases. In each circumstance, using the predictive capabilities of the model in the reconstruction of events, the obvious source of exposure could be absolved.
The dynamic landscape of fission yeast meiosis alternative-splice isoforms (2016)

Abstract Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here we exploit a single-molecule long-read sequencing technique and develop an open-source software program called SpliceHunter, to characterize the transcriptome in the meiosis of fission yeast. We reveal 17017 alternative splicing events in 19741 novel isoforms at different stages of meiosis, including antisense and read-through transcripts. Intron retention is the major type of alternative splicing, followed by “alternate intron in exon”. 887 novel transcription units are detected; 60 of the predicted proteins show homology in other species and form theoretical stable structures. We compare the dynamics of novel isoforms based on the number of supporting full-length reads with those of annotated isoforms and explore the translational capacity and quality of novel isoforms. The evaluation of these factors indicates that the majority of novel isoforms are unlikely to be both condition-specific and translatable but the possibility of functional novel isoforms is not excluded. Moreover, the co-option of these unusual transcripts into newly born genes seems likely. Together, this study highlights the diversity and dynamics at the isoform level in the sexual development of fission yeast.
Robust CON-type zeolite nanocatalyst in methanol-to-olefins reaction: downsizing, recrystallisation and defect-healing treatments toward prolonged lifetime (2022)

A CON-type zeolite underwent bead-milling, recrystallisation and defect-healing treatments to yield highly crystalline zeolite nanoparticles, showing prolonged lifetime in MTO reactions.
Co-design for Tunability of a Bulk Acoustic Wave Filters with 65nm CMOS Switch (2011)

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