gebhart/patrepeval huggingface dataset:
Data-centric execution of speculative parallel programs (2016)

Multicore systems must exploit locality to scale, scheduling tasks to minimize data movement. While locality-aware parallelism is well studied in non-speculative systems, it has received little attention in speculative systems (e.g., HTM or TLS), which hinders their scalability. We present spatial hints, a technique that leverages program knowledge to reveal and exploit locality in speculative parallel programs. A hint is an abstract integer, given when a speculative task is created, that denotes the data that the task is likely to access. We show it is easy to modify programs to convey locality through hints. We design simple hardware techniques that allow a state-of-the-art, tiled speculative architecture to exploit hints by: (i) running tasks likely to access the same data on the same tile, (ii) serializing tasks likely to conflict, and (iii) balancing tasks across tiles in a locality-aware fashion. We also show that programs can often be restructured to make hints more effective. Together, these techniques make speculative parallelism practical on large-scale systems: at 256 cores, hints achieve near-linear scalability on nine challenging applications, improving performance over hint-oblivious scheduling by 3.3× gmean and by up to 16×. Hints also make speculation far more efficient, reducing wasted work by 6.4× and traffic by 3.5× on average.
Quantum Chemical Mass Spectrometry: Verification and Extension of the Mobile Proton Model for Histidine (2017)

The quantum chemical mass spectrometry for materials science (QCMS<sup>2</sup>) method is used to verify the proposed mechanism for proton transfer - the Mobile Proton Model (MPM) - by histidine for ten XHS tripeptides, based on quantum chemical calculations at the DFT/B3LYP/6-311+G* level of theory. The fragmentations of the different intermediate structures in the MPM mechanism are studied within the QCMS<sup>2</sup> framework, and the energetics of the proposed mechanism itself and those of the fragmentations of the intermediate structures are compared, leading to the computational confirmation of the MPM. In addition, the calculations suggest that the mechanism should be extended from considering only the formation of five-membered ring intermediates to include larger-ring intermediates. Graphical Abstract ᅟ.
Microglia Regulate Neuroglia Remodeling in Various Ocular and Retinal Injuries (2018)

Reactive microglia and infiltrating peripheral monocytes have been implicated in many neurodegenerative diseases of the retina and CNS. However, their specific contribution in retinal degeneration remains unclear. We recently showed that peripheral monocytes that infiltrate the retina after ocular injury in mice become permanently engrafted into the tissue, establishing a proinflammatory phenotype that promotes neurodegeneration. In this study, we show that microglia regulate the process of neuroglia remodeling during ocular injury, and their depletion results in marked upregulation of inflammatory markers, such as <i>Il17f</i>, <i>Tnfsf11, Ccl4, Il1a, Ccr2, Il4, Il5</i>, and <i>Csf2</i> in the retina, and abnormal engraftment of peripheral CCR2<sup>+</sup> CX3CR1<sup>+</sup> monocytes into the retina, which is associated with increased retinal ganglion cell loss, retinal nerve fiber layer thinning, and pigmentation onto the retinal surface. Furthermore, we show that other types of ocular injuries, such as penetrating corneal trauma and ocular hypertension also cause similar changes. However, optic nerve crush injury-mediated retinal ganglion cell loss evokes neither peripheral monocyte response in the retina nor pigmentation, although peripheral CX3CR1<sup>+</sup> and CCR2<sup>+</sup> monocytes infiltrate the optic nerve injury site and remain present for months. Our study suggests that microglia are key regulators of peripheral monocyte infiltration and retinal pigment epithelium migration, and their depletion results in abnormal neuroglia remodeling that exacerbates neuroretinal tissue damage. This mechanism of retinal damage through neuroglia remodeling may be clinically important for the treatment of patients with ocular injuries, including surgical traumas.
Split tolerance induced by the intrathymic adoptive transfer of thymocyte stem cells. (1988)

The intrathymic transfer of semiallogeneic CD4/CD8 double-negative (DN) thymocyte stem cells into irradiated host mice resulted in a transient state of chimerism in adoptive host thymus, spleen, and lymph nodes. Host-derived T cells, isolated from the thymus and periphery of the chimeric mice, were found to be specifically nonresponsive to the MHC antigens of the semiallogeneic DN donor in cytotoxicity assays. This nonresponsiveness was not permanent, but persisted as long as appreciable numbers of Thy-1 alloantigen-positive progeny of the DN donor cells could be detected in the spleen and lymph nodes of adoptive host mice. FACS sorting of DN donor cells before intrathymic transfer indicated that nonresponsiveness could be induced by Thy-1+ cells and was therefore not attributable to contaminating thymic macrophages, dendritic cells, or B cells. When FACS-sorted Thy-1+ (bm5 x bm12)F1 DN cells were transferred intrathymically into C57BL/6 hosts, nonresponsiveness to DN donor MHC class I but not class II alloantigen (split tolerance) was observed. These experiments were repeated using FACS-sorted Thy-1+ DN donor cells that were semiallogeneic to the irradiated adoptive host at either MHC class I or class II locus with similar results. Limiting dilution analysis showed that host-derived CTL precursors were tolerant of DN donor MHC class I alloantigen and no evidence for the involvement of suppressor T cells was found. The data indicate that murine thymocytes themselves are capable of tolerizing to MHC class I but not class II alloantigen after intrathymic transfer. The implications for intrathymic T cell differentiation and maintenance of self tolerance are discussed.
A continuum of Ins<i>P</i><sub>3</sub>‐mediated elementary Ca<sup>2+</sup> signalling events in <i>Xenopus</i> oocytes (1998)

1. The elementary release events underlying inositol 1,4, 5-trisphosphate (InsP3)-mediated calcium signalling were investigated in Xenopus oocytes by means of high-resolution confocal linescan imaging together with flash photolysis of caged InsP3. 2. Weak photolysis flashes evoked localized, transient calcium signals that arose at specific sites following random latencies of up to several seconds. The duration, spatial spread and amplitude of these elementary events varied widely. Event durations (at half-maximal amplitude) were distributed exponentially between about 100 and 600 ms. Fluorescence magnitudes (F/F0 of Oregon Green 488 BAPTA-1) showed a skewed distribution with a peak at about 1.5 and a tail extending as high as 3.5. 3. Individual release sites exhibited both small events (blips) and large events (puffs). The spatiotemporal distribution of calcium signals during puffs was consistent with calcium diffusion from a point source (< a few hundred nanometres), rather than with propagation of a microscopic calcium wave. 4. Estimates of the calcium flux associated with individual events were made by integrating fluorescence profiles along the scan line in three dimensions to derive the 'signal mass' at each time point. The smallest resolved events corresponded to liberation of < 2 x 10-20 mol Ca2+, and large events to about 2 x 10-18 mol Ca2+. The rise of signal mass was more prolonged than that of the fluorescence intensity, suggesting that calcium liberation persists even while the fluorescence begins to decline. Rates of rise of signal mass corresponded to Ca2+ currents of 0.4-2.5 pA. 5. Measurements of signal mass from different events showed a continuous, exponential distribution, arising through variability in magnitude and duration of calcium flux. 6. We conclude that localized calcium transients in the oocyte represent a continuum of events involving widely varying amounts of calcium liberation, rather than falling into separate populations of 'fundamental' and 'elementary' events (blips and puffs) involving, respectively, single and multiple InsP3 receptor channels. This variability probably arises through stochastic variation in both the number of channels recruited and the duration of channel opening.
Site-Specific Interaction between α-Synuclein and Membranes Probed by NMR-Observed Methionine Oxidation Rates (2013)

α-Synuclein (αS) is an intrinsically disordered protein that is water-soluble but also can bind negatively charged lipid membranes while adopting an α-helical conformation. Membrane affinity is increased by post-translational N-terminal acetylation, a common modification in all eukaryotic cells. In the presence of lipid vesicles containing a small fraction of peroxidized lipids, the N-terminal Met residues in αS (Met1 and Met5) rapidly oxidize while reducing the toxic lipid hydroperoxide to a nonreactive lipid hydroxide, whereas C-terminal Met residues remain unaffected. Met oxidation can be probed conveniently and quantitatively by NMR spectroscopy. The results show that oxidation of Met1 reduces the rate of oxidation of Met5 and vice versa as a result of decreased membrane affinity of the partially oxidized protein. The effect of Met oxidation on the αS-membrane affinity extends over large distances, as in the V49M mutant, oxidation of Met1 and Met5 strongly impacts the oxidation rate of Met49 and vice versa. When not bound to membrane, oxidized Met1 and Met5 of αS are excellent substrates for methionine sulfoxide reductase (Msr), thereby providing an efficient vehicle for water-soluble Msr enzymes to protect the membrane against oxidative damage.
ecMTCP: An Energy-Aware Congestion Control Algorithm for Multipath TCP (2011)

In this paper, we develop an energy-aware congestion control algorithm for multipath TCP, called ecMTCP. ecMTCP moves traffic from the most congested paths to the more lightly loaded paths, as well as from higher energy cost paths to the lower ones, thus achieving load-balancing and energy-savings. Our simulation results show that ecMTCP can achieve greater energy-savings compared to MPTCP, and preserve fairness to regular TCP.
Analysis of a thermal method for assessing endothelial dysfunction. (2004)

The presence of atherosclerosis not only affects the normal functioning of the coronary blood vessels but also of the peripheral vasculature. Property measurements made in the peripheral vasculature hence do reflect the condition of the coronary blood vessels. The endothelial cells form the inner lining of the blood vessels, and are responsible for the release of nitric oxide (NO) in order to control the vascular tone. Under normal conditions the artery will dilate in response to increased blood flow, mediated by the release of NO. The hampering of this normal response, caused by certain cardiovascular diseases, is referred to as endothelial dysfunction (EDF). Occlusion of the arm using a standard blood pressure cuff for five minutes followed by sudden release of the occlusion is known to create a reactive hyperemia in a normally functioning vasculature. We propose to measure the EDF by attempting to create this reactive hyperemia in the arm and measuring the temperature response in the hand and forearm, using a computer-based data acquisition system. The rate of temperature fall during occlusion and the temperature rate of rise after release are combined to assess EDF. An engineering analysis of the instrument was performed. Initial studies on normal subjects have indicated that the rate of rise is significantly higher than the rate of fall of temperature.
Ultrasensitive molecular absorption detection using metal slot antenna arrays (2015)

We theoretically study the transmission reduction of light passing through absorptive molecules embedded in a periodic metal slot array in a near infrared wavelength regime. From the analytically solved transmitted light, we present a simple relation given by the attenuation length of light at the resonance wavelength of the slot antennas with respect to the spectral width of the resonant transmission peak. This relation clearly explains that the control of the transmission reduction even with very low absorptive materials is possible. We investigate also the transmission reduction by absorptive molecules in a real metallic slot antenna array on a dielectric substrate and compare the results with finite difference time domain calculations. In numerical calculations, we demonstrate that the same amount of transmission reduction by a bulk absorptive material can be achieved only with one-hundredth thickness of the same material when it is embedded in an optimized Fano-resonant slot antenna array. Our relation presented in this study can contribute to label-free chemical and biological sensing as an efficient design and performance criterion for periodic slot antenna arrays.
<i>α</i>-MON: Traffic Anonymizer for Passive Monitoring (2021)

Packet measurements at scale are essential for several applications, such as cyber-security, accounting and troubleshooting. They, however, threaten users’ privacy by exposing sensitive information. Anonymization has been the answer to this challenge, i.e., replacing sensitive information with obfuscated copies. Anonymization of packet traces, however, comes with some challenges and drawbacks. First, it reduces the value of data. Second, it requires to consider diverse protocols because information may leak from many non-encrypted fields. Third, it must be performed at high speeds directly at the monitor, to prevent private data from leaking, calling for real-time solutions. We present <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\alpha $ </tex-math></inline-formula> -MON, a flexible tool for privacy-preserving packet monitoring. It replicates input packet streams to different consumers while anonymizing protocol fields according to flexible policies that cover all protocol layers. Beside classic anonymization mechanisms such as IP address obfuscation, <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\alpha $ </tex-math></inline-formula> -MON supports <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${z}$ </tex-math></inline-formula> -anonymization, a novel solution to obfuscate rare values that can be uniquely traced back to limited sets of users. Differently from classic anonymization approaches, <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z-anonymity</i> works on a streaming fashion, with zero delay, operating at high-speed links on a packet-by-packet basis. We quantify the impact of <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z-anonymity</i> on traffic measurements, finding that it introduces minimal error when it comes to finding heavy-hitter services. We evaluate <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\alpha $ </tex-math></inline-formula> -MON performance using packet traces collected from an ISP network and show that it achieves a sustainable rate of 40 Gbit/s on a Commercial Off-the Shelf server. <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\alpha $ </tex-math></inline-formula> -MON is available to the community as an open-source project.
Implicit Neural Spatial Representations for Time-dependent PDEs (2022)

Implicit Neural Spatial Representation (INSR) has emerged as an effective representation of spatially-dependent vector fields. This work explores solving time-dependent PDEs with INSR. Classical PDE solvers introduce both temporal and spatial discretizations. Common spatial discretizations include meshes and meshless point clouds, where each degree-of-freedom corresponds to a location in space. While these explicit spatial correspondences are intuitive to model and understand, these representations are not necessarily optimal for accuracy, memory usage, or adaptivity. Keeping the classical temporal discretization unchanged (e.g., explicit/implicit Euler), we explore INSR as an alternative spatial discretization, where spatial information is implicitly stored in the neural network weights. The network weights then evolve over time via time integration. Our approach does not require any training data generated by existing solvers because our approach is the solver itself. We validate our approach on various PDEs with examples involving large elastic deformations, turbulent fluids, and multi-scale phenomena. While slower to compute than traditional representations, our approach exhibits higher accuracy and lower memory consumption. Whereas classical solvers can dynamically adapt their spatial representation only by resorting to complex remeshing algorithms, our INSR approach is intrinsically adaptive. By tapping into the rich literature of classic time integrators, e.g., operator-splitting schemes, our method enables challenging simulations in contact mechanics and turbulent flows where previous neural-physics approaches struggle. Videos and codes are available on the project page: http://www.cs.columbia.edu/cg/INSR-PDE/
Exploiting Transport Activity of P-Glycoprotein at the Blood–Brain Barrier for the Development of Peripheral Cannabinoid Type 1 Receptor Antagonists (2012)

Although the CB1 receptor antagonist/inverse agonist rimonabant has positive effects on weight loss and cardiometabolic risk factors, neuropsychiatric side effects have prompted researchers to develop peripherally acting derivatives. Here, we investigated for a series of 3,4-diarylpyrazoline CB1 receptor antagonists if transport by the brain efflux transporter P-gp could be used as a selection criterion in the development of such drugs. All 3,4-diarylpyrazolines and rimonabant inhibited P-gp transport activity in membrane vesicles isolated from HEK293 cells overexpressing the transporter, but only the 1,1-dioxo-thiomorpholino analogue 23 exhibited a reduced accumulation (-38 ± 2%) in these cells, which could be completely reversed by the P-gp/BCRP inhibitor elacridar. In addition, 23 appeared to be a BCRP substrate, whereas rimonabant was not. In rats, the in vivo brain/plasma concentration ratio of 23 was significantly lower than for rimonabant (0.4 ± 0.1 vs 6.2 ± 1.6, p < 0.001). Coadministration of elacridar resulted in an 11-fold increase of the brain/plasma ratio for 23 (p < 0.01) and only 1.4-fold for rimonabant (p < 0.05), confirming the involvement of P-gp and possibly BCRP in limiting the brain entrance of 23 in vivo. In conclusion, these data support the conception that efflux via transporters such as P-gp and BCRP can limit the brain penetration of CB1 receptor antagonists, and that this property could be used in the development of peripheral antagonists.
Thermal Decomposition Study on Li2O2 for Li2NiO2 Synthesis as a Sacrificing Positive Additive of Lithium-Ion Batteries (2019)

Herein, thermal decomposition experiments of lithium peroxide (Li<sub>2</sub>O<sub>2</sub>) were performed to prepare a precursor (Li<sub>2</sub>O) for sacrificing cathode material, Li<sub>2</sub>NiO<sub>2</sub>. The Li<sub>2</sub>O<sub>2</sub> was prepared by a hydrometallurgical reaction between LiOH·H<sub>2</sub>O and H<sub>2</sub>O<sub>2</sub>. The overall reaction during annealing was found to involve the following three steps: (1) dehydration of LiOH·H<sub>2</sub>O, (2) decomposition of Li<sub>2</sub>O<sub>2</sub>, and (3) pyrolysis of the remaining anhydrous LiOH. This stepwise reaction was elucidated by thermal gravimetric and quantitative X-ray diffraction analyses. Furthermore, over-lithiated lithium nickel oxide (Li<sub>2</sub>NiO<sub>2</sub>) using our lithium precursor was synthesized, which exhibited a larger yield of 90.9% and higher irreversible capacity of 261 to 265 mAh g<sup>-1</sup> than the sample prepared by commercially purchased Li<sub>2</sub>O (45.6% and 177 to 185 mAh g<sup>-1</sup>, respectively) due to optimal powder preparation conditions.
Vision-sensorimotor abstraction and imagination towards exploring robot&amp;#x2019;s inner world (2008)

Based on indications from the neuroscience and psychology, both perception and action can be internally simulated by activating sensor and motor areas in the brain without external sensory input or without any resulting overt behavior. This hypothesis, however, can be highly useful in the real robot applications. The robot, for instance, can cover some of the corrupted sensory inputs by replacing them with its internal simulation. The accuracy of this hypothesis is strongly based on the agentpsilas experiences. As much as the agent knows about the environment, as much as it can build a strong internal representation about it. Although many works have been presented regarding to this hypothesis with various levels of success. At the sensorimotor abstraction level, where extracting data from the environment occur, however, none of them have so far used the robotpsilas vision as a sensory input. In this study, vision-sensorimotor abstraction is presented through memory-based learning in a real mobile robot ldquoHemissonrdquo to investigate the possibilities of explaining its inner world based on internal simulation of perception and action at the abstract level. The analysis of the experiments illustrate that our robot with vision sensory input has developed some kind of simple associations or anticipation mechanism through interacting with the environment, which enables, based on its history and the present situation, to guide its behavior in the absence of any external interaction.
Evaluation of a photodynamic therapy agent using a canine prostate cancer model (2023)

We have successfully established a PSMA-expressing canine orthotopic prostate tumor model and used the model to evaluate the PSMA-targeted nano agents (AuNPs-Pc158) in the application of FL imaging and PDT. It was demonstrated that the nano agents allowed visualization of the cancer cells and enabled their destruction when they were irradiated with a specific wavelength of light.
Culture-Based Virus Isolation To Evaluate Potential Infectivity of Clinical Specimens Tested for COVID-19 (2020)

Real-time reverse transcription-PCR (RT-PCR) is currently the most sensitive method to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19). However, the correlation between detectable viral RNA and culturable virus in clinical specimens remains unclear. Here, we performed virus culture for 60 specimens that were confirmed to be positive for SARS-CoV-2 RNA by real-time RT-PCR. The virus could be successfully isolated from 12 throat and nine nasopharyngeal swabs and two sputum specimens. The lowest copy number required for virus isolation was determined to be 5.4, 6.0, and 5.7 log<sub>10</sub> genome copies/ml sample for detecting the <i>nsp12</i>, <i>E</i>, and <i>N</i> genes, respectively. We further examined the correlation of genome copy number and virus isolation in different regions of the viral genome, demonstrating that culturable specimens are characterized by high copy numbers with a linear correlation observed between copy numbers of amplicons targeting structural and nonstructural regions. Overall, these results indicate that in addition to the copy number, the integrity of the viral genome should be considered when evaluating the infectivity of clinical SARS-CoV-2 specimens.