gebhart/patrepeval huggingface dataset:
Manifestation of nonlinear elasticity in rock: convincing evidence over large frequency and strain intervals from laboratory studies (1996)

Abstract. Nonlinear elastic response in rock is established as a robust and representative characteristic rock rather than a curiosity. We show measurements of this behaviour from a variety of experiments on rock taken over many orders of magnitude in strain and frequency. The evidence leads to a pattern of unifying behaviour in rock: (1) Nonlinear response in rock is ubiquitous. (2) The response takes place over a large frequency interval (dc to 105 kHz at least). (3) The response not only occurs, as is commonly appreciated, large strains but also at small strains where this behaviour and the manifestations of this behaviour are commonly disregarded.
Characterizing Scheduling Delay for Low-Latency Data Analytics Workloads (2018)

Data analytics workloads are shifting to shorter task execution time, higher degree of parallelism, and execution on faster hardware. As a result, job scheduling is becoming a bottleneck, which needs to offer extreme low-latency, massive throughput, and high scalability. However, few efforts have been focused on systematically understanding the scheduling delay. In this paper, we propose a method and develop a tool, SD-checker, that decomposes the job scheduling delay into multiple components and characterizes each by extensive experiments. SDchecker extracts event messages through mining both cluster scheduler logs and application logs, and constructs a scheduling order graph for the ease of analysis. We use SDchecker to evaluate Spark-SQL on a popular cluster scheduler Yarn. Results show that the scheduling delay may account for 60% of the job runtime of small data analytics workloads. After decomposing the total scheduling delay, we find Spark itself contributes 70% of the delay. Through the evaluation and analysis, we conclude that (1) The causes of scheduling delay are determined by many factors, and (2) The job scheduling is not well optimized yet, and far from ideal for low-latency data analytics workloads.
Shallow trench isolation scatterometry metrology in a high volume fab (2002)

Focuses on the current roles of metrology systems associated with a shallow trench isolation (STI) run-to-run (RtR) controller and recent advances AMD has made applying new, ODP scatterometry-based metrology to this application. It will compare industry standard metrology techniques to ODP, with the objective of identifying the STI metrology system or systems that will produce timely and reliable data streams with the largest quantity of process information at the highest possible signal to noise (S/N) ratio.
Myocardial temperature in acute myocardial infarction: protection with mild regional hypothermia (1997)

This study tests the hypothesis that a 2-4 degrees C reduction in myocardial temperature, obtained by using topical regional hypothermia (TRH), reduces infarct size. Anesthetized rabbits received coronary artery occlusion and reperfusion. We cooled hearts in the TRH group by applying an ice bag directly over the risk zone; the control group received no intervention. Risk zone myocardial temperature (MT) in the TRH group was reduced at occlusion by 2 degrees C from baseline and after 5 min of occlusion by 3.6 degrees C. In the control group, MT in the risk region remained within 0.3 degree C of baseline. The ischemic area was similar in both groups, yet infarct size in the TRH group was reduced by an average of 65% compared with the control group. Infarct size closely correlated with MT in the risk region at the time of occlusion. In a second protocol in which all hearts were paced, infarct size was 21% of the risk region in TRH hearts compared with 44% in controls. These results strongly support the important role of MT in the progression of necrosis and demonstrate that the application of local cooling to the risk region profoundly reduces myocardial infarct size.
Trends, challenges and opportunities for performance engineering with modern business software (2003)

The author looks at trends in software and systems, and the current and likely implications of these trends on the discipline of performance engineering. In particular, he examines software complexity growth and its consequences for performance engineering for enhanced understanding, more efficient analysis and effective performance improvement. The pressures for adaptive and autonomous systems introduce further opportunities for performance innovation. The promise of aspect oriented software development technologies for assisting with some of these challenges is introduced.
DFT Calculations of Photoabsorption Spectra in the VUV Region for Design of Photoresist Materials for 157 nm Lithography. (2002)

Time-dependent density functional theory (TD-DFT) calculations using the B3LYP hybrid functional were performed to investigate the transparencies of organic molecules and polymers in the vacuum ultraviolet (VUV) region. The calculated photoabsorption spectra obtained from the combination of geometry optimization using the 6-311G(d) basis set and subsequent calculations of transition energies and oscillator strengths using the 6-311++G(d, p) basis set agree well with the experimental spectra. This method is a useful to infer the transparency of polymers in the VUV region, and in particular helpful for design of photoresist materials for F2 lithography (157nm). The transparencies of the model compounds relating to the representative polymer platforms were estimated, and the calculated spectra demonstrate the effectiveness of judicious introduction of -F and -CF3 groups in reducing optical absorption at the wavelength. In addition, the absorption spectra of model compounds having a sulfonyl fluoride (-SO2F) and sulfonyl ester (-SO2OR) groups, which were proposed by the present authors as novel resist platforms, were calculated and compared with the experimental spectra of corresponding homopolymers.
The prognostic impacts of IMRT combined with chemotherapy with different platinums and paclitaxel in advanced esophageal carcinoma (2016)

Objective
To analyze the prognosis of advanced esophageal carcinoma treated with paclitaxel and different platinum-based chemotherapy regimens plus intensity-modulated radiotherapy (IMRT), and to explore an optimal chemotherapy regimen.


Methods
A total of 242 patients with advanced esophageal carcinoma who were admitted to our hospital and treated with paclitaxel and cisplatin (68 patients), nedaplatin (85 patients), lobaplatin (58 patients), or oxaliplatin (31 patients) plus IMRT from 2008 to 2014 were enrolled as subjects. The prognosis of the four groups was analyzed after 2, 3, and ≥4 cycles of chemotherapy. The survival rates were calculated by the Kaplan-Meier method and analyzed by the log-rank test. The Cox model was used for the multivariate prognostic analysis.


Results
The sample number of 3 years was 168 cases. In all the 242 patients, the medium survival time was 31.1 months and the 3-year overall survival (OS) rate was 47.4%. There was no significant difference in the 3-year OS rate between the cispaltin, nedaplatin, lobaplatin, and oxaliplatin groups (46.2% vs. 56.4% vs. 45.7% vs. 29.0%, P=0.090). The stratified analysis showed that the cisplatin, nedaplatin, and lobaplatin groups had a significantly higher OS rate than the oxaliplatin group (50.1% vs. 29.0%, P=0.021). There was no significant difference in the 3-year OS rate between patients receiving 2, 3, and ≥4 cycles of chemotherapy (40.1% vs. 49.5% vs. 50.8%, P=0.264). The multivariate analysis showed that esophageal tumor volume and the maximal size of metastatic lymph node were independent prognostic factors.


Conclusions
Combined with IMRT, paclitaxel plus cisplatin, nedaplatin, or lobaplatin-based chemotherapy achieves improved survival rates than paclitaxel plus oxaliplatin-based chemotherapy. Esophageal tumor volume and the maximal size of metastatic lymph node are independent prognostic factors.


Key words: 
Esophageal neoplasms/chemotherapy; Esophageal neoplasms/intensity-modulated radiotherapy; Prognostic analysis
Noninvasive Monitoring of Blood Glucose with Raman Spectroscopy (2017)

The successful development of a noninvasive blood glucose sensor that can operate reliably over sustained periods of time has been a much sought after but elusive goal in diabetes management. Since diabetes has no well-established cure, control of elevated glucose levels is critical for avoiding severe secondary health complications in multiple organs including the retina, kidney and vasculature. While fingerstick testing continues to be the mainstay of blood glucose detection, advances in electrochemical sensing-based minimally invasive approaches have opened the door for alternate methods that would considerably improve the quality of life for people with diabetes. In the quest for better sensing approaches, optical technologies have surfaced as attractive candidates as researchers have sought to exploit the endogenous contrast of glucose, notably its absorption, scattering, and polarization properties. Vibrational spectroscopy, especially spontaneous Raman scattering, has exhibited substantial promise due to its exquisite molecular specificity and minimal interference of water in the spectral profiles acquired from the blood-tissue matrix. Yet, it has hitherto been challenging to leverage the Raman scattering signatures of glucose for prediction in all but the most basic studies and under the least demanding conditions. In this Account, we discuss the newly developed array of methodologies that address the key challenges in measuring blood glucose accurately using Raman spectroscopy and unlock new prospects for translation to sustained noninvasive measurements in people with diabetes. Owing to the weak intensity of spontaneous Raman scattering, recent research has focused on enhancement of signals from the blood constituents by designing novel excitation-collection geometries and tissue modulation methods while our attempts have led to the incorporation of nonimaging optical elements. Additionally, invoking mass transfer modeling into chemometric algorithms has not only addressed the physiological lag between the actual blood glucose and the measured interstitial fluid glucose values but also offered a powerful tool for predictive measurements of hypoglycemia. This framework has recently been extended to provide longitudinal tracking of glucose concentration without necessitating extensive a priori concentration information. These findings are advanced by the results of recent glucose tolerance studies in human subjects, which also hint at the need for designing nonlinear calibration models that can account for subject-to-subject variations in skin heterogeneity and hematocrit levels. Together, the emerging evidence underscores the promise of a blood withdrawal-free optical platform-featuring a combination of high-throughput Raman spectroscopic instrumentation and data analysis of subtle variations in spectral expression-for diabetes screening in the clinic and, ultimately, for personalized monitoring.
A practical method to determine the light source distribution in bioluminescent imaging (2004)

Optical signatures of tumor cells may be generated by expression of reporter genes encoding bioluminescent/fluorescent proteins. Bioluminescent imaging is a novel technique that identifies such light sources from the light flux detected on the surface of a small animal. This technique can effectively evaluate tumor cell growth and regression in response to various therapies in medical research, drug development and gene therapy. In this paper, the diffusion approximation is employed to describe the propagation of photons through biological tissues. Then, a practical method is proposed for localizing and quantifying bioluminescent sources from external bioluminescent signals. This method incorporates prior knowledge on permissible source regions, and transforms the inverse bioluminescent problem into a finite element-based constrained optimization procedure. This approach is validated and evaluated with ideal and noise data in numerical simulation.
The Effect of a Fixed Foil on Ship Propulsion and Motions (2013)

In this paper, we study a ship employing a fixed horizontal foil for motion reduction and thrust generation in waves. Although simple, such a foil may substantially reduce the ship motions and resistance in waves. Model tests of a 1:16 scale model of a 90 m long offshore vessel with a fixed foil of 29 m span in the bow were performed. For a ship speed of 12 knots, the fixed foil resulted in a resistance reduction of 60% in regular head sea waves with height 3.7 m and period 8.6 s. For the same wave and ship speed, the vessel’s heave and pitch motions were reduced by 42% and 45%, respectively. The effect of the foil was implemented in the MARINTEK Vessel Simulator (VeSim), which solves the equations of motion for a ship in the time domain. Simulations are compared with the model tests. The ship resistance was underpredicted in the simulations for most wave periods, but this was found to be due to the foil not being entirely fixed in the model tests. The effects of longitudinal position of the foil and wave direction on the foil thrust are also studied theoretically.
Human eosinophils constitutively express multiple Th1, Th2, and immunoregulatory cytokines that are secreted rapidly and differentially (2008)

Eosinophils are innate immune leukocytes implicated in the initiation and maintenance of type 2 immune responses, including asthma and allergy. The ability to store and rapidly secrete preformed cytokines distinguishes eosinophils from most lymphocytes, which must synthesize cytokine proteins prior to secretion and may be a factor in the apparent Th2 bias of eosinophils. Multiple studies confirm that human eosinophils from atopic or hypereosinophilic donors can secrete over 30 cytokines with a varying and often opposing immune-polarizing potential. However, it remains unclear whether all of these cytokines are constitutively preformed and available for rapid secretion from eosinophils in the circulation of healthy individuals or are restricted to eosinophils from atopic donors. Likewise, the relative concentrations of cytokines stored within eosinophils have not been studied. Here, we demonstrate that human blood eosinophils are not singularly outfitted with Th2-associated cytokines but rather, constitutively store a cache of cytokines with nominal Th1, Th2, and regulatory capacities, including IL-4, IL-13, IL-6, IL-10, IL-12, IFN-gamma, and TNF-alpha. We demonstrate further rapid and differential release of each cytokine in response to specific stimuli. As agonists, strong Th1 and inflammatory cytokines elicited release of Th2-promoting IL-4 but not Th1-inducing IL-12. Moreover, a large quantity of IFN-gamma was secreted in response to Th1, Th2, and inflammatory stimuli. Delineations of the multifarious nature of preformed eosinophil cytokines and the varied stimulus-dependent profiles of rapid cytokine secretion provide insights into the functions of human eosinophils in mediating inflammation and initiation of specific immunity.
Testing an ‘aging gene’ in long‐lived <i>Drosophila</i> strains: increased longevity depends on sex and genetic background (2003)

Molecular advances of the past decade have led to the discovery of a myriad of 'aging genes' (methuselah, Indy, InR, Chico, superoxide dismutase) that extend Drosophila lifespan by up to 85%. Despite this life extension, these mutants are no longer lived than at least some recently wild-caught strains. Typically, long-lived mutants are identified in relatively short-lived genetic backgrounds, and their effects are rarely tested in genetic backgrounds other than the one in which they were isolated or derived. However, the mutant's high-longevity phenotype may be dependent on interactions with alleles that are common in short-lived laboratory strains. Here we set out to determine whether one particular mutant could extend lifespan in long-lived genetic backgrounds in the fruit fly, Drosophila melanogaster. We measured longevity and resistance to thermal stress in flies that were transgenically altered to overexpress human superoxide dismutase (SOD) in the motorneurones in each of 10 genotypes. Each genotype carried the genetic background from a different naturally long-lived wild-caught Drosophila strain. While SOD increased lifespan on average, the effect was genotype- and sex-specific. Our results indicate that naturally segregating genes interact epistatically with the aging gene superoxide dismutase to modify its ability to extend longevity. This study points to the need to identify mutants that increase longevity not only in the lab strain of origin but also in naturally long-lived genetic backgrounds.
CRISPR/Cas9 Technology as an Emerging Tool for Targeting Amyotrophic Lateral Sclerosis (ALS) (2018)

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9) is a genome editing tool that has recently caught enormous attention due to its novelty, feasibility, and affordability. This system naturally functions as a defense mechanism in bacteria and has been repurposed as an RNA-guided DNA editing tool. Unlike zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), CRISPR/Cas9 takes advantage of an RNA-guided DNA endonuclease enzyme, Cas9, which is able to generate double-strand breaks (DSBs) at specific genomic locations. It triggers cellular endogenous DNA repair pathways, contributing to the generation of desired modifications in the genome. The ability of the system to precisely disrupt DNA sequences has opened up new avenues in our understanding of amyotrophic lateral sclerosis (ALS) pathogenesis and the development of new therapeutic approaches. In this review, we discuss the current knowledge of the principles and limitations of the CRISPR/Cas9 system, as well as strategies to improve these limitations. Furthermore, we summarize novel approaches of engaging the CRISPR/Cas9 system in establishing an adequate model of neurodegenerative disease and in the treatment of SOD1-linked forms of ALS. We also highlight possible applications of this system in the therapy of ALS, both the inherited type as well as ALS of sporadic origin.
PDZ Domains: Structural Modules for Protein Complex Assembly (2002)

PDZ domains1 are modular protein interaction domains that play a role in protein targeting and protein complex assembly. Once termed Discs-large homology regions (DHRs) or GLGF repeats (after a conserved Gly-Leu-Gly-Phe sequence found within the domain), these domains of ∼90 amino acids are now primarily known by an acronym of the first three PDZ-containing proteins identified: the postsynaptic protein PSD-95/SAP90, theDrosophila septate junction protein Discs-large, and the tight junction protein ZO-1.
Mechanism for rapid growth of organic–inorganic halide perovskite crystals (2016)

Optoelectronic devices based on hybrid halide perovskites have shown remarkable progress to high performance. However, despite their apparent success, there remain many open questions about their intrinsic properties. Single crystals are often seen as the ideal platform for understanding the limits of crystalline materials, and recent reports of rapid, high-temperature crystallization of single crystals should enable a variety of studies. Here we explore the mechanism of this crystallization and find that it is due to reversible changes in the solution where breaking up of colloids, and a change in the solvent strength, leads to supersaturation and subsequent crystallization. We use this knowledge to demonstrate a broader range of processing parameters and show that these can lead to improved crystal quality. Our findings are therefore of central importance to enable the continued advancement of perovskite optoelectronics and to the improved reproducibility through a better understanding of factors influencing and controlling crystallization.
Next-generation multimedia messaging (2002)

This paper discusses some technical aspects of multimedia messaging systems. By 'messages', we mean non-real-time communications containing various media (text, speech, FAXed document images, video, electronic ink, etc.), passing between users over enterprise-wide telephony and data networks, and collecting in 'multimedia mailboxes'. Messaging, like 'digital libraries', is an application domain for indexing, retrieval, searching, etc.-but it offers some significantly different challenges and opportunities. We discuss some technical implications of the expected contents of messages, waiting time in mailboxes, and the particular needs of messaging users.
Development of plasmid cloning vectors for Thermus thermophilus HB8: expression of a heterologous, plasmid-borne kanamycin nucleotidyltransferase gene (1992)

While several Thermus genes have been cloned and T. thermophilus has been shown to be transformable, molecular genetic studies of these thermophiles have been hampered by the absence of selectable cloning vectors. We have constructed a selectable plasmid by random insertion of a heterologous gene encoding a thermostable kanamycin nucleotidyltransferase activity into a cryptic, multicopy plasmid from T. thermophilus HB8. This plasmid should serve as a suitable starting point for the development of a gene expression system for T. thermophilus.
Interplay Between Innate Immunity and the Plant Microbiota (2017)

The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.