gebhart/patrepeval huggingface dataset:
Evict on write, a management strategy for a prefetch unit and/or first level cache in a multiprocessor system with speculative execution (2023)

In a multiprocessor system with at least two levels of cache, a speculative thread may run on a core processor in parallel with other threads. When the thread seeks to do a write to main memory, this access is to be written through the first level cache to the second level cache. After the write though, the corresponding line is deleted from the first level cache and/or prefetch unit, so that any further accesses to the same location in main memory have to be retrieved from the second level cache. The second level cache keeps track of multiple versions of data, where more than one speculative thread is running in parallel, while the first level cache does not have any of the versions during speculation. A switch allows choosing between modes of operation of a speculation blind first level cache.
The Effect of Thermal Non-Uniformity on Coherent Structures in Supersonic Free Jets (2023)

View Video Presentation: https://doi.org/10.2514/6.2023-3352.vid Prior work has shown total temperature non-uniformity to be an effective noise reduction technique which introduces a stream of cold flow into the heated jet. This method resulted in changes in the exhaust plume and reduced peak sound pressure levels by 2±0.5 dB. The goal of this work is to reveal underlying changes in the spatial-temporal structure of plume instability and turbulence caused by non-uniform total temperature distributions. Time-Resolved Doppler Global Velocimetry (TR-DGV) with a sampling frequency of 50 kHz is used to collect flow velocity data that is resolved in both time and space. Comparison of the mean velocity fields shows that the introduction of the cooler temperature flow in the thermally non-uniform case results in a velocity deficit of about 10% compared to the thermally uniform case. The method of spectral proper orthogonal decomposition (SPOD) was used to reveal the large-scale, coherent noise producing mechanisms. SPOD results indicate that the thermally non-uniform case showed a decrease in turbulent kinetic energy compared to the uniform case at all frequencies. Coherent fluctuations start developing further upstream in the thermally non-uniform case. The addition of the unheated plume results in a disruption in the propagation of the Mach waves from the shear layer into the ambient. The results indicate that the total temperature non-uniformity results in a modified exhaust plume and mean flow distribution at the nozzle exit, compared to that of a thermally uniform flow, which past studies have indicated is a method to reduce jet noise.
Supplementary Table 2 from Targeting the PI3K Pathway in the Brain—Efficacy of a PI3K Inhibitor Optimized to Cross the Blood–Brain Barrier (2023)

&lt;p&gt;PDF file - 60K, Plasma Concentrations, Brain Concentrations and Brain-to-Plasma Ratio Measured at the End of Study (42 days) 2 hours Following the Last Daily PO Administration of GNE-317 (40 mg/kg), GDC-0941 (250 mg/kg) or GDC-0980 (10 mg/kg) to GS2 Tumor-Bearing Mice&lt;/p&gt;
Crystal Structure Analysis Using Annular Dark-Field Imaging with High Precision (2009)

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009
ChemInform Abstract: THE EFFECT OF THE α‐CYANO MOIETY IN NEIGHBORING GROUP PARTICIPATION BY THE CYCLOPROPYL GROUP (1982)

Abstract The Effect of the α‐Cyano Moiety on Neighboring Group Participation by the Cyclopropyl Group.
Improving Quality Metrics in Radiation Oncology: Implementation of Pretreatment Peer Review for Stereotactic Body Radiation Therapy in Patients with Thoracic Cancer (2022)

We successfully implemented a sustainable workflow for detailed pre-Tx contour/plan review for thoracic SBRT cases in the context of twice-weekly disease site-specific peer-review meetings. We reached our quality improvement objective to peer review ≥90% of SBRT cases before exceeding 25% of the dose delivered. This process was feasible to conduct in an integrated network of sites across our system.
Accuracy of a Hybrid Fast Physical Optics Scheme for the Analysis of Dual Reflector Antennas (2006)

A novel hybrid Fast Physical Optics (FPO) algorithm for the analysis of dual reflector antennas is presented. A two-level FPO algorithm for the subreflector to main reflector propagation is proposed and combined with the multilevel FPO that is used for the main reflector to far-field computation. The accuracy of the proposed method is studied by comparison with the direct physical optics evaluation of the near and far fields.
The catalytic subunits of protein phosphatase‐1 and protein phosphatase 2A are distinct gene products (1984)

Three forms of protein phosphatase-1 were isolated from rabbit skeletal muscle that had Mr values of 37 000, 34 000 and 33 000 determined by sodium dodecyl sulphate (SDS) gel electrophoresis. Each species dephosphorylated the beta-subunit of phosphorylase kinase very much faster than the alpha-subunit, was inhibited by inhibitors 1 and 2 with equal potency, and was converted to a form dependent on glycogen synthase kinase-3 and Mg-ATP for activity by incubation with inhibitor-2. Digestion with cyanogen bromide or Staphylococcus aureus proteinase followed by SDS gel electrophoresis showed a very similar pattern of cleavage products for all three forms. The Mr-37 000 and Mr-34 000 species were converted to the Mr-33 000 form by incubation with chymotrypsin. It is concluded that the Mr-33 000 and Mr-34 000 forms are derived from the Mr-37 000 component by limited proteolysis. Conversion of the Mr-37 000 to the Mr-33 000 form was accompanied by a two-fold increase in activity, indicating that an Mr-4000 fragment at one end of the polypeptide is an inhibitory domain that decreases enzyme activity. The catalytic subunit of protein phosphatase 2A from rabbit skeletal muscle had an Mr of 36 000 determined by SDS gel electrophoresis and its specific activity (3 kU/mg) was much lower than that of the Mr-37 000 (15-20 kU/mg) or Mr-33/34 000 (40-50 kU/mg) forms of protein phosphatase-1. It dephosphorylated the alpha-subunit of phosphorylase kinase 4-5-fold faster than the beta-subunit, was unaffected by inhibitor-1 or inhibitor-2, and preincubation with the latter protein did not result in the production of a glycogen synthase kinase-3 and Mg-ATP-dependent form of the enzyme. Digestion with chymotrypsin did not alter the electrophoretic mobility of protein phosphatase 2A under conditions that caused quantitative conversion of the Mr-37 000 form of protein phosphatase-1 to the Mr-33 000 species. Digestion with cyanogen bromide or S. aureus proteinase, followed by SDS gel electrophoresis, showed a quite different pattern of cleavage products to those observed with protein phosphatase 1. Antibody to protein phosphatase-2A raised in sheep did not cross-react with any of the forms of protein phosphatase-1, as judged by immunoelectrophoretic and immunotitration experiments. It is concluded that protein phosphatase-1 and protein phosphatase-2A are distinct gene products.
A Dominant Mutation in Nuclear Receptor Interacting Protein 1 Causes Urinary Tract Malformations via Dysregulation of Retinoic Acid Signaling (2017)

Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of CKD in the first three decades of life. However, for most patients with CAKUT, the causative mutation remains unknown. We identified a kindred with an autosomal dominant form of CAKUT. By whole-exome sequencing, we identified a heterozygous truncating mutation (c.279delG, p.Trp93fs*) of the nuclear receptor interacting protein 1 gene (<i>NRIP1</i>) in all seven affected members. <i>NRIP1</i> encodes a nuclear receptor transcriptional cofactor that directly interacts with the retinoic acid receptors (RARs) to modulate retinoic acid transcriptional activity. Unlike wild-type NRIP1, the altered NRIP1 protein did not translocate to the nucleus, did not interact with RAR<i>α</i>, and failed to inhibit retinoic acid-dependent transcriptional activity upon expression in HEK293 cells. Notably, we also showed that treatment with retinoic acid enhanced NRIP1 binding to RAR<i>α</i> RNA <i>in situ</i> hybridization confirmed <i>Nrip1</i> expression in the developing urogenital system of the mouse. In explant cultures of embryonic kidney rudiments, retinoic acid stimulated <i>Nrip1</i> expression, whereas a pan-RAR antagonist strongly reduced it. Furthermore, mice heterozygous for a null allele of <i>Nrip1</i> showed a CAKUT-spectrum phenotype. Finally, expression and knockdown experiments in <i>Xenopus laevis</i> confirmed an evolutionarily conserved role for <i>NRIP1</i> in renal development. These data indicate that dominant <i>NRIP1</i> mutations can cause CAKUT by interference with retinoic acid transcriptional signaling, shedding light on the well documented association between abnormal vitamin A levels and renal malformations in humans, and suggest a possible gene-environment pathomechanism in this disease.
Pulse Current Measurements and Rabi Oscillations in a dc SQUID Phase Qubit (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We have used 2 ns pulses of current to read out the states of a Nb/AlOx/Nb dc SQUID phase qubit at 25 mK. Plotting the number of escape events that occur versus the size of the current pulse reveals a series of steps corresponding to the occupancy of different energy levels. After calibrating the measurement pulses, we fit these steps to determine the population in each level. Rabi oscillations were viewed using this technique. The single-shot measurement fidelity was theoretically analysed and the optimal single pulse in our device was determined. </para>
Biofiltration of volatile pollutants: Engineering mechanisms for improved design, long-term operation, prediction and implementation. 1998 annual progress report (1998)

'Biofiltration systems can be used for treatment of volatile organic compounds (VOCs); however, the systems are poorly understood and are currently operated as black boxes. Common operational problems associated with biofilters include fouling, deactivation, and overgrowth, all of which make them ineffective for continuous, long-term use. The objective of this investigation is to develop generic methods for long-term stable operation, in particular by using selective limitation of supplemental nutrients while maintaining high activity. As part of this effort, the author will provide deeper fundamental understanding of the important biological and transport mechanisms in biodestruction of sparingly soluble VOCs and extend this approach and mathematical models to additional systems of high priority EM relevance--direct degradation and cometabolic degradation of priority pollutants such as BTEX and chlorinated organics. This report summarizes work after 2 years of a 3-year project. Major results are enumerated and discussed'
Retinal nerve fiber bundle tracing and analysis in human eye by polarization sensitive OCT (2015)

We present a new semi-automatic processing method for retinal nerve fiber bundle tracing based on polarization sensitive optical coherence tomography (PS-OCT) data sets. The method for tracing is based on a nerve fiber orientation map that covers the fovea and optic nerve head (ONH) regions. In order to generate the orientation map, two types of information are used: optic axis orientation based on polarization data, and complementary information obtained from nerve fiber layer (NFL) local thickness variation to reveal fiber bundle structures around the fovea. The corresponding two orientation maps are fused into a combined fiber orientation map. En face maps of NFL retardation, thickness, and unit-depth-retardation (UDR, equivalent to birefringence) are transformed into "along-trace" maps by using the obtained traces of the nerve fiber bundles. The method is demonstrated in the eyes of healthy volunteers, and as an example of further analyses utilizing this method, maps illustrating the gradients of NFL retardation, thickness, and UDR are demonstrated.
Additions and Corrections: Synthesis of Two Bis-m-quinomethanes. An Experimental Study of Connectivity Effects on the Equal-Parity Criterion for Low-Spin Ground States in Alternant Non-Kekule Molecules (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdditions and Corrections: Synthesis of Two Bis-m-quinomethanes. An Experimental Study of Connectivity Effects on the Equal-Parity Criterion for Low-Spin Ground States in Alternant Non-Kekule MoleculesDavid E. Seeger, Paul M. Lahti, Angelo R. Rossi, and Jerome A. BersonCite this: J. Am. Chem. Soc. 1986, 108, 19, 6100Publication Date (Print):September 1, 1986Publication History Published online8 March 2004Published inissue 1 September 1986https://pubs.acs.org/doi/10.1021/ja00279a604https://doi.org/10.1021/ja00279a604research-articleACS PublicationsRequest reuse permissionsArticle Views38Altmetric-Citations-LEARN 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-Alertsclose Get e-Alerts
PULSE-WAVEFORM AND LASER-DOPPLER INDICES FOR IDENTIFYING COLORECTAL-CANCER PATIENTS (2020)

This study aimed to determine the effectiveness of using noninvasive arterial pulse-wave and laser-Doppler flowmetry (LDF) measurements to discriminate between colorectal-cancer (CC) patients and healthy control subjects. Radial-artery blood pressure waveform (BPW), finger photoplethysmography (PPG), and skin-surface LDF signals were measured noninvasively in 12 CC patients and 25 control subjects. Beat-to-beat, spectral, and variability analyses were applied to 20-minute-long recorded signals. Significant intergroup differences were found. In BPW, [Formula: see text]–[Formula: see text] amplitude indices were significantly larger while [Formula: see text]–[Formula: see text] phase-angle indices were significantly smaller in the CC patients than in the controls. The PPG and LDF variability indices were significantly larger and smaller, respectively, in CC patients. The relative energy contributions of the endothelial-, neural-, and myogenic-related frequency bands in LDF were significantly smaller in CC patients. The present findings indicate that pulse and LDF waveform analysis can be used to evaluate the arterial pulse-wave transmission condition, the responses of the blood-flow perfusion, and its regulatory activities in CC patients. There could be some similarities and differences in the present indices for different types of cancer. These findings could be utilized in the development of a rapid, noninvasive, and objective technique for evaluating the CC-induced blood-flow responses.
Identification of genomic variants causing sperm abnormalities and reduced male fertility (2018)

Whole genome sequencing has identified millions of bovine genetic variants; however, there is currently little understanding about which variants affect male fertility. It is imperative that we begin to link detrimental genetic variants to sperm phenotypes via the analysis of semen samples and measurement of fertility for bulls with alternate genotypes. Artificial insemination (AI) bulls provide a useful model system because of extensive fertility records, measured as sire conception rates (SCR). Genetic variants with moderate to large effects on fertility can be identified by sequencing the genomes of fertile and subfertile or infertile sires identified with high or low SCR as adult AI bulls or yearling bulls that failed Breeding Soundness Evaluation. Variants enriched in frequency in the sequences of subfertile/infertile bulls, particularly those likely to result in the loss of protein function or predicted to be severely deleterious to genes involved in sperm protein structure and function, semen quality or sperm morphology can be designed onto genotyping assays for validation of their effects on fertility. High throughput conventional and image-based flow cytometry, proteomics and cell imaging can be used to establish the functional effects of variants on sperm phenotypes. Integrating the genetic, fertility and sperm phenotype data will accelerate biomarker discovery and validation, improve routine semen testing in bull studs and identify new targets for cost-efficient AI dose optimization approaches such as semen nanopurification. This will maximize semen output from genetically superior sires and will increase the fertility of cattle. Better understanding of the relationships between male genotype and sperm phenotype may also yield new diagnostic tools and treatments for human male and idiopathic infertility.
Prevalence and characteristics of pain in early and late stages of ALS (2013)

The purpose of this study was to compare pain frequency in early and late stages of ALS and to describe the relationship between pain intensity and functional status. Sixty-four patients in different stages of ALS were asked to complete the Neuropathic Pain Scale and to draw the localization of their pain on a body cartoon. The Amyotrophic Lateral Sclerosis Functional Rating Scale-Revised (ALSFRS-R) and Forced Vital Capacity (FVC) values were obtained from the medical record. A χ(2) correlation was used to compare the proportion of patients with pain in different stages of ALS. Correlation coefficient was used to describe the relationship between pain intensity and functional status (ALSFRS-R). Pain was reported by about half the patients. Using FVC values, patients were subdivided into early, intermediate and late stage of the disease. There was a negative correlation between pain intensity and functional status. There was no statistically significant difference in the presence of pain among patients in the different stages of ALS. In conclusion, our study showed that pain is common in ALS patients. Although pain intensity did correlate negatively with functional status, as expected, we were surprised to find that pain was also present in the early stages of the disease.
Modeling analytics as knowledge work: Computing meets organizational psychology (2015)

This paper reports on an ongoing interdisciplinary study of analytic workflow, describing our preliminary understanding and findings as well as some directions for further investigation and validation. Specifically, we exploit knowledge from organizational psychology to develop a computational organizational model. Our proposed organizational model provides a framework to understand the impact of organizational level variables and worker characteristics on workflow performance, providing a view to create justifiable interventions to improve performance. To evaluate the viability of the model, we develop a multiagent simulation framework and design an experimental study.
Autonomous Algorithms for Centralized and Distributed Interference Coordination: A Virtual Layer Based Approach (2013)

Interference mitigation techniques are essential for improving the performance of interference limited wireless networks. In this paper, we introduce novel interference mitigation schemes for wireless cellular networks with space division multiple access (SDMA). The schemes are based on a virtual layer that captures and simplifies the complicated interference situation in the network and that is used for power control. We show how optimization in this virtual layer generates gradually adapting power control settings that lead to autonomous interference minimization. Thereby, the granularity of control ranges from controlling frequency sub-band power via controlling the power on a per-beam basis, to a granularity of only enforcing average power constraints per beam. In conjunction with suitable short-term scheduling, our algorithms gradually steer the network towards a higher utility. We use extensive system-level simulations to compare three distributed algorithms and evaluate their applicability for different user mobility assumptions. In particular, it turns out that larger gains can be achieved by imposing average power constraints and allowing opportunistic scheduling instantaneously, rather than controlling the power in a strict way. Furthermore, we introduce a centralized algorithm, which directly solves the underlying optimization and shows fast convergence, as a performance benchmark for the distributed solutions. Moreover, we investigate the deviation from global optimality by comparing to a branch-and-bound-based solution.
Prognostic role of mid-treatment PET/CT and plasma cytokines in patients undergoing chemoradiation for locally advanced non-small cell lung cancer (LA-NSCLC). (2020)

9040 Background: Patients with unresectable LA-NSCLC are treated with concurrent chemoradiation (CRT) and consolidation immunotherapy with survival that range from months to years or even decades. Early predictive biomarkers have potential to identify patients who are unlikely to benefit from continuing standard of care therapy and require a change in management. We investigated biomarkers that are widely available (PET/CT scan and plasma cytokine levels) to develop early predictors (mid-CRT) of survival in a phase II clinical trial of chemoradiation for LA-NSCLC. Methods: 37 Patients with AJCC v7 stage IIB-IIIB NSCLC were prospectively enrolled on the FLARE-RT trial (NCT02773238) from 2016-9. All patients underwent chemoradiation; 18 also received adjuvant durvalumab. PET/CT exams were performed at week 3 of CRT and response status was pre-defined by published metrics. 21 patients consented to peripheral blood collection at baseline and week 3, and plasma levels of 43 common inflammatory cytokines were measured. Bootstrapping over 100 iterations of the least absolute shrinkage and selection operator (LASSO) was performed to reduce feature dimensionality and guard against false discoveries. Cox regression of selected cytokine levels and PET response status, as well as time-dependent receiver-operating characteristic (ROC) analysis, were evaluated for associations to overall survival (OS). Results: Median follow-up was 18 months with 1-year OS 81% and PFS 52%. Mid-CRT PET response (as determined by pre-defined metrics) was strongly associated with OS (HR 5.6 [1.4-22.0], p = 0.015) after adjusting for radiation target volume, with 1-yr OS 94% for responders vs. 68% for non-responders (p = 0.017). Plasma TNFα level was also prognostic for OS (HR 1.9 [1.1-3.5], p = 0.030). TNFα retained significance for OS (HR 2.3 [1.2-4.6], p = 0.016) after adjusting for PET response. Bivariate mid-CRT PET response and TNFα generated a parsimonious model to predict OS (AUC = 0.85, 18-month horizon). Conclusions: Risk stratification for long-term survival after chemoradiation in patients with LA-NSCLC may be achievable based on mid-chemoradiation assessment of widely available biomarkers (PET imaging and plasma TNFα level). Combined functional imaging and peripheral blood biomarkers will be validated in a larger sample of our trial cohort, along with other independent patient populations. Clinical trial information: NCT02773238.