gebhart/patrepeval huggingface dataset:
Clickable Analogue of Cerulenin as Chemical Probe to Explore Protein Palmitoylation (2014)

Dynamic palmitoylation is an important post-translational modification regulating protein localization, trafficking, and signaling activities. The Asp-His-His-Cys (DHHC) domain containing enzymes are evolutionarily conserved palmitoyl acyltransferases (PATs) mediating diverse protein S-palmitoylation. Cerulenin is a natural product inhibitor of fatty acid biosynthesis and protein palmitoylation, through irreversible alkylation of the cysteine residues in the enzymes. Here, we report the synthesis and characterization of a "clickable" and long alkyl chain analogue of cerulenin as a chemical probe to investigate its cellular targets and to label and profile PATs in vitro and in live cells. Our results showed that the probe could stably label the DHHC-family PATs and enable mass spectrometry studies of PATs and other target proteins in the cellular proteome. Such probe provides a new chemical tool to dissect the functions of palmitoylating enzymes in cell signaling and diseases and reveals new cellular targets of the natural product cerulenin.
Komplexone VI. Neue einfache Titriermethoden zur Bestimmung der Wasserhärte (1946)

Abstract Es werden vier neue Methoden zur bestimmung der Wasser‐härte beschrieben. Besonders empfehlenswert sind die Methoden A und C, von denen die eine die Kalkhärte und die andere die Gesamthärte liefert. Diese beiden Methoden sind einfacher als diejenigen von Wartha ‐ Pfeifer und Blacher , liefern genauere Resultate und beanspruchen für die Durchführung weniger Zeig. Die Methode B ist etwas weniger genau und nur anwendbar, wenn kein Magnesiumion vorliegt. Für die vierte Methode D, die ebenfalls gute Resultate liefert, ist das notwendige Komplexon im Handel nicht erhältlich.
Isothiazoles II: 5‐chloro‐4‐isothiazolin‐3‐ones (1971)

Abstract Quantitative gas chromatographic analysis of the 3‐hydroxyisothiazole product distributions formed in the chlorine induced cyclization of 3,3′ ‐dithiodipropionamide and 3‐mercaptopropion‐arnide has led to reaction conditions which yield respectively 3‐hydroxyisothiazole, 5‐chloro‐3‐hydroxyisothiazole, or 4,5‐dichloro‐3‐hydroxyisothiazole as the predominant product. The 4‐chloro analog was found in only small quantity. Similar glc analysis of the cyclization of N,N ′‐dimethyl‐3,3′‐dilhiodipropionamide showed 5‐ehloro‐2‐methyl‐4‐isothiazolin‐3‐one to he the major 4‐isothiazolin‐3‐one product under varied conditions. Also, a representative series of 5‐chloro‐2‐subtiuted‐4‐isohiazolin‐3‐oncs were prepared under extrapolated reaction conditions.
Snf1 Protein Kinase Regulates Phosphorylation of the Mig1 Repressor in <i>Saccharomyces cerevisiae</i> (1998)

In glucose-grown cells, the Mig1 DNA-binding protein recruits the Ssn6-Tup1 corepressor to glucose-repressed promoters in the yeast Saccharomyces cerevisiae. Previous work showed that Mig1 is differentially phosphorylated in response to glucose. Here we examine the role of Mig1 in regulating repression and the role of the Snf1 protein kinase in regulating Mig1 function. Immunoblot analysis of Mig1 protein from a snf1 mutant showed that Snf1 is required for the phosphorylation of Mig1; moreover, hxk2 and reg1 mutations, which relieve glucose inhibition of Snf1, correspondingly affect phosphorylation of Mig1. We show that Snf1 and Mig1 interact in the two-hybrid system and also coimmunoprecipitate from cell extracts, indicating that the two proteins interact in vivo. In immune complex assays of Snf1, coprecipitating Mig1 is phosphorylated in a Snf1-dependent reaction. Mutation of four putative Snf1 recognition sites in Mig1 eliminated most of the differential phosphorylation of Mig1 in response to glucose in vivo and improved the two-hybrid interaction with Snf1. These studies, together with previous genetic findings, indicate that the Snf1 protein kinase regulates phosphorylation of Mig1 in response to glucose.
Wafer Topography-Aware Optical Proximity Correction (2006)

Depth of focus is the major contributor to lithographic process margin. One of the major causes of focus variation is imperfect planarization of fabrication layers. Presently, optical proximity correction (OPC) methods are oblivious to the predictable nature of focus variation arising from wafer topography. As a result, designers suffer from manufacturing yield loss as well as loss of design quality through unnecessary guardbanding. In this paper, the authors propose a novel flow and method to drive OPC with a topography map of the layout that is generated by chemical-mechanical polishing simulation. The wafer topography variations result in local defocus, which the authors explicitly model in the OPC insertion and verification flows. In addition, a novel topography-aware optical rule check to validate the quality of result of OPC for a given topography is presented. The experimental validation in this paper uses simulation-based experiments with 90-nm foundry libraries and industry-strength OPC and scattering bar recipes. It is found that the proposed topography-aware OPC (TOPC) can yield up to 67% reduction in edge placement errors. TOPC achieves up to 72% reduction in worst case printability with little increase in data volume and OPC runtime. The electrical impact of the proposed TOPC method is investigated. The results show that TOPC can significantly reduce timing uncertainty in addition to process variation
Input Technologies and Techniques (2007)

Input devices sense physical properties of people, places, or things. Yet any treatment of input devices without regard to the corresponding visual feedback is like trying to use a pen without paper. Small-screen devices with integrated sensors underscore the indivisibility of input and output. This chapter treats input technologies at the level of interaction techniques, which provide a way for users to accomplish tasks by combining input with appropriate feedback. An interaction designer must consider the physical sensor, the feedback presented to the user, the ergonomic and industrial design of the device, and the interplay between all of the interaction techniques supported by a system. This chapter enumerates properties of input devices and provides examples of how these properties apply to common pointing devices as well as mobile devices with touch or pen input. We will discuss how to use input signals in applications, and cover models and theories that help to evaluate interaction techniques and reason about design options. We will also discuss discrete symbolic entry, including mobile and keyboard-based text entry. The chapter concludes with some thoughts about future trends.
Differences in the metabolism of the antitumour agents amsacrine and its derivative CI-921 in rat and mouse (1992)

1. Rats and mice were treated with the antitumour agent CI-921 (I), and parent compound amsacrine, with all biliary metabolites being analysed. 2. In both rat and mouse the major biliary metabolites of amsacrine are the 5'- and 6'-glutathione (GSH) conjugates, with no C9-GSH conjugate being detected. 3. 5'- and 6'-GSH conjugates of I are also formed in both species. However, two additional products were detected and their structures confirmed by liquid secondary ion mass spectrometry and 1H-n.m.r. spectrometry, and by comparison with synthetic standards. 4. Additional metabolites of I are the C9-GSH conjugate and the 4-hydroxymethyl derivative which, either as the aglycone or glucuronide, is the predominant product in rat bile (comprising 56% of the dose eliminated over 3.5 h). 5. Relative amounts of the C9-GSH conjugate to the 5'- and 6'-GSH conjugates to the 4-hydroxymethyl derivatives, were 24:65:10 in mouse bile and 2:8:90 in rat bile. 6. These differences indicate first, likely enzyme involvement in the formation of the C9-GSH conjugate of I, and second, in comparison with amsacrine, alternative pathways which may decrease formation of the reactive quinone diimine intermediate of I and consequent hepatotoxicity.
Development of neutral and bifunctional radiopharmaceuticals using 62Cu-dithiosemicarbazone (DTS) chelate - Basic studies on 64Cu chelates. (1986)

Recent plausibility of generator produced 62Cu, a positron emitter is attracting the interest of those working in the development of bifunctional radiopharmaceuticals (BR). In our development of bifunctional radiopharmaceuticals containing a neutral dithiosemicarbazone (DTS) metal chelate, tertiary (p-DPA-DTS) and quaternary (p-TPA-DTS) amino DTS derivatives were synthesized. As for the basic understanding of their divalent metal (Cu2+, Ni2+, Zn2+) complex formation and stability, spectrophotometrical studies were carried out, comparatively with KTS. Upon assessment of preferential behavior of Cu chelate, the radiolabeled 64Cu-DTS derivative chelates were tested in mice, and potential use with 62Cu in positron nuclear medicine is discussed.
Flow-Controlled Vertical Deposition Method for the Fabrication of Photonic Crystals (2003)

10.1021/la035686y
The effects of probiotic supplementation on lean body mass, strength, and power, and health indicators in resistance trained males: a pilot study (2014)

Background While growing evidence suggests beneficial effects of probiotics on the gut-brain-axis, only a limited number of studies have investigated the impact of gut microbiota modulation on muscle physiology (gut-muscle-axis). The probiotic BC30 (Ganeden Biotech Inc., Maryfield Heights, OH) has been shown to increase protein absorption and the anabolic potential of a respective protein source has been directly linked to peak plasma leucine levels. Postworkout administration of slow digesting proteins such as casein show inferior results on muscle protein synthesis in comparison to fast absorbed proteins such as whey. Thus, the purpose of this investigation was to determine if the co-administration of a probiotic with a slow digested protein has a beneficial effect on body composition, performance, and measures of perceived health. Methods 10 healthy resistance-trained individuals volunteered to participate in this study (mean+/-SD; age: 22.0 ± 2.4 yr; height: 181.8 ± 4.1 cm; weight: 85.6 ± 12.9 kg). Subjects were randomly assigned to consume either 20g of casein (Control = CON) or 20g of casein plus probiotic (500M BC30, =BC30) twice daily. Subjects were instructed to consume one serving in the morning upon waking while the second serving was consumed after training or before bed on non-training days. With assistance from a dietician, macronutrients were controlled to 50% carbohydrate, 25% protein, and 25% fat between groups using the Mifflin-St Jeor formula. Subjects performed full body workouts 4-times per week for 8 weeks consisting of hypertrophy (8-12 RM loads and 60 seconds rest), and strength (1-5 RM loads with 3-5 minutes rest) under supervision of the researchers in order to ensure compliance. Body composition (Dual X-Ray Absorptiometry; DXA), quadriceps thickness (ultrasound), peak power (Monark Wingate Cycle), vertical jump power (Tendo unit), 1-RM bench press, and 1-RM leg press were measured at baseline and after the eighth week of supplementation. Perceived GI health (GSRS) was measured weekly and upper respiratory health (WURSS-21) daily. Consent to publish the results was obtained from all participants.
In vivo fate-tracing studies using the Scl stem cell enhancer: embryonic hematopoietic stem cells significantly contribute to adult hematopoiesis (2004)

Evidence for the lineage relationship between embryonic and adult hematopoietic stem cells (HSCs) in the mouse is primarily indirect. In order to study this relationship in a direct manner, we expressed the tamoxifen-inducible Cre-ER(T) recombinase under the control of the stem cell leukemia (Scl) stem-cell enhancer in transgenic mice (HSC-SCL-Cre-ER(T)). To determine functionality, HSC-SCL-Cre-ER(T) transgenics were bred with Cre reporter mice. Flow cytometric and transplantation studies revealed tamoxifen-dependent recombination occurring in more than 90% of adult long-term HSCs, whereas the targeted proportion within mature progenitor populations was significantly lower. Moreover, the transgene was able to irreversibly tag embryonic HSCs on days 10 and 11 of gestation. These cells contributed to bone marrow hematopoiesis 5 months later. In order to investigate whether the de novo HSC generation is completed during embryogenesis, HSC-SCL-Cre-ER(T)-marked fetal liver cells were transplanted into adult recipients. Strikingly, the proportion of marked cells within the transplanted and the in vivo-remaining HSC compartment was not different, implying that no further HSC generation occurred during late fetal and neonatal stages of development. These data demonstrate for the first time the direct lineage relationship between midgestation embryonic and adult HSCs in the mouse. Additionally, the HSC-SCL-Cre-ER(T) mice will provide a valuable tool to achieve temporally controlled genetic manipulation of HSCs.
A Comprehensive Wellbore/Reservoir Simulator (1989)

ABSTRACT This paper describes a fully implicit, three dimensional thermal numerical model for simulating flow through a porous media and through a wellbore. Darcy's law is used together with conservation of energy and mass to model flow in the porous media. The wellbore simulator is a time dependent, thermal, three-phase, one dimensional model which conserves energy, momentum of all phases and mass. Wellbore grid blocks are embedded in reservoir grid blocks. Variables in the reservoir and wellbore are solved for simultaneously. Many options are included in the wellbore simulator including the ability to model parallel flow in inner tubing and outer annuli and specification of slant angles or other parameters per wellbore grid block. This coupled model is targeted mainly at horizontal well or other applications in which a high degree of dynamic interaction occurs between the wellbore and reservoir.
A case study of file system workload in a large-scale distributed environment (1994)

No abstract available.
The aethereal network on chip after ten years (2010)

The goals for the Æthereal network on silicon, as it was then called, were set in 2000 and its concepts were defined early 2001. Ten years on, what has been achieved? Did we meet the goals, and what is left of the concepts? In this paper we answer those questions, and evaluate different implementations, based on a new performance: cost analysis. We discuss and reflect on our experiences, and conclude with open issues and future directions.
Web-based therapeutic exercise resource center as a treatment for knee osteoarthritis: a prospective cohort pilot study (2014)

This pilot study demonstrated the web-based TERC to be feasible and efficacious in improving clinical outcomes for patients with mild/moderate knee OA and supports future studies to compare TERC to current standard of care, such as educational brochures.
Probabilistic reliability based view synthesis for FTV (2010)

View synthesis using depth maps is an important application in 3D image processing. In this paper, a novel method is proposed for the plausible view synthesis of Free-viewpoint TV (FTV), using two input images and their depth maps. The depth estimation based on stereo matching is known to be error-prone, leading to noticeable artifacts in the synthesized new views. To produce high-quality view synthesis, we introduce a probabilistic framework which constrains the reliability of each pixel of new view by Maximizing Likelihood (ML). The spatial adaptive reliability is provided by incorporating Gamma hyper-prior and the synthesis error approximation. Furthermore, we generate the virtual view by solving a Maximum a Posterior (MAP) problem using graph cuts. We compare the proposed method with other depth based view synthesis approaches on MPEG test sequences. The results show the outperformance of our method both at subjective artifacts reduction and objective PSNR improvement.
Learning-Based Robust Optimization: Procedures and Statistical Guarantees (2020)

Robust optimization (RO) is a common approach to tractably obtain safeguarding solutions for optimization problems with uncertain constraints. In this paper, we study a statistical framework to integrate data into RO based on learning a prediction set using (combinations of) geometric shapes that are compatible with established RO tools and on a simple data-splitting validation step that achieves finite-sample nonparametric statistical guarantees on feasibility. We demonstrate how our required sample size to achieve feasibility at a given confidence level is independent of the dimensions of both the decision space and the probability space governing the stochasticity, and we discuss some approaches to improve the objective performances while maintaining these dimension-free statistical feasibility guarantees. This paper was accepted by Yinyu Ye, optimization.
Superantigens: Bacterial and Viral Proteins that Manipulate the Immune System (1993)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
A Modified Water Fat Separation Algorithm Based on Region Growing (2009)

An efficient algorithm for water fat separation on low field MRI is presented in this paper. Based on the DIXON algorithm, in phase and opposed phase images are acquired by spin echo (SE) sequence. From these images the water only and fat only images can be extracted by the chemical shift principle .The algorithm is region growing based. The modification is proposed on how to process background noises. The pixels of background noises are push into an additional stack which has the lowest priority so as to get a more robust performance. Experiments on low field system show good results.
Risks of radiation-induced cancer at high doses and dose rates (1993)

The Armitage-Doll model of carcinogenesis is fitted to the Japanese bomb survivors with the DS86 dosimetry. It is found to provide an adequate description of solid cancer incidence (but not that of leukaemia) as a function of radiation dose when up to two radiation-affected stages are assumed; the optimal model for solid cancers is one in which there are two radiation-affected stages separated by two additional stages. Leukaemia is best modelled by assuming a single radiation-affected stage. The fit of the Armitage-Doll model is contrasted with that of a less biologically based (relative risk) model which is fitted jointly to the leukaemia data in the Japanese cohort and in the UK spondylitics, as well as to solid cancer data in the Japanese. The literature on exposure to high doses at high dose-rates from therapeutic irradiation is surveyed with a view to determining patterns for variation in risk by age at exposure, time since exposure and evidence for curvilinearity of dose-response. Reductions in relative risk with increasing age at exposure are documented for all cancer types.
Models of Working Memory: An Introduction (1999)

Working memory plays an essential role in complex cognition. Everyday cognitive tasks – such as reading a newspaper article, calculating the appropriate amount to tip in a restaurant, mentally rearranging furniture in one's living room to create space for a new sofa, and comparing and contrasting various attributes of different apartments to decide which to rent – often involve multiple steps with intermediate results that need to be kept in mind temporarily to accomplish the task at hand successfully. "Working memory" is the theoretical construct that has come to be used in cognitive psychology to refer to the system or mechanism underlying the maintenance of task-relevant information during the performance of a cognitive task (Baddeley & Hitch, 1974; Daneman & Carpenter, 1980). As reflected by the fact that it has been labeled "the hub of cognition" (Haberlandt, 1997, p. 212) and proclaimed as "perhaps the most significant achievement of human mental evolution" (Goldman-Rakic, 1992, p. 111), it is a central construct in cognitive psychology and, more recently, cognitive neuroscience.
Easily Manufacturable Shallow Trench Isolation for Gigabit Dynamic Random Access Memory (1996)

A simple and easily manufacturable shallow trench isolation (STI) process is developed for 1 Gbit dynamic random access memory (DRAM) and possibly DRAMs with ever greater capacity. The main features of this STI scheme are dual slope trench formation and selective dry-etching-assisted chemical mechanical polishing (CMP) planarization. The dual slope trench is formed by utilizing polymer generation during trench etching to improve the sub-threshold conduction characteristics (hump-free sub-threshold) and reduce the threshold voltage variation. The basic elements of dry-etching-assisted planarization are to locally form oxide mesas using a highly selective dry etching, and to minimize the amount of CMP simply by removing the locally formed oxide mesas. This new dry-etching-assisted CMP planarization significantly reduces dishing in the large field area and improves the flatness between the high and low pattern density areas such as the cell array and periphery region in a high-density DRAM.
Levodopa‐induced dyskinesia (1990)

This review will consider the classification and phenomenology, the acute pharmacology, and the etiology of levodopa-induced dyskinesias
Communication, protection and diagnostics for cement power systems (2002)

Recent technological advancements have produced intelligent final control devices. These devices communicate operating and diagnostic information along dedicated networks to the distributed computer control system that is used for process control. This level of integration is described, and the many benefits are investigated in greater detail. The integral communications provide device status and diagnostic information, a simple twisted pair connection to a distributed control systems (DCS) I/O interface. The DCS collects this information for monitoring the overall electrical distribution system status centrally but also uses it in conjunction with other process plant information to allow the process to be operated in an optimum way.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Parallel direct solution of linear equations on FPGA-based machines (2004)

The efficient solution of large systems of linear equations represented by sparse matrices appears in many tasks. LU factorization followed by backward and forward substitutions is widely used for this purpose. Parallel implementations of this computation-intensive process are limited primarily to supercomputers. New generations of field-programmable gate array (FPGA) technologies enable the implementation of system-on-a-programmable-chip (SOPC) computing platforms that provide many opportunities for configurable computing. We present the design and implementation of a parallel machine for LU factorization on an SOPC board, using multiple instances of a soft processor. A highly parallel block-diagonal-bordered (BDB) algorithm for LU factorization is mapped to our multiprocessor. Our results prove the viability of our FPGA-based approach.