gebhart/patrepeval huggingface dataset:
Exploring Protein Phosphorylation in Response to DNA Damage Using Differentially Tagged Yeast Arrays (2008)

Two collections of chromosomally tagged yeast Saccharomyces cerevisiae strains were previously designed to detect protein-protein interactions via the Cross-and-Capture system. Here, we used these strain collections in a different application to screen for proteins that are phosphorylated in response to DNA damage by electrophoretic shift analysis. Modification of a number of proteins that are known targets for checkpoint kinases was confirmed this way. Furthermore, we identified the mismatch repair protein Pms1 as a novel target for phosphorylation in the response to DNA damage and replication fork arrest. Genetic analysis revealed that this phosphorylation is dependent on checkpoint activation by ATM and ATR (yeast Mec1p and Tel1p) kinase. Hence, we demonstrated that the Cross-and-Capture system could be efficiently used to detect posttranslational modifications that modulate and control protein function in eukaryotic cells.
Spike anneal for NiSi formation (2005)

The design of wafer processing equipment needs to continuously evolve and respond to the challenges of the future. In this article, we present the evolution of rapid thermal processing (RTP) in the transistor manufacturing environment with emphasis on production-worthy performance over a temperature regime that addresses the sub-400/spl deg/C processing requirements. Temperature and thermal budget control is increasingly critical for contact material processing for sub-65 nm nodes. We present low temperature spike anneal as an application to address thermal budget challenges and demonstrate the extendibility of lamp-based RTP to low temperature processes.
The repressor personality and avoidant information processing: A dichotic listening study (1991)

The present research was designed to investigate the proposition that repressors, operationally defined by the conjunction of low anxiety and high defensiveness, are particularly adept at avoiding the processing of information when motivated to do so. Four groups of participants (nondefensive-low anxious, high anxious, repressors, and defensive-high anxious) were administered a dichotic listening task involving neutral or negative affective words presented in the unattended ear. Participants shadowed the material presented to the attended ear and simultaneously responded to a probe task presented on a video monitor. Results revealed that repressors made significantly fewer shadowing errors than high anxious and defensive-high anxious participants and marginally significantly fewer shadowing errors than low anxious participants for both neutral and negative words. High anxious participants, however, were later able to recognize the negative words that had been presented to the unattended ear at well above chance levels, whereas the recognition memory of repressors for such negative unattended words was at chance levels. In addition, repressors' responses to a postexperiment questionnaire indicated a significantly greater number of distracting thoughts during the experiment relative to other participants. Repressors, it seems, are indeed skillful at avoidant information processing and this capacity may well be related to the emotional memory deficits they have displayed in previous research.
Growth of AlN Films by Hot-Wall CVD and Sublimation Techniques: Effect of Growth Cell Pressure (2002)

Aluminum nitride (AlN) films were grown on off-axis, Si-terminated 4H-SiC substrates by hot-wall CVD and sublimation techniques. The films were investigated by Infrared reflectance, Optical microscopy, Energy Dispersive X-ray analysis and Cathodoluminescence in a Scanning Electron Microscope with respect to their thickness, morphological, compositional and luminescence properties, in order to examine the influence of the growth cell pressure in either of the two deposition methods. Good quality thick AlN films were obtained by hot-wall CVD at temperature of 1200degreesC and reduced pressure of 100 mbar as reflected in the near stoichiometric N/Al ratio in these layers and in the appearance of the characteristic AlN near band edge emission. The AlN sublimation grown films at temperature of 2100degreesC suffered from island growth irrespective of the background pressure. The supersaturation conditions that affect strongly the growth mode became more favorable when the temperature was reduced to 1900degreesC.
Selection and performance of the levonorgestrel-releasing intrauterine system. (1997)

LNg IUS can be successfully used by women who cannot use a CU IUD or who have experienced hormonal side effects with oral contraceptives.
Serviceability of Coiled Tubing in Corrosive Workover and Production Environments (2005)

Abstract This paper presents some of the findings from a joint industry research program supported by major oil and gas producers, coiled tubing (CT) manufacturers and material producers. Phase I of this program determined the cracking resistance of CT material in wet H2S environments which included a database of field failure scenarios. In Phase II of this program, cyclic fatigue tests were conducted on specimens pre-exposed to aerated brine, sour brine, sweet brine, and stimulated acid service environments. Tests showed that the duration of exposure in aerated brine and sour brine environments did not affect the average number of cycles to failure. There was no significant difference among the different grades of coiled tubing in each separate environment. However, exposure to the evaluated environmental conditions severely decreased the fatigue life of the coiled tubing in comparison to the as-received (control) set of samples.
Impaired cardiovascular function in primary biliary cirrhosis (2010)

Cardiovascular system dysregulation in the form of autonomic dysfunction is common at all stages of the disease process in the autoimmune liver disease primary biliary cirrhosis (PBC) and associates with the symptom of fatigue. The mechanisms underpinning autonomic dysfunction in PBC are, however, at present unclear. In this study we set out to explore, for the first time, cardiac structure and function in PBC using impedance cardiography (ICG) and magnetic resonance methodologies. ICG was assessed beat to beat in response to orthostasis (by head-up tilt) in age and sex case-matched high-fatigue and low-fatigue PBC groups (assessed by Fatigue Impact Scale), normal control subjects (n = 15 each group) and a liver disease control cohort (primary sclerosing cholangitis). Cardiac structure and bioenergetics were examined in 15 of the PBC subjects and 8 of the normal control subjects by magnetic resonance spectroscopy and cine imaging. Capacity of the left ventricle to respond to orthostasis [left ventricular ejection time (LVET)] was impaired in PBC compared with matched normal control subjects (P = 0.05). This was a PBC-specific phenomenon unrelated to fatigue status. PBC patients exhibited significantly lower cardiac muscle phosphocreatine-to-ATP ratio (PCr/ATP ratio; measure of cardiac bioenergetic integrity) compared with control subjects (P < 0.01). PCr/ATP <1.6 (indicative of increased risk of death in cardiomyopathy) was present in 6/15 (40%) PBC patients (0/8 control subjects; P < 0.05). Cardiac structure and function were similar in all measures of left ventricular morphology between control subjects and PBC. The close relationship between PCr/ATP and LVET seen in normal subjects (r(2) = 0.6; P < 0.05) was lost in PBC patients, a finding compatible with myocardial dysfunction. Significant correlation was seen between fatigue severity in PBC and fall in cardiac output on orthostasis (r(2) = 0.25; P = 0.005). Our findings suggest the presence of altered myocardial function in PBC. Autonomic "dysfunction" may, rather than being an abnormal process, represent a compensatory mechanism to increase cardiac return to mitigate these effects.
Substrate Specificity of the Adenylation Enzyme SgcC1 Involved in the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 (2006)

C-1027 is an enediyne antitumor antibiotic composed of a chromophore with four distinct chemical moieties, including an (S)-3-chloro-4,5-dihydroxy-beta-phenylalanine moiety that is derived from l-alpha-tyrosine. SgcC4, a novel aminomutase requiring no added co-factor that catalyzes the formation of the first intermediate (S)-beta-tyrosine and subsequently SgcC1 homologous to adenylation domains of nonribosomal peptide synthetases, was identified as specific for the SgcC4 product and did not recognize any alpha-amino acids. To definitively establish the substrate for SgcC1, a full kinetic characterization of the enzyme was performed using amino acid-dependent ATP-[(32)P]PP(i) exchange assay to monitor amino acid activation and electrospray ionization-Fourier transform mass spectroscopy to follow the loading of the activated beta-amino acid substrate to the peptidyl carrier protein SgcC2. The data establish (S)-beta-tyrosine as the preferred substrate, although SgcC1 shows promiscuous activity toward aromatic beta-amino acids such as beta-phenylalanine, 3-chloro-beta-tyrosine, and 3-hydroxy-beta-tyrosine, but all were <50-fold efficient. A putative active site mutant P571A adjacent to the invariant aspartic acid residue of all alpha-amino acid-specific adenylation domains known to date was prepared as a preliminary attempt to probe the substrate specificity of SgcC1; however the mutation resulted in a loss of activity with all substrates except (S)-beta-tyrosine, which was 142-fold less efficient relative to the wild-type enzyme. In total, SgcC1 is now confirmed to catalyze the second step in the biosynthesis of the (S)-3-chloro-4,5-dihydroxy-beta-phenylalanine moiety of C-1027, presenting downstream enzymes with an (S)-beta-tyrosyl-S-SgcC2 thioester substrate, and represents the first beta-amino acid-specific adenylation enzyme characterized biochemically.
Nucleophilic addition of the pentafluoroethyl group to aldehydes, ketones, and esters (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleophilic addition of the pentafluoroethyl group to aldehydes, ketones, and estersPaul G. Gassman and Neil J. O'ReillyCite this: J. Org. Chem. 1987, 52, 12, 2481–2490Publication Date (Print):June 1, 1987Publication History Published online1 May 2002Published inissue 1 June 1987https://pubs.acs.org/doi/10.1021/jo00388a025https://doi.org/10.1021/jo00388a025research-articleACS PublicationsRequest reuse permissionsArticle Views1001Altmetric-Citations108LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Preliminary Assessment of Natural Fracture Patterns in Frontier Formation Sandstones, Southwestern Wyoming (1992)

Abstract Sets of fractures having north, west-northwest to east-northeast, and northeast strikes are present in outcrops of Cretaceous Frontier Formation sandstone along the western margin of the Green River Basin in southwestern Wyoming. The oldest fractures strike north and likely result from lateral stretching associated with Cretaceous subsidence of the northtrending foredeep, and possibly indentation of the Uinta Mountains from the south. Fractures with an easterly strike are younger; they cut across or abut north-striking fractures where the two sets occur together. East-striking fractures may reflect east-west shortening during Cretaceous/early Tertiary orogenesis, although they predate local folds and faults. Both within beds and on the scale of several beds, fracture networks have attributes that could govern the way fractures transmit fluids. Two or more fracture sets occur together only locally; more commonly, adjacent beds contain only one or the other set, causing the preferred direction of potential fluid-flow in fractures to switch by about 90° between adjacent beds. Where only one fracture set is present, fracture connectivity is low. Fractures generally terminate within beds or at bed boundaries, so networks are vertically partitioned. Commonly, fractures are arranged in swarms characterized by abrupt variations in fracture density.
The calcium channel blocker nisoldipine minimizes the release of tumor necrosis factor and interleukin-6 following rat liver transplantation (1992)

Kupffer cells, when activated, release toxic cytokines such as tumor necrosis factor (TNF), which can cause tissue injury. Takei et al. have reported that nisoldipine, a calcium channel blocker which decreases phagocytotic activity by Kupffer cells, also diminishes liver and lung injury and dramatically improves survival following liver transplantation [27]. Therefore, we studied the effect of nisoldipine on the time course of TNF and interleukin-6 (IL-6) release following cold storage and liver transplantation in the rat. Livers were stored under survival and non-survival conditions in cold Euro-Collins solution in the presence or absence of nisoldipine (1.4 µM). After storage, the effluent was collected for determination of cytokines. The liver was then transplanted orthotopically and serum was collected at various time intervals for up to 5 h. In the effluent, TNF levels were very low in both the control and nisoldipine-treated groups and IL-6 was not measurable. Furthermore, when livers were stored under survival conditions and transplanted (liver stored in the cold for 4 h), serum TNF (2 U/ml) and IL-6 (350 U/ml) values were minimal in both the control and nisoldipine-treated groups. In contrast, when livers were stored under non-survival conditions and transplanted (liver stored in the cold for 10 h), TNF levels increased to 15 ± 2 U/ml, 150 min after graft reperfusion, an increase which was prevented by nisoldipine (6.5 U/ml). Serum IL-6 levels were also elevated 300 min after transplantation in livers stored for 10 h. Nisoldipine also reduced the release of this cytokine. Serum transaminases (SGOT) were elevated to values around 2000 U/l 5 h following transplantation. In the nisoldipine-treated group, values were lower between 60 and 300 min. In the lung, interstitial and alveolar edema and cellular infiltration were detectable 5 h post-operatively and were diminished by nisoldipine. These data confirmed that TNF and IL-6 release were minimal following cold storage and transplantation of livers stored under survival conditions, but were elevated transiently after transplantation under non-survival conditions. Nisoldipine prevented cytokine release, most likely by blocking the activation of Kupffer cells, which may explain how it decreases liver and lung injury very early following liver transplantation.
Unit-cell determination from randomly oriented electron-diffraction patterns (2009)

Unit-cell determination is the first step towards the structure solution of an unknown crystal form. Standard procedures for unit-cell determination cannot cope with data collections that consist of single diffraction patterns of multiple crystals, each with an unknown orientation. However, for beam-sensitive nanocrystals these are often the only data that can be obtained. An algorithm for unit-cell determination that uses randomly oriented electron-diffraction patterns with unknown angular relationships is presented here. The algorithm determined the unit cells of mineral, pharmaceutical and protein nanocrystals in orthorhombic high- and low-symmetry space groups, allowing (well oriented) patterns to be indexed.
In Vitro Progesterone Stimulates the Release of Luteinizing Hormone-Releasing Hormone from Superfused Hypothalamic Tissue from Ovariectomized Estradiol-Primed Prepuberal Rats* (1982)

This study was designed to determine if in vitro treatment with progesterone (P4) would activate the LHRH apparatus in hypothalmic fragments from ovariectomized, estradiol- primed rats. Immature, 28-day-old female rats were ovariectomized and implanted with Silastic capsules containing estradiol. At 30 days of age, the animals were decapitated, and the mediobasal hypothalamic-anterior hypothalamic-preoptic area fragments were removed and transferred to supervision chambers. These hypothalamic units received P4, delivered either in pulses (10 min on, 20 min off; 10 ng/ml) or in a continuous mode. LHRH was determined in perfusates and postsuperfusion tissues by RIA. The intermittent mode of P4 administration unequivocally stimulated episodic LHRH release. A maximal stimulatory effect of P4 (close to a 4-fold increment over pretreatment levels) was observed about 1 h after initial P4 administration. After a decline in LHRH release to approximately initial levels, it took about 1 h more for the intermittent P4 pulses to once again stimulate the LHRH secretory apparatus. In contrast to the intermittent mode, continuous P4 infusions were not effective in increasing LHRH release. Furthermore, the release profile was sustained at a stable low level without any pulsatile fluctuation. Intermittent superfusion of hypothalamic fragments with cholesterol did not stimulate LHRH release. A single P4 pulse of 10-min duration augmented the LHRH release rate (>150% increment over pretreatment levels), while that of 1-min duration and similar strength (10 ng/ml) failed to change the LHRH release rate. The stimulatory effectiveness of P4 on the LHRH release rate in vitro was reduced when hypothalamic units were superfused at 30 C instead of 37 C and was not present in hypothalamic fragments from intact prepuberal rats. These observations demonstrated for the first time that an in vitro intermittent infusion of P4, but not a continuous administration, can directly activate the neural LHRH secretory apparatus from hypothalamic fragments from ovariectomized, estradiol-primed prepuberal rats.
A Telemetry System Embedded in Clothes for Indoor Localization and Elderly Health Monitoring (2013)

This paper presents a telemetry system used in a combined trilateration method for the precise indoor localization of the elderly who need health monitoring. The system is based on the association of two wireless technologies: ultrasonic and 802.15.4. The use of the 802.15.4 RF signal gives the reference starting time of the ultrasonic emission (time difference of arrival method). A time of flight measurement of the ultrasonic pulses provides the distances between the mobile node and three anchor points. These distance measurements are then used to locate the mobile node using the trilateration method with an accuracy of a few centimetres. The originality of our work lies in embedding the mobile node in clothes. The system is embedded in clothes in two ways: on a shoe in order to form a "smart" shoe and in a hat in order to form a "smart" hat. Both accessories allow movements, gait speed and distance covered to be monitored for health applications. Experiments in a test room are presented to show the effectiveness of our system.
Abstract 3160: Stromal markers of activated tumor associated fibroblasts predict poor survival and are associated with necrosis in non-small cell lung cancer (2019)

Abstract Tumor associated fibroblasts (TAFs) are essential contributors of the progression of non-small cell lung cancer (NSCLC). Most lung TAFs exhibit an activated phenotype characterized by the expression of α-SMA and fibrillar collagens. However, the prognostic value of these activation markers in NSCLC remains unclear. To address this question we conducted a retrospective multicentric study of the prognostic value of the standard markers of activated fibroblasts. For this purpose, we conducted a quantitative image analysis of α-SMA immunostaining and picrosirius red staining of fibrillar collagens imaged by bright-field and polarized microscopy, respectively, using tissue microarrays with samples from 220 surgical patients, which elicited a percentage of positive staining area for each marker and patient. Kaplan-Meier curves showed that all TAF activation markers were significantly associated with poor survival, and their prognostic value was independent of TNM staging as revealed by multivariate analysis, which elicited an adjusted increased risk of death after 3 years of 129% and 94% for fibrillar collagens imaged with bright-field (p = 0.004) and polarized light (p = 0.003), respectively, and of 89% for α-SMA (p = 0.009). We also found a significant association between all TAF activation markers and tumor necrosis, which is often indicative of hypoxia, supporting a pathologic link between tumor desmoplasia and necrosis/hypoxia. Our findings identify patients with large histologic coverage of fibrillar collagens and α-SMA+ TAFs to be at higher risk of recurrence and death, supporting that they could be considered for adjuvant therapy. Moreover it supports that antifibrotic drugs aiming to target tumor fibrosis may be an effective therapeutic approach to improve survival in NSCLC. Citation Format: Jordi Alcaraz, Josep-Lluís Carrasco, Laura Millares, Iuliana-Cristiana Benchea, Francisco-Javier Fernández, Anabel Martínez, María José Pajares, Julio Sánchez de Cos, Ramon Rami-Porta, Luis Seijo, Josep Ramírez, Noemí Reguart, Esther Barreiro, Eduard Monsó. Stromal markers of activated tumor associated fibroblasts predict poor survival and are associated with necrosis in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3160.