gebhart/patrepeval huggingface dataset:
Cooperative Network Coding for Distributed Storage using Base Stations\n with Link Constraints (2021)

In this work, we consider a novel distributed data storage/caching scenario\nin a cellular setting where multiple nodes may fail/depart at the same time. In\norder to maintain the target reliability, we allow cooperative regeneration of\nlost nodes with the help of base stations allocated in a set of hierarchical\nlayers. Due to this layered structure, a symbol download from each base station\nhas a different cost, while the link capacities connecting the nodes of the\ncellular system and the base stations are also limited. In this more practical\nand general scenario, we present the fundamental trade-off between repair\nbandwidth cost and the storage space per node. Particularly interesting\noperating points are the minimum storage as well as bandwidth cost points in\nthis trade-off curve. We provide closed-form expressions for the corresponding\nbandwidth (cost) and storage space per node for these operating points.\nFinally, we provide an explicit optimal code construction for the minimum\nstorage regeneration point for a given set of system parameters.\n
Free-electron interactions with photonic GKP states: error correction and universal quantum computation (2023)

We find that interactions of coherently-shaped free electrons with photons enable universal quantum computation and error correction with GKP qubits. The electron can entangle multiple GKP qubits, creating GHZ and cluster states.
Repeatability of dose painting by numbers treatment planning in prostate cancer radiotherapy based on multiparametric magnetic resonance imaging (2017)

Dose painting by numbers (DPBN) refers to a voxel-wise prescription of radiation dose modelled from functional image characteristics, in contrast to dose painting by contours which requires delineations to define the target for dose escalation. The direct relation between functional imaging characteristics and DPBN implies that random variations in images may propagate into the dose distribution. The stability of MR-only prostate cancer treatment planning based on DPBN with respect to these variations is as yet unknown. We conducted a test-retest study to investigate the stability of DPBN for prostate cancer in a semi-automated MR-only treatment planning workflow. Twelve patients received a multiparametric MRI on two separate days prior to prostatectomy. The tumor probability (TP) within the prostate was derived from image features with a logistic regression model. Dose mapping functions were applied to acquire a DPBN prescription map that served to generate an intensity modulated radiation therapy (IMRT) treatment plan. Dose calculations were done on a pseudo-CT derived from the MRI. The TP and DPBN map and the IMRT dose distribution were compared between both MRI sessions, using the intraclass correlation coefficient (ICC) to quantify repeatability of the planning pipeline. The quality of each treatment plan was measured with a quality factor (QF). Median ICC values for the TP and DPBN map and the IMRT dose distribution were 0.82, 0.82 and 0.88, respectively, for linear dose mapping and 0.82, 0.84 and 0.94 for square root dose mapping. A median QF of 3.4% was found among all treatment plans. We demonstrated the stability of DPBN radiotherapy treatment planning in prostate cancer, with excellent overall repeatability and acceptable treatment plan quality. Using validated tumor probability modelling and simple dose mapping techniques it was shown that despite day-to-day variations in imaging data still consistent treatment plans were obtained.
Data from Dual mTORC1/2 and HER2 Blockade Results in Antitumor Activity in Preclinical Models of Breast Cancer Resistant to Anti-HER2 Therapy (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The PI3K/Akt/mTOR pathway is an attractive target in HER2-positive breast cancer that is refractory to anti-HER2 therapy. The hypothesis is that the suppression of this pathway results in sensitization to anti-HER2 agents. However, this combinatorial strategy has not been comprehensively tested in models of trastuzumab and lapatinib resistance.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We analyzed &lt;i&gt;in vitro&lt;/i&gt; cell viability and induction of apoptosis in five different cell lines resistant to trastuzumab and lapatinib. Inhibition of HER2/HER3 phosphorylation, PI3K/Akt/mTOR, and extracellular signal-regulated kinase (ERK) signaling pathways was evaluated by Western blotting. Tumor growth inhibition after treatment with lapatinib, INK-128, or the combination of both agents was evaluated in three different animal models: two cell-based xenograft models refractory to both trastuzumab and lapatinib and a xenograft derived from a patient who relapsed on trastuzumab-based therapy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The addition of lapatinib to INK-128 prevented both HER2 and HER3 phosphorylation induced by INK-128, resulting in inhibition of both PI3K/Akt/mTOR and ERK pathways. This dual blockade produced synergistic induction of cell death in five different HER2-positive cell lines resistant to trastuzumab and lapatinib. &lt;i&gt;In vivo&lt;/i&gt;, both cell line–based and patient-derived xenografts showed exquisite sensitivity to the antitumor activity of the combination of lapatinib and INK-128, which resulted in durable tumor shrinkage and exhibited no signs of toxicity in these models.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The simultaneous blockade of both PI3K/Akt/mTOR and ERK pathways obtained by combining lapatinib with INK-128 acts synergistically in inducing cell death and tumor regression in breast cancer models refractory to anti-HER2 therapy. &lt;i&gt;Clin Cancer Res; 18(9); 2603–12. ©2012 AACR.&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Microwave Absorption and Molecular Structure in Liquids. XIII. The Critical Wavelengths of Some Aliphatic Ethers and Long-Chain Ketones (1956)

The dielectric constants and losses of ethyl ether, n-decyl ether, n-heptanone-2, n-pentadecanone-8, n-heptadecanone-9, and benzophenone, and of solutions of benzophenone in heptane and in a 50–50 mixture of heptane and benzene have been measured at wavelengths of 1.25, 3.22, and 10.0 cm at temperatures between 4 and 85°. The arc plots constructed from these data and the measured low-frequency dielectric constants have been used to calculate the critical wavelengths at which the loss is a maximum. Several molecules of similar sizes and shapes are shown to possess similar viscosities and critical wavelengths. For the pure polar liquids, a rough proportionality between the critical wavelengths or dielectric relaxation times and the viscosities is observed.
<title>10-Gb/s VCSEL-based data links</title> (2000)

Standards activities for the next generation of Ethernet, 10 Gigabit Ethernet, are underway. Vertical Cavity Surface Emitting Lasers (VCSELs) offer significant advantages for realizing cost-effective, high speed optical data links. The progress towards achieving 10 Gb/s VCSEL-based links is reviewed.
Flightless-1 inhibits ER stress-induced apoptosis in colorectal cancer cells by regulating Ca2+ homeostasis (2020)

The endoplasmic reticulum (ER) stress response is an adaptive mechanism that is activated upon disruption of ER homeostasis and protects the cells against certain harmful environmental stimuli. However, critical and prolonged cell stress triggers cell death. In this study, we demonstrate that Flightless-1 (FliI) regulates ER stress-induced apoptosis in colon cancer cells by modulating Ca<sup>2+</sup> homeostasis. FliI was highly expressed in both colon cell lines and colorectal cancer mouse models. In a mouse xenograft model using CT26 mouse colorectal cancer cells, tumor formation was slowed due to elevated levels of apoptosis in FliI-knockdown (FliI-KD) cells. FliI-KD cells treated with ER stress inducers, thapsigargin (TG), and tunicamycin exhibited activation of the unfolded protein response (UPR) and induction of UPR-related gene expression, which eventually triggered apoptosis. FliI-KD increased the intracellular Ca<sup>2+</sup> concentration, and this upregulation was caused by accelerated ER-to-cytosolic efflux of Ca<sup>2+</sup>. The increase in intracellular Ca<sup>2+</sup> concentration was significantly blocked by dantrolene and tetracaine, inhibitors of ryanodine receptors (RyRs). Dantrolene inhibited TG-induced ER stress and decreased the rate of apoptosis in FliI-KD CT26 cells. Finally, we found that knockdown of FliI decreased the levels of sorcin and ER Ca<sup>2+</sup> and that TG-induced ER stress was recovered by overexpression of sorcin in FliI-KD cells. Taken together, these results suggest that FliI regulates sorcin expression, which modulates Ca<sup>2+</sup> homeostasis in the ER through RyRs. Our findings reveal a novel mechanism by which FliI influences Ca<sup>2+</sup> homeostasis and cell survival during ER stress.
Optical Properties of A-Plane InGaN/GaN Multiple Quantum Wells Grown on Nanorod Lateral Overgrowth Templates (2011)

A-plane InGaN/GaN multiple-quantum wells (MQWs) were grown on a series of nanorod epitaxial lateral overgrowth (NRELOG) templates with varied nanorod depth. Optical properties of these samples were investigated by excitation power and temperature-dependent photoluminescence (PL). Due to the absence of quantum-confined Stark effect, the negligible PL emission peak shift and nearly identical power index for all samples were observed. In contrast to the as-grown MQWs, the thermal activation energy and internal quantum efficiency of NRELOG MQWs exhibit 1.6-fold and 4-fold increases, respectively, which are attributed to the improvement of crystal quality by NRELOG. Furthermore, the Shockley-Read-Hall nonradiative coefficient, determined from the fits of power-dependent PL quantum efficiency, is also apparently reduced while MQWs are grown on NRELOG GaN template. The results show the feasibility to fabricate high radiative efficiency a-plane devices via NRELOG.
Palliation of Esophageal Carcinoma with a New Self-Expanding Plastic Stent (2003)

These results show that SEPS are effective for the palliation of dysphagia in patients with esophageal malignancies. The immediate results are similar to those observed with SEMS, and the observed low rate of late obstruction suggests that their long-term efficacy might be superior to that of SEMS. This device warrants evaluation in a controlled prospective trial.
Systematic Review and Meta-Analysis: Clinical, Endoscopic, Histological and Safety Placebo Rates in Induction and Maintenance Trials of Ulcerative Colitis (2021)

Placebo rates in ulcerative colitis trials vary according to the endpoint assessed, whether it is for assessment of response or remission, and whether the trial is designed for induction or maintenance. These contemporary rates across different endpoints and drug classes will help to inform trial design.
Rapid Laser Induced Crystallization of Amorphous NiTi Films Observed by Nanosecond Dynamic Transmission Electron Microscopy (DTEM) (2010)

The crystallization processes of the as-deposited, amorphous NiTi thin films have been studied in detail using techniques such as differential scanning calorimetry and, in-situ TEM. The kinetic data have been analyzed in terms of Johnson-Mehl-Avrami-Kolomogrov (JMAK) semi-empirical formula. The kinetic parameters determined from this analysis have been useful in defining process control parameters for tailoring microstructural features and shape memory properties. Due to the commercial push to shrink thin film-based devices, unique processing techniques have been developed using laser-based annealing to spatially control the microstructure evolution down to sub-micron levels. Nanosecond, pulse laser annealing is particularly attractive since it limits the amount of peripheral heating and unwanted microstructural changes to underlying or surrounding material. However, crystallization under pulsed laser irradiation can differ significantly from conventional thermal annealing, e.g., slow heating in a furnace. This is especially true for amorphous NiTi materials and relevant for shape memory thin film based microelectromechanical systems (MEMS) applications. There is little to no data on the crystallization kinetics of NiTi under pulsed laser irradiation, primarily due to the high crystallization rates intrinsic to high temperature annealing and the spatial and temporal resolution limits of standard techniques. However, with the high time and spatial resolution capabilities of the dynamic transmission electron microscope (DTEM) constructed at Lawrence Livermore National Laboratory, the rapid nucleation events occurring from pulsed laser irradiation can be directly observed and nucleation rates can be quantified. This paper briefly explains the DTEM approach and how it used to investigate the pulsed laser induced crystallization processes in NiTi and to determine kinetic parameters.
Microfluidic origami: a new device format for in-line reaction monitoring by nanoelectrospray ionization mass spectrometry (2013)

Microfluidics is an attractive platform for chemical synthesis because it offers fast reaction times, reduced reagent usage, and the ability to integrate multiple functions on a single device. Digital Microfluidics (DMF) is particularly well-suited for microscale chemical synthesis, as it permits discretized sample handling, allowing for total process control. However, a limitation of DMF-based synthesis is analysis, which is often performed offline. To this end, we have developed "microfluidic origami", a new device format that integrates DMF with in-line analysis by mass spectrometry (MS). This format comprises a DMF platform and a folded nanoelectrospray ionization (nanoESI) emitter formed on a single flexible polyimide film substrate. Additionally, the device contains a two-plate-to-one-plate DMF interface, which allows for straightforward coupling of micro-reaction operations and product delivery to the emitter for analysis. The integrated platform was used to perform the Morita-Baylis-Hillman (MBH) reaction using DMF followed by inline MS analysis for monitoring the reaction progress in real-time. We propose that this platform has potential as a new tool for real-time monitoring of reaction rates and reaction pathways and could be a useful addition to the synthetic organic chemistry laboratory.
Externalization of the Leaderless Cytokine IL-1F6 Occurs in Response to Lipopolysaccharide/ATP Activation of Transduced Bone Marrow Macrophages (2009)

An interesting trait shared by many members of the IL-1 cytokine family is the absence of a signal sequence that can direct the newly synthesized polypeptides to the endoplasmic reticulum. As a result, these cytokines accumulate intracellularly. Recent studies investigating IL-1beta export established that its release is facilitated via activation of an intracellular multiprotein complex termed the inflammasome. The purpose of the current study was to explore the mechanism by which murine IL-1F6 is released from bone marrow-derived macrophages (BMDMs) and to compare this mechanism to that used by IL-1beta. BMDMs were engineered to overexpress IL-1F6 by retroviral transduction; cells overexpressing GFP also were generated to provide a noncytokine comparator. The transduced cells constitutively expressed IL-1F6 and GFP, but they did not constitutively release these polypeptides to the medium. Enhanced release of IL-1F6 was achieved by treating with LPS followed by ATP-induced activation of the P2X(7) receptor; GFP also was released under these conditions. No obvious proteolytic cleavage of IL-1F6 was noted following P2X(7) receptor-induced release. Stimulus-induced release of IL-1F6 and GFP demonstrated comparable susceptibility to pharmacological modulation. Therefore, transduced IL-1F6 is released in parallel with endogenous mature IL-1beta from LPS/ATP-treated BMDMs, but this externalization process is not selective for cytokines as a noncytokine (GFP) shows similar behavior. These findings suggest that IL-1F6 can be externalized via a stimulus-coupled mechanism comparable to that used by IL-1beta, and they provide additional insight into the complex cellular processes controlling posttranslational processing of the IL-1 cytokine family.
Adaptive Hamiltonian estimation using Bayesian experimental design (2012)

Using Bayesian experimental design techniques, we have shown that for a single twolevel quantum mechanical system under strong (projective) measurement, the dynamical parameters of a model Hamiltonian can be estimated with exponentially improved accuracy over offline estimation strategies. To achieve this, we derive an adaptive protocol which finds the optimal experiments based on previous observations. We show that the risk associated with this algorithm is close to the global optimum, given a uniform prior. Additionally, we show that sampling at the Nyquist rate is not optimal.
Improvements in automated PNA synthesis using Boc/Z monomers (1997)

An optimized automated PNA synthesis protocol is reported. Under optimal conditions the product yield of a test 17-mer PNA is approximately 90%. The average coupling yield is 99.4%. The synthesis strategy is Boc/Z and the deprotected amine is neutralized in situ. The monomers are added in molar excess to HATU and pre-activated for 60 s before delivery to the resin. The concentration of the activated monomers is 0.08 M during the couplings. Heteroselective solvation provides the highest coupling yields. Acetic anhydride is used as capping reagent followed by a piperidine wash. The protocol has been developed in a 5 mumol scale but is easily scaled up to 10-50 mumol scale syntheses on the automated synthesizer (ABI 433A).
The Mitochondrion Is a Site of Trypanocidal Action of the Aromatic Diamidine DB75 in Bloodstream Forms of Trypanosoma brucei (2007)

Human African trypanosomiasis (HAT) is a fatal tropical disease caused by infection with protozoans of the species Trypanosoma brucei gambiense and T. b. rhodesiense. An oral prodrug, DB289, is a promising new therapy undergoing phase III clinical trials for early-stage HAT. DB289 is metabolically converted to the active trypanocidal diamidine DB75 [2,5-bis(4-amidinophenyl)furan]. We previously determined that DB75 inhibits yeast mitochondrial function (C. A. Lanteri, B. L. Trumpower, R. R. Tidwell, and S. R. Meshnick, Antimicrob. Agent Chemother. 48:3968-3974, 2004). The purpose of this study was to investigate if DB75 targets the mitochondrion of T. b. brucei bloodstream forms. DB75 rapidly accumulates within the mitochondria of living trypanosomes, as indicated by the fluorescent colocalization of DB75 with a mitochondrion-specific dye. Fluorescence-activated cell sorting analysis of rhodamine 123-stained living trypanosomes shows that DB75 and other trypanocidal diamidines (pentamidine and diminazene) collapse the mitochondrial membrane potential. DB75 inhibits ATP hydrolysis within T. brucei mitochondria and appears to inhibit the oligomycin-sensitive F 1 F 0-ATPase and perhaps other ATPases. DB75 is most likely not an inhibitor of electron transport within trypanosome mitochondria, since DB75 fails to inhibit mitochondrial respiration when glycerol-3-phosphate is used as the respiratory substrate. However, DB75 inhibits whole-cell respiration (50% inhibitory concentration, 20 microM) at drug concentrations and incubation durations that also result in the dissipation of the mitochondrial membrane potential. Taken together, these findings suggest that the mitochondrion is a target of the trypanocidal action of DB75.
Novel Eukaryotes from the Permanently Anoxic Cariaco Basin (Caribbean Sea) (2003)

Present knowledge of microbial diversity is decidedly incomplete (S. J. Giovannoni and M. S. Rappé, p. 47-84, in D. Kirchman, ed., Microbial Ecology of the Oceans, 2000; E. Stackebrandt and T. M. Embley, p. 57-75, in R. R. Colwell and D. J. Grimes, ed., Nonculturable Microorganisms in the Environment, 2000). Protistan phylogenies are particularly deficient and undoubtedly exclude clades of principal ecological and evolutionary importance (S. L. Baldauf, Science 300:1703-1706, 2003). The rRNA approach has been extraordinarily successful in expanding the global prokaryotic record (S. J. Giovannoni and M. S. Rappé, p. 47-84, in D. Kirchman, ed., Microbial Ecology of the Oceans, 2000; E. Stackebrandt and T. M. Embley, p. 57-75, in R. R. Colwell and D. J. Grimes, ed., Nonculturable Microorganisms in the Environment, 2000) but has rarely been used in protistan discovery. Here we report the first application of the 18S rRNA approach to a permanently anoxic environment, the Cariaco Basin off the Venezuelan coast. On the basis of rRNA sequences, we uncovered a substantial number of novel protistan lineages. These included new clades of the highest taxonomic level unrelated to any known eukaryote as well as deep branches within established protistan groups. Three novel lineages branch at the base of the eukaryotic evolutionary tree preceding, contemporary with, or immediately following the earliest eukaryotic branches. These newly discovered protists may retain traits reminiscent of an early eukaryotic ancestor(s).
Performance Analysis of the IEEE 802.11s PSM (2012)

With the introduction of IEEE 802.11 power save mode (PSM), a lot of work has been done to enhance the energy saving ability of the wireless nodes. The ultimate goal of the research is to make the networking equipment carbon neutral and prolong the lifetime of the energy limited device for various applications; in some cases it is a trade-off between energy efficiency and delay. However, few studies have been made until now in the area of IEEE 802.11s based link specific power mode. The essence of this method is the ability of a node to maintain different power modes with its different peer nodes at the same time. A new peer service period (PSP) mechanism is also proposed in IEEE 802.11s amendment for transmitting to a receiver operating in PSM. In this paper the performance of the link specific power mode is studied for a single- and a multilink network in terms of energy, delay throughput, and sleep duration. It is found that at small load the energy saving could be as high as eighty percent when compared with the active mode operation. A stochastic model, based on discrete time discrete state Markov chain, is developed for one peer link operation to study the system behavior closely during PSM operation.
Real-time IP-10 measurements as a new tool for inflammation regulation within a clinical decision support protocol for managing severe COVID-19 patients (2020)

The challenge of treating severely ill COVID-19 patients is particularly great due to the need to simultaneously manage oxygenation and the inflammatory state without compromising viral clearance. Currently, there are many tools to aid in oxygen management and in monitoring viral replication. However, predictive biomarkers for monitoring the host immune response across COVID-19 disease stages and specifically, for titrating immunomodulatory therapy are lacking. We utilized a recently cleared platform (MeMed Key™) that enables rapid and easy serial measurement of IP-10, a host protein implicated in lung injury due to viral-induced hyperinflammation. A dynamic clinical decision support protocol was employed for managing SARS-CoV-2 positive patients admitted to a COVID-19 dedicated medical center run by Clalit Health Services. This is the first protocol to include real-time measurements of IP-10 as a potential aid for regulating inflammation. Overall, 502 serial real-time IP-10 measurements were performed on 52 patients recruited between 7 th April 2020 to 10 th May 2020, with 12 patients admitted to the intensive care unit (ICU). IP-10 levels correlated with increased COVID-19 severity score and ICU admission. Within the ICU admitted patients, the number of days with IP-10 measurements &gt;1,000 pg/ml was associated with mortality. Upon administration of corticosteroid immunomodulatory therapy, a significant decrease in IP-10 levels was observed. Real-time IP-10 monitoring represents a new tool to aid in management and therapeutic decisions relating to the inflammatory status of COVID-19 patients.