gebhart/patrepeval huggingface dataset:
Skewless Network Clock Synchronization (2012)

This paper examines synchronization of computer clocks connected via a data network and proposes a skewless algorithm to synchronize them. Unlike existing solutions, which either estimate and compensate the frequency difference (skew) among clocks or introduce offset corrections that can generate jitter and possibly even backward jumps, our algorithm achieves synchronization without these problems. We first analyze the convergence property of the algorithm and provide necessary and sufficient conditions on the parameters to guarantee synchronization. We then implement our solution on a cluster of IBM BladeCenter servers running Linux and study its performance. In particular, both analytically and experimentally, we show that our algorithm can converge in the presence of timing loops. This marks a clear contrast with current standards such as NTP and PTP, where timing loops are specifically avoided. Furthermore, timing loops can even be beneficial in our scheme. For example, it is demonstrated that highly connected subnetworks can collectively outperform individual clients when the time source has large jitter. It is also experimentally demonstrated that our algorithm outperforms other well-established software-based solutions such as the NTPv4 and IBM Coordinated Cluster Time (IBM CCT).
Gyramides Prevent Bacterial Growth by Inhibiting DNA Gyrase and Altering Chromosome Topology (2014)

Antibiotics targeting DNA gyrase have been a clinical success story for the past half-century, and the emergence of bacterial resistance has fueled the search for new gyrase inhibitors. In this paper we demonstrate that a new class of gyrase inhibitors, the gyramides, are bacteriostatic agents that competitively inhibit the ATPase activity of Escherichia coli gyrase and produce supercoiled DNA in vivo. E. coli cells treated with gyramide A have abnormally localized, condensed chromosomes that blocks DNA replication and interrupts chromosome segregation. The resulting alterations in DNA topology inhibit cell division through a mechanism that involves the SOS pathway. Importantly, gyramide A is a specific inhibitor of gyrase and does not inhibit the closely related E. coli enzyme topoisomerase IV. E. coli mutants with reduced susceptibility to gyramide A do not display cross-resistance to ciprofloxacin and novobiocin. The results demonstrate that the gyramides prevent bacterial growth by a mechanism in which the topological state of chromosomes is altered and halts DNA replication and segregation. The specificity and activity of the gyramides for inhibiting gyrase makes these compounds important chemical tools for studying the mechanism of gyrase and the connection between DNA topology and bacterial cell division.
In‐line optical monitoring of polymer injection molding (1994)

Abstract An optical sensor, consisting of optical fibers to transmit light to and from the mold cavity, was constructed for the purpose of measuring the onset of polymer solidification during injection molding. The sensor was used to detect characteristic fluorescence radiation from a dye which had been doped into the resin at very low concentration. By measuring changes in fluorescence intensity it was possible to detect whether the state of the resin was liquid or solid. We observed that, as the resin cooled in the mold, the onset of solidification was indicated by highly characteristic and distinct changes in the fluorescence intensity/time profile. Application of the method involved the use of a calibration relationship between the fluorescence intensity and temperature of the doped polymer in order to determine the distict features which characterize the onset of solidification. Injection molding of a glass forming polymer (polystyrene) and a crystallizable polymer (polyethylene) was monitored by this technique.
A New Family of Pyridine-Appended Multidentate Polymers As Hydrophilic Surface Ligands for Preparing Stable Biocompatible Quantum Dots (2014)

The growing utility of semiconductor quantum dots (QDs) in biochemical and cellular research necessitates, in turn, continuous development of surface functionalizing ligands to optimize their performance for ever more challenging and diverse biological applications. Here, we describe a new class of multifunctional polymeric ligands as a stable, compact and high affinity alternative to multidentate thiolated molecules. The polymeric ligands are designed with a poly(acrylic acid) backbone where pyridines are used as anchoring groups that are not sensitive to degradation by air and light, along with short poly(ethylene glycol) (PEG) pendant groups which are coincorporated for aqueous solubility, biocompatibility and colloidal stability. The percentages of each of the latter functional groups are controlled during initial synthesis along with incorporation of carboxyl groups which serve as chemical handles for subsequent covalent modification of the QD surface. A detailed physicochemical characterization indicates that the multiple pyridine groups are efficiently bound on the QD surface since they provide for relatively small overall hydrodynamic sizes along with good colloidal stability and strong fluorescence over a wide pH range, under high salt concentration and in extremely dilute conditions at room temperature under room light over extended timeframes. Covalent conjugation of dyes and metal-affinity coordination with functional enzymes to the QD surfaces were also demonstrated. Biocompatibility and long-term stability of the pyridine polymer coated QDs were then confirmed in a battery of relevant assays including cellular delivery by both microinjection and peptide facilitated uptake along with intracellular single QD tracking studies and cytotoxicity testing. Cumulatively, these results suggest this QD functionalization strategy is a viable alternative that provides some desirable properties of both compact, discrete ligands and large amphiphilic polymers.
MCDB-R (2010)

Enterprises often need to assess and manage the risk arising from uncertainty in their data. Such uncertainty is typically modeled as a probability distribution over the uncertain data values, specified by means of a complex (often predictive) stochastic model. The probability distribution over data values leads to a probability distribution over database query results, and risk assessment amounts to exploration of the upper or lower tail of a query-result distribution. In this paper, we extend the Monte Carlo Database System to efficiently obtain a set of samples from the tail of a query-result distribution by adapting recent "Gibbs cloning" ideas from the simulation literature to a database setting.
TAS0314, a novel multi-epitope long peptide vaccine, showed synergistic antitumor immunity with PD-1/PD-L1 blockade in HLA-A*2402 mice (2020)

Cancer peptide vaccines are a promising cancer immunotherapy that can induce cancer-specific cytotoxic T lymphocytes (CTLs) in tumors. However, recent clinical trials of cancer vaccines have revealed that the efficacy of the vaccines is limited. Targeting single antigens and vaccination with short peptides are partly the cause of the poor clinical outcomes. We synthesized a novel multi-epitope long peptide, TAS0314, which induced multiple epitope-specific CTLs in HLA knock-in mice. It also showed superior epitope-specific CTL induction and antitumor activity. We also established a combination treatment model of vaccination with PD-1/PD-L1 blockade in HLA-A*2402 knock-in mice, and it showed a synergistic antitumor effect with TAS0314. Thus, our data indicated that TAS0314 treatment, especially in combination with PD-1/PD-L1 blockade, is a promising therapeutic candidate for cancer immunotherapy.
On‐line ultrasonic monitoring of the injection molding process (1997)

Abstract On‐line ultrasonic monitoring of injection molding of a simple polymer box is studied using pulse‐echo techniques. The flow front of molten polymers inside the mold has been probed by a multiple‐channel probing system with a time resolution of 2 ms. This information can be used to control the plunger movements. The gap development, because of the shrinkage of the part in the mold, is also monitored. This information, which is important for the understanding of the part's cooling process, has been found to be superior than that measured by a conventional pressure probe. The relation between the gap formation time and the packing pressure has been investigated at various part locations characterized by different thicknesses. The velocity and the amplitude variations of ultrasonic waves, in a reflection as well as in a transmission configuration, have also been measured in the part's material during its solidification. The behavior of these ultrasonic parameters contributes to the interpretation of the solidification process.
Do Not Predict – Recompute! How Value Recomputation Can Truly Boost the Performance of Invisible Speculation (2021)

Recent architectural approaches that address speculative side-channel attacks aim to prevent software from exposing the microarchitectural state changes of transient execution. The Delay-on-Miss technique is one such approach, which simply delays loads that miss in the L1 cache until they become non-speculative, resulting in no transient changes in the memory hierarchy. However, this costs performance, prompting the use of value prediction (VP) to regain some of the delay.However, the problem cannot be solved by simply introducing a new kind of speculation (value prediction). Value-predicted loads have to be validated, which cannot be commenced until the load becomes non-speculative. Thus, value-predicted loads occupy the same amount of precious core resources (e.g., reorder buffer entries) as Delay-on-Miss. The end result is that VP only yields marginal benefits over Delay-on-Miss.In this paper, our insight is that we can achieve the same goal as VP (increasing performance by providing the value of loads that miss) without incurring its negative side-effect (delaying the release of precious resources), if we can safely, non-speculatively, recompute a value in isolation (without being seen from the outside), so that we do not expose any information by transferring such a value via the memory hierarchy. Value Recomputation, which trades computation for data transfer was previously proposed in an entirely different context: to reduce energy-expensive data transfers in the memory hierarchy. In this paper, we demonstrate the potential of value recomputation in relation to the Delay-on-Miss approach of hiding speculation, discuss the trade-offs, and show that we can achieve the same level of security, reaching 93% of the unsecured baseline performance (5% higher than Delay-on-miss), and exceeding (by 3%) what even an oracular (100% accuracy and coverage) value predictor could do.
Improving Perceived QoS of Delay-sensitive Video Against A Weak Last-mile: A Practical Approach (2021)

We present a novel approach to improve the perceived QoS for video-feeds in delay-sensitive interactive applications under practical last-mile impairments. Conventional approaches consume additional communication and computation resources in the effort to regain the PSNR of the frames by trying to recover the lost information. Such approaches undermine the strict latency requirements leading to eventual frame-drop and reduction in overall system QoE. Instead, we aim to create an approximation of the corrupted frame by regaining the structural information and minimizing the effect of the lost packet(s). The objective is to minimize the possibility of frame drop under weakened last-mile connection so that the remote user can have a better perceived QoS at the application level and can have better probability of reacting to remote scene despite lossy condition. We prove the efficiency of the system under real-life situations with impairments in real field deployment. The benchmarking is performed in terms of full referential video quality metrics against established state-of-the art like WebRTC and RTP.
High-dynamic-range transmission-mode detection of synchrotron radiation\n using X-ray excited optical luminescence in diamond (2020)

We demonstrate enhancement of X-ray excited optical luminescence in a\n100-micron-thick diamond plate by introduction of defect states via electron\nbeam irradiation and subsequent high-temperature annealing. The resulting X-ray\ntransmission-mode scintillator features a linear response to incident photon\nflux in the range of 7.6$\\times$10$^8$ to 1.26$\\times10^{12}$ photons/s/mm$^2$\nfor hard X-rays (15.9 keV) using exposure times from 0.01 to 5 s. These\ncharacteristics enable a real-time transmission-mode imaging of X-ray photon\nflux density without disruption of X-ray instrument operation.\n
Speculative precomputation: long-range prefetching of delinquent loads (2002)

This paper explores Speculative Precomputation, a technique that uses idle thread contexts in a multithreaded architecture to improve performance of single-threaded applications. It attacks program stalls from data cache misses by pre-computing future memory accesses in available thread contexts, and prefetching these data. This technique is evaluated by simulating the performance of a research processor based on the Itanium/sup TM/ ISA supporting Simultaneous Multithreading. Two primary forms of Speculative Precomputation are evaluated. If only the non-speculative thread spawns speculative threads, performance gains of up to 30% are achieved when assuming ideal hardware. However, this speedup drops considerably with more realistic hardware assumptions. Permitting speculative threads to directly spawn additional speculative threads reduces the overhead associated with spawning threads and enables significantly more aggressive speculation, overcoming this limitation. Even with realistic costs for spawning threads, speedups as high as 169% are achieved, with an average speedup of 76%.
Poly(methyl acrylate‐co‐hydroxyethyl acrylate) hydrogel implant material of strength and softness (1981)

The physiochemical properties of a hydrogel used as a scleral buckling implant for retinal detachment surgery are described. The new material was prepared by simultaneous polymerization and crosslinking of 2-hydroxyethyl acrylate with methyl acrylate and ethylene diacrylate, in the presence of an inert diluent, ethylene glycol. At equilibrium swelling, the hydrogen absorbed 17% water and had a durometer hardness (DH) of 15 (Shore Durometer A-2). A unique property of this material was its swelling hysteresis; when the gel swollen in 70% ethanol was placed in water, it retained a high level of hydration (75% water) and softness (DH 8), and most of its elasticity and strength as well. Then the swelling decreased very slowly so that the implant reached its ultimate size at equilibrium swelling in ca. 1 year. This property is especially useful in the scleral buckling procedure, in which a soft implant indents the sclera over the detached retina until reattachment is achieved. In addition to this advantage, this hydrogel is more elastic and stronger than available hydrogels of similar softness.
Abstract 5587: Ultra-deep targeted sequencing of cell-free DNA and patient-matched white blood cells for treatment response evaluation in patients with metastatic colorectal cancer (2023)

Abstract Background: Treatment response monitoring of patients with metastatic colorectal cancer is currently performed by computed tomography (CT) imaging, which assesses tumor volume. Circulating tumor DNA (ctDNA) testing has the potential to replace or complement CT imaging by assessing the presence and abundance of tumor-specific mutations, allowing for personalized treatment and early adaptation of treatment regimens through risk stratification and the emergence of therapy resistance mutations. However, germline and clonal hematopoiesis-associated alterations can confound the identification of tumor-specific alterations in cell-free DNA (cfDNA), often requiring additional sequencing of tumor tissue. Aim: The present study assessed whether ctDNA-based treatment response monitoring could be performed in a tumor tissue-independent manner by combining ultra-deep targeted sequencing analyses of cfDNA with patient-matched white blood cell (WBC) derived DNA. Methods: In total, 183 cfDNA and 49 WBC samples, along with 28 tissue samples, from 52 metastatic colorectal cancer patients participating in the prospective phase III CAIRO5 clinical trial were analyzed using an ultra-deep targeted sequencing liquid biopsy assay. Results: The combined cfDNA and WBC analysis prevented the reporting of false positives due to germline or hematopoietic variants in 40% of patients. Patient-matched tumor tissue sequencing did not provide additional information. Longitudinal analyses of ctDNA were more predictive of overall survival than standard-of-care radiological response evaluation. ctDNA mutations related to primary or acquired resistance to the EGFR inhibitor panitumumab were identified in 42% of patients. Conclusions: Accurate ctDNA mutation detection by combined cfDNA and WBC genomic DNA analyses in a tumor tissue-independent manner mitigates sample logistics challenges in the clinical setting, and the application of this approach for evaluation of therapeutic response and resistance opens new avenues for early adaptation of treatment regimens. Citation Format: Iris van 't Erve, Jamie E. Medina, Alessandro Leal, Eniko Papp, Jillian Phallen, Vilmos Adleff, Elaine Jiayuee Chiao, Adith S. Arun, Karen Bolhuis, John K. Simmons, Aanavi Karandikar, Kenneth C. Valkenburg, Mark Sausen, Samuel V. Angiuoli, Robert B. Scharpf, Cornelis J. Punt, Gerrit J. Meijer, Victor E. Velculescu, Remond J. Fijneman. Ultra-deep targeted sequencing of cell-free DNA and patient-matched white blood cells for treatment response evaluation in patients with metastatic colorectal cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5587.
Low‐Overpotential Electrocatalytic Water Splitting with Noble‐Metal‐Free Nanoparticles Supported in a sp<sup>3</sup> N‐Rich Flexible COF (2016)

Covalent organic frameworks (COFs) are crystalline organic polymers with tunable structures. Here, a COF is prepared using building units with highly flexible tetrahedral sp 3 nitrogens. This flexibility gives rise to structural changes which generate mesopores capable of confining very small (<2 nm sized) non‐noble‐metal‐based nanoparticles (NPs). This nanocomposite shows exceptional activity toward the oxygen‐evolution reaction from alkaline water with an overpotential of 258 mV at a current density of 10 mA cm −2 . The overpotential observed in the COF‐nanoparticle system is the best in class, and is close to the current record of ≈200 mV for any noble‐metal‐free electrocatalytic water splitting system—the Fe–Co–Ni metal‐oxide‐film system. Also, it possesses outstanding kinetics (Tafel slope of 38.9 mV dec −1 ) for the reaction. The COF is able to stabilize such small‐sized NP in the absence of any capping agent because of the COF–Ni(OH) 2 interactions arising from the N‐rich backbone of the COF. Density‐functional‐theory modeling of the interaction between the hexagonal Ni(OH) 2 nanosheets and the COF shows that in the most favorable configuration the Ni(OH) 2 nanosheets are sandwiched between the sp 3 nitrogens of the adjacent COF layers and this can be crucial to maximizing their synergistic interactions.
Design, fabrication, and performance of integrated miniature SQUID susceptometers (1989)

The design, construction, and performance of miniature SQUID (superconducting quantum interference device) susceptometers is discussed. Spins (in units of mu /sub beta /) per square root Hz has been identified as an important figure of merit. Simple expressions for S/sub n/ (spin sensitivity) in miniature SQUID susceptometers are developed and the implications of dimensional scaling explored. The details of several existing and proposed designs are reviewed, including versions that utilize commercial SQUIDs. With thin-film DC SQUIDs, S/sub n/ values of a few thousand spins/ square root Hz have already been obtained, and it is projected that values of a few hundred will be achieved soon.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
On the Properties of Bit-Reversal Shortening in Polar Codes (2018)

Puncturing and shortening are widely used methods employed to design arbitrary rate codes from a mother code of given rate. In the context of polar codes, the encoding process has to be completely redone based on the codelength and coding rate for any given shortening/puncturing pattern which makes the implementation of a rate-compatible polar code system very complex. This happens as reliability ordering of the polarized bit-channels gets altered post shortening/puncturing; thus making it necessary to recompute the bit-channel reliabilities tailored to the new reduced codelength followed by sorting them again (in other words, a complete reconstruction). It has been noted before that a bit reversal shortening (BRS) scheme has a special property: it does not require the said reordering of bit-channels, which makes the encoder implementation significantly simple and pragmatic. While this property is extremely intriguing both theoretically and practically, no detailed study on this subject is available in literature. In this paper, we show the relation of BRS with prior art, highlight the said property across wide range of code parameters and then delve deep into what leads up to that property. We observe that like all other schemes, BRS also changes the reliability order of indices, but in a very localized manner. Consequently, the non-frozen set for bit-reverse shortened polar code is nearly same as that of the mother code. Extensive simulation of polar codes is provided to validate the findings.
TailoredBRIEF: Online per-feature descriptor customization (2015)

Image feature descriptors composed of a series of binary intensity comparisons yield substantial memory and runtime improvements over conventional descriptors, but are sensitive to viewpoint changes in ways that vary per feature. We propose a method to improve the matching performance of such descriptors by specifically reasoning about the reliability of test results on a feature-by-feature basis. We demonstrate an intuitive method to learn improved descriptor structures for individual features. Further, these learned results can be efficiently applied during matching with little increase in runtime. We provide an evaluation using a standard, ground-truthed, multi-image dataset.