gebhart/patrepeval huggingface dataset:
TicToc: Enabling Bandwidth-Efficient DRAM Caching for both Hits and\n Misses in Hybrid Memory Systems (2019)

This paper investigates bandwidth-efficient DRAM caching for hybrid DRAM +\n3D-XPoint memories. 3D-XPoint is becoming a viable alternative to DRAM as it\nenables high-capacity and non-volatile main memory systems; however, 3D-XPoint\nhas 4-8x slower read, and worse writes. As such, effective DRAM caching in\nfront of 3D-XPoint is important to enable a high-capacity, low-latency, and\nhigh-write-bandwidth memory. There are two major approaches for DRAM cache\ndesign: (1) a Tag-Inside-Cacheline (TIC) organization that optimizes for hits,\nby storing tag next to each line such that one access gets both tag and data,\nand (2) a Tag-Outside-Cacheline (TOC) organization that optimizes for misses,\nby storing tags from multiple data-lines together such that one tag-access gets\ninfo for several data-lines. Ideally, we desire the low hit-latency of TIC, and\nthe low miss-bandwidth of TOC. To this end, we propose TicToc, an organization\nthat provisions both TIC and TOC to get hit and miss benefits of both.\n However, we find that naively combining both actually performs worse than\nTIC, because one needs to pay bandwidth to maintain both metadata. The main\ncontribution of this work is developing architectural techniques to reduce the\nbandwidth of maintaining both TIC and TOC metadata. We find the majority of the\nbandwidth cost is due to maintaining TOC dirty bits. We propose DRAM Cache\nDirtiness Bit, which carries DRAM cache dirty info to last-level caches, to\nprune repeated dirty-bit checks for known dirty lines. We then propose\nPreemptive Dirty Marking, which predicts which lines will be written and\nproactively marks dirty bit at install time, to amortize the initial dirty-bit\nupdate. Our evaluations on a 4GB DRAM cache with 3D-XPoint memory show that\nTicToc enables 10% speedup over baseline TIC, nearing 14% speedup possible with\nan idealized DRAM cache w/ 64MB of SRAM tags, while needing only 34KB SRAM.\n
Proposal of Effective Damage Identification Method for Truss Structures Using Successive Iteration Method of Bounding Domain and Domain Decomposition Finite Element Technique (2004)

Damage identification methods based on changes in natural frequencies and mode shapes using finite element methods have received wide attention for their high applicability to complex structures. In this paper, for truss structures we develop an effective damage identification method with a successive iteration method of bounding domain and a domain decomposition finite element technique. By means of the successive iteration method of bounding domain, a truss structure is subdivided successively into subdomains of truss structures, and finally a damaged truss member is identified. In order to reduce computational time, the domain decomposition finite element technique is also developed to give frequencies and mode shapes of the whole structure by assembling subdomain frequencies and mode shapes. We examine the validity of the domain decomposition finite element technique by performing the vibration analysis for a subdivided two-dimensional truss structure, and then a numerical damage identification study for a two-dimensional truss structure is conducted. It is recognized that the present damage identification method is effective and computationally efficient.
Measurement of the CP-violating phase and decay-width difference in $B_s^0\to\psi(2S)\phi$ decays (2016)

A time-dependent angular analysis of $B_s^0\to\psi(2S)\phi$ decays is performed using data recorded by the LHCb experiment. The data set corresponds to an integrated luminosity of 3.0\invfb collected during Run 1 of the LHC. The CP-violating phase and decay-width difference of the $B_s^0$ system are measured to be $\phi_s = 0.23^{+0.29}_{-0.28} \pm 0.02$ rad and $\Delta\Gamma_s = 0.066^{+0.041}_{-0.044} \pm 0.007$ ps$^{-1}$, respectively, where the first uncertainty is statistical and the second systematic. This is the first time that $\phi_s$ and $\Delta\Gamma_s$ have been measured in a decay containing the $\psi(2S)$ resonance.
Direction of Arrival Filters for Improved Aberration Estimation (2008)

Successful adaptive imaging requires accurate measurements of the aberration profile across the array surface. Two-dimensional spatial filters are used to obtain more accurate estimates of aberrating layers by suppressing wavefronts emanating from off-axis scatterers. Application of these filters to the rf signals of the individual elements rejects wavefronts arriving from angles other than the look direction of the array and results in an increase in element-to-element correlation. Spatial filtering reduced the amount of error in the measured aberration profiles and adaptive spatial filtering further improved the estimates. The improvements in aberration estimation obtained with these methods are verified using simulations and experiments in tissue-mimicking phantoms. The technique is applied to signals obtained from in vivo human thyroid.
Learning Task Specific Web Services Compositions with Loops and Conditional Branches from Example Executions (2010)

Majority of the existing approaches to service composition, including the widely popular planning based techniques, are not able to automatically compose practical workflows that include complex repetitive behaviors (loops), taking into account possibility of failures and non-determinism of web service execution results. In this work, we present a learning based approach for composing task specific workflows. We present an approach for learning task specific web service compositions from a very small number of observations (one or more) of example service execution sequences (traces) that solve a given goal. The workflows learned by this approach generalize to the tasks justified by the observed execution trace. The generalization captures the repetitive executions of service sequences, conditional branching executions, and repetitions and branching resulting from failures. We evaluate the approach on a complex web services application involving arbitrary number of repetitive executions and failed executions.
Synthesis, Structural Characterization, and Unusual Field-Effect Behavior of Organic Transistor Semiconductor Oligomers: Inferiority of Oxadiazole Compared with Other Electron-Withdrawing Subunits (2009)

A new series of heterocyclic oligomers based on the 1,3,4-oxadiazole ring were synthesized. Other electron-deficient cores (fluorenone and fumaronitrile) were introduced to investigate the oligomers as n-channel materials. The physical properties, thin film morphologies, and field-effect transistor characteristics of the oligomers were evaluated. Thin films were deposited at different substrate temperatures and on variously coated Si/SiO(2) for device optimization. Contrary to our expectations, the thin film devices of 4 revealed p-channel behavior, and the average hole mobility was 0.14 cm(2) V(-1) s(-1) (maximum value 0.18 cm(2) V(-1) s(-1)). Compound 11 is the first example of an oxadiazole-containing organic semiconductor (OSC) oligomer in an n-channel organic field-effect transistor (OFET) and shows moderate mobilities. Non-oxadiazole-containing oligomers 9 and 12 showed n-channel OFET behavior on hexamethyldisilazane-treated and Cytop spin-coated SiO(2) in vacuum. These are the first fluorenone- and fumaronitrile-based n-OSCs demonstrated in transistors. However, oxadiazole-core materials 14 and 16 were inactive in transistor devices.
Gigahertz ambipolar frequency multiplier based on CVD graphene (2010)

Ambipolar transport in graphene offers great opportunities for novel device and circuit applications. This paper discusses the RF performance of CVD grown graphene transistors for the first time. Then, a new graphene ambipolar frequency multiplier that can operate at 1.4 GHz with extremely high output spectral purity (> 90%) is demonstrated. These GHz graphene frequency multipliers, made from wafer-scale graphene synthesis and fabrication processes, demonstrate the great potential of graphene-based ambipolar devices for RF and mixed-signal applications.
Production of Bio-oil from Alfalfa Stems by Fluidized-Bed Fast Pyrolysis (2008)

This study focused on the production of bio-oil from alfalfa stem material. Two alfalfa maturity stages, harvested at the early bud and full flower stages of development, were examined to evaluate the impact of variation in cell wall polysaccharide and lignin content on pyrolysis oil yields, production efficiency, and bio-oil and char quality, in terms of their use as combustion fuel and for chemicals. Findings included a lower-than-average yield of bio-oil and a higher-than-average yield of charcoal from alfalfa stems, compared to previous results for other biomass feedstocks. The bio-oil showed a decrease in oxygen content from the alfalfa stems, leading to a higher-than-average energy content in the bio-oil. Bio-oil yields were slightly higher for the more-mature alfalfa, which had higher levels of cell wall cellulose and lignin. Overall, when all the pyrolysis products were considered, energy recovery was better for the more-mature alfalfa stems.
Revolutionize livestock breeding in the future: an animal embryo-stem cell breeding system in a dish (2018)

Meat and milk production needs to increase ~ 70-80% relative to its current levels for satisfying the human needs in 2050. However, it is impossible to achieve such genetic gain by conventional animal breeding systems. Based on recent advances with regard to in vitro induction of germ cell from pluripotent stem cells, herein we propose a novel embryo-stem cell breeding system. Distinct from the conventional breeding system in farm animals that involves selecting and mating individuals, the novel breeding system completes breeding cycles from parental to offspring embryos directly by selecting and mating embryos in a dish. In comparison to the conventional dairy breeding scheme, this system can rapidly achieve 30-40 times more genetic gain by significantly shortening generation interval and enhancing selection intensity. However, several major obstacles must be overcome before we can fully use this system in livestock breeding, which include derivation and mantaince of pluripotent stem cells in domestic animals, as well as in vitro induction of primordial germ cells, and subsequent haploid gametes. Thus, we also discuss the potential efforts needed in solving the obstacles for application this novel system, and elaborate on their groundbreaking potential in livestock breeding. This novel system would provide a revolutionary animal breeding system by offering an unprecedented opportunity for meeting the fast-growing meat and milk demand of humans.
Dynamic scheduling strategies for shared-memory multiprocessors (2002)

Efficiently scheduling parallel tasks on to the processors of a shared-memory multiprocessor is critical to achieving high performance. Given perfect information at compile-time, a static scheduling strategy can produce an assignment of tasks to processors that ideally balances the load among the processors while minimizing the run-time scheduling overhead and the average memory referencing delay. Since perfect information is seldom available, however, dynamic scheduling strategies distribute the task assignment function to the processors by having idle processors allocate work to themselves from a shared queue. While this approach can improve the load balancing compared to static scheduling, the time required to access the shared work queue adds directly to the overall execution time. To overlap the time required to dynamically schedule tasks with the execution of the tasks, we examine a class of self-adjusting dynamic scheduling (SADS) algorithms that centralizes the assignment of tasks to processors. These algorithms dedicate a single processor of the multiprocessor to perform a novel on-line branch-and-bound technique that dynamically computes partial schedules based on the loads of the other processors and the memory locality (affinity) of the tasks and the processors. Our simulation results show that this centralized scheduling outperforms self-scheduling algorithms even when using only a small number of processors.
Estimating the internal structure of reservoirs with shear-wave VSPs (1986)

In the past 10 years, vertical seismic profiles (VSPs) have played an increasingly important role in identifying and delineating in situ layers. Such VSPs have usually recorded P-wave data. Three-component shear wave trains carry three or four times more information about the source and structure of the rocks along the raypath than the equivalent P-wave train so, in principle, shear-wave VSPs should be a particularly valuable technique for examining in situ layers.
Development of a Highly Sensitive Serum Neurofilament Light Chain Assay on an Automated Immunoassay Platform (2022)

ABSTRACT Background Neurofilament light chain (NfL) is an axonal cytoskeletal protein that is released into the extracellular space following neuronal or axonal injury associated with neurological conditions such as multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), and other diseases. NfL is detectable in cerebrospinal fluid (CSF) and blood. Numerous studies in MS have demonstrated that NfL correlates with disease activity, predicts disease progression, and is reduced by treatment with MS disease-modifying drugs, making NfL an attractive candidate to supplement existing clinical and imaging measures in MS. However, for NfL to achieve its potential as a clinically useful biomarker for clinical decision-making or drug development, a standardized, practical, widely accessible assay is needed. Our objective was to validate the analytical performance of the novel serum neurofilament light (sNfl) assay on the ADVIA Centaur® XP immunoassay system. Methods The research assay was evaluated on the ADVIA Centaur XP immunoassay system from Siemens Healthineers. The lower limit of quantitation (LLoQ), intra-assay variation, assay range, cross-reactivity with neurofilament medium and heavy chains, and effect of interfering substances were determined. NfL assay values in serum and CSF were compared with radiological and clinical disease activity measures in patients with MS and ALS, respectively. This assay was further optimized to utilize serum, plasma, and CSF sample types and transferred to Siemens’ CLIA laboratory, where it was analytically validated as a laboratory-developed test. Results In this study, a LLoQ of 1.85 pg/mL, intra-assay variation of &lt;6%, and an assay range of up to 646 pg/mL were demonstrated. A cross-reactivity of &lt;0.7% with neurofilament medium and heavy chains was observed, and the assay was not significantly affected by various interfering substances encountered in clinical specimens. Serum and CSF NfL assay values were associated with radiological and clinical disease activity measures in patients with MS and ALS, respectively. Conclusion The analytical performance of the NfL assay fulfilled all acceptance criteria; therefore, we believe the assay is acceptable for use in both research and clinical practice settings to determine elevated sNfL levels in patients.
On Integrated Access and Backhaul Networks: Current Status and Potentials (2020)

In this article, we introduce and study the potentials and challenges of integrated access and backhaul (IAB) as one of the promising techniques for evolving 5G networks. We study IAB networks from different perspectives. We summarize the recent Rel-16 as well as the upcoming Rel-17 3GPP discussions on IAB, and highlight the main IAB-specific agreements on different protocol layers. Also, concentrating on millimeter wave-based communications, we evaluate the performance of IAB networks in both dense and suburban areas. Using a finite stochastic geometry model, with random distributions of IAB nodes as well as user equipments (UEs) in a finite region, we study the service coverage rate defined as the probability of the event that the UEs' minimum rate requirements are satisfied. We present comparisons between IAB and hybrid IAB/fiber-backhauled networks where a part or all of the small base stations are fiber-connected. Finally, we study the robustness of IAB networks to weather and various deployment conditions and verify their effects, such as blockage, tree foliage, rain as well as antenna height/gain on the coverage rate of IAB setups, as the key differences between the fiber-connected and IAB networks. As we show, IAB is an attractive approach to enable the network densification required by 5G and beyond.
Sphingosine‐1‐Phosphate Modulates the Effect of Estrogen in Human Osteoblasts (2018)

Production of sphingosine-1-phosphate (S1P) is linked to 17β-estradiol (E2) activity in many estrogen-responsive cells; in bone development, the role of S1P is unclear. We studied effects of S1P on proliferation and differentiation of human osteoblasts (hOB). Ten nM E2, 1 μM S1P, or 1 μM of the S1P receptor 1 (S1PR1) agonist SEW2871 increased hOB proliferation at 24 hours. S1PR 1, 2, and 3 mRNAs are expressed by hOB but not S1PR4 or S1PR5. Expression of S1PR2 was increased at 7 and 14 days of differentiation, in correspondence with osteoblast-related mRNAs. Expression of S1PR1 was increased by E2 or S1P in proliferating hOB, whereas S1PR2 mRNA was unaffected in proliferating cells; S1PR3 was not affected by E2 or S1P. Inhibiting sphingosine kinase (SPHK) activity with sphingosine kinase inhibitor (Ski) greatly reduced the E2 proliferative effect. Both E2 and S1P increased SPHK mRNA at 24 hours in hOB. S1P promoted osteoblast proliferation via activating MAP kinase activity. Either E2 or S1P increased S1P synthesis in a fluorescent S1P assay. Interaction of E2 and S1P signaling was indicated by upregulation of E2 receptor mRNA after S1P treatment. E2 and S1P also promoted alkaline phosphatase expression. During osteoblast differentiation, S1P increased bone-specific mRNAs, similarly to the effects of E2. However, E2 and S1P showed differences in the activation of some osteoblast pathways. Pathway analysis by gene expression arrays was consistent with regulation of pathways of osteoblast differentiation; collagen and cell adhesion proteins centered on Rho/Rac small GTPase signaling and Map kinase or signal transducer and activator of transcription (Stat) intermediates. Transcriptional activation also included significant increases in superoxide dismutase 1 and 2 transcription by either S1P or E2. We demonstrate that the SPHK system is a co-mediator for osteoblast proliferation and differentiation, which is mainly, but not entirely, complementary to E2, whose effects are mediated by S1PR1 and S1PR2.
Distinguishing Failure to Cure From Complication After Penile Prosthesis Implantation (2017)

Patient-reported outcome assessments can vary greatly from what physicians determine to be successful PPI. An assessment of POPs encompasses more than just complication rates; it also reflects FTC. Even when POPs occur, patients can still derive satisfaction if they are correctively managed. Factors that possibly predispose to POPs include previous PPI surgery, body mass index greater than 30 kg/m<sup>2</sup>, and history of intracorporal injections. Pineda M, Burnett AL. Distinguishing Failure to Cure From Complication After Penile Prosthesis Implantation. J Sex Med 2017;14:731-737.
A Conventional Beagle Dog Model for Acute and Chronic Infection withHelicobacter pylori (1999)

Helicobacter pylori has been widely recognized as an important human pathogen responsible for chronic gastritis, peptic ulcers, gastric cancer, and mucosa-associated lymphoid tissue (MALT) lymphoma. Little is known about the natural history of this infection since patients are usually recognized as having the infection only after years or decades of chronic disease. Several animal models of H. pylori infection, including those with different species of rodents, nonhuman primates, and germ-free animals, have been developed. Here we describe a new animal model in which the clinical, pathological, microbiological, and immunological aspects of human acute and chronic infection are mimicked and which allows us to monitor these aspects of infection within the same individuals. Conventional Beagle dogs were infected orally with a mouse-adapted strain of H. pylori and monitored for up to 24 weeks. Acute infection caused vomiting and diarrhea. The acute phase was followed by polymorphonuclear cell infiltration, interleukin 8 induction, mononuclear cell recruitment, and the appearance of a specific antibody response against H. pylori. The chronic phase was characterized by gastritis, epithelial alterations, superficial erosions, and the appearance of the typical macroscopic follicles that in humans are considered possible precursors of MALT lymphoma. In conclusion, infection in this model mimics closely human infection and allows us to study those phases that cannot be studied in humans. This new model can be a unique tool for learning more about the disease and for developing strategies for treatment and prevention.
STED with wavelengths closer to the emission maximum (2012)

In stimulated emission depletion (STED) nanoscopy the wavelength of the STED beam is usually tuned towards the red tail of the emission maximum of the fluorophore. Shifting the STED wavelength closer to the emission peak, i.e. towards the blue region, favorably increases the stimulated emission cross-section. However, this blue-shifting also increases the probability to excite fluorophores that have remained in their ground state, compromising the image contrast. Here we present a method to exploit the higher STED efficiency of blue-shifted STED beams while maintaining the contrast in the image. The method is exemplified by imaging immunolabeled features in mammalian cells with an up to 3-fold increased STED efficiency compared to that encountered in standard STED nanoscopy implementations.
Long-term critical dimension measurement performance for a new mask CD-SEM, S-9380M (2007)

To realize good repeatability in CD measurements, many issues have to be addressed including system stability, sample charging and contamination, measurement conditions, and image processing. The S-9380M is a mask CD-SEM (Critical Dimension Scanning Electron Microscope) system developed for measurement and inspection of 45 nm node photomask. The S-9380M has several innovations like a newly designed optical system to minimize sample charge-up and drift effects, ultra-high resolution (3nm) imaging to enable measurements at high magnification, and an integrated ultra-violet (UV) unit for pre-treatment of the mask to rid the surface of organic contaminants. This paper presents measurements carried out using the S-9380M system, and showed that superior performance is achieved with short-term dynamic repeatability of 3&sigma; less than 0.6 nm (for line patterns), and long-term dynamic repeatability of 3&sigma; less than 1.0 nm without trend modification.
Modulation of Immune Cell Reactivity with Cis-Binding Siglec Agonist (2020)

Primary inflammatory pathologies caused by phagocytes lead to numerous debilitating conditions, including chronic pain and blindness due to age-related macular degeneration. Many members of the sialic acid-binding immunoglobulin-like lectin (Siglec) family are immunoinhibitory receptors whose agonism is an attractive approach to for anti-inflammatory therapy. Here, we show that synthetic lipid-conjugated glycopolypeptides can insert into cell membranes and engage Siglec receptors in cis, leading to inhibitory signaling. Specifically, we construct a cis-binding agonist of Siglec-9 and show that it modulates MAPK signaling in reporter cell lines, immortalized macrophage and microglial cell lines, and primary human macrophages. These cis-binding agonists of Siglecs present a new modality for therapeutic suppression of immune cell reactivity.