gebhart/patrepeval huggingface dataset:
POWER prototype: towards integrated policy-based management (2002)

A policy-based management system is only really useful if it allows not only high level description of abstract policy, but also enables such policy to be refined and eventually mapped into an appropriate configuration for controlling devices in the managed system. Such a full integration has only been discussed in the literature but not realised so far. Our approach, implemented as the POWER prototype, demonstrates a way towards making it a reality in practice.
Chemical modification of A1 adenosine receptors in rat brain membranes. Evidence for histidine in different domains of the ligand binding site. (1988)

Chemical modification of amino acid residues was used to probe the ligand recognition site of A1 adenosine receptors from rat brain membranes. The effect of treatment with group-specific reagents on agonist and antagonist radioligand binding was investigated. The histidine-specific reagent diethylpyrocarbonate (DEP) induced a loss of binding of the agonist R-N6-[3H] phenylisopropyladenosine ([3H]PIA), which could be prevented in part by agonists, but not by antagonists. DEP treatment induced also a loss of binding of the antagonist [3H]8-cyclopentyl-1,3-dipropylxanthine ([3H]DPCPX). Antagonists protected A1 receptors from this inactivation while agonists did not. This result provided evidence for the existence of at least 2 different histidine residues involved in ligand binding. Consistent with a modification of the binding site, DEP did not alter the affinity of [3H]DPCPX, but reduced receptor number. From the selective protection of [3H] PIA and [3H]DPCPX binding from inactivation, it is concluded that agonists and antagonists occupy different domains at the binding site. Sulfhydryl modifying reagents did not influence antagonist binding, but inhibited agonist binding. This effect is explained by modification of the inhibitory guanine nucleotide binding protein. Pyridoxal 5-phosphate inactivated both [3H]PIA and [3H]DPCPX binding, but the receptors could not be protected from inactivation by ligands. Therefore, no amino group seems to be located at the ligand binding site. In addition, it was shown that no further amino acids with polar side chains are present. The absence of hydrophilic amino acids from the recognition site of the receptor apart from histidine suggests an explanation for the lack of hydrophilic ligands with high affinity for A1 receptors.
On the MAC for Power-Line Communications: Modeling Assumptions and Performance Tradeoffs (Technical Report 205771, EPFL) (2014)

INDY2
Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations (2019)

A medium-sized and highly flexible inhibitor to the enzyme β-secretase 1 (BACE), which produces the amyloid β-peptide by cleavage of its precursor protein, was dynamically docked into the large and wide catalytic cleft of BACE that binds to the amyloid-precursor by employing multicanonical molecular dynamics (McMD) simulations. We applied our method to predict the native binding configuration and sample the intermediary structures connecting this natively bound state to the unbound one. Representative structures located at free energy minima obtained from McMD were taken and subjected to canonical simulations to refine and validate them, reproducing the native complex structure in agreement with the experimental data in the most stable structure, i.e., the one at the global minimum. In addition, the binding free energy was estimated by umbrella sampling (US) simulations along representative pathways obtained from the McMD ensemble, followed by weighted histogram analysis to estimate the affinity, which also reproduced the experimental inhibitory affinity. Interestingly, the loss of interactions between the two molecules along the pathway was clearly shown in the free energy landscape, reiterating the fundamental importance of atomistic interactions to the binding affinity between receptor and drug compound. The sampled ensemble by the US simulations smoothly connected the bound and unbound states, refining the binding pathway while staying true to the McMD ensemble.
Photorefractive characterization of polymers (1993)

The polymer Bisphenol A 4,4'-nitroaminostilbene mixed with 40 wt. % benzaldehyde-diphenyl hydrazone is typical of the epoxy-based photorefractive polymers recently shown to be photorefractive. 1
Phylogenetic Analyses of Meloidogyne Small Subunit rDNA. (2002)

Phylogenies were inferred from nearly complete small subunit (SSU) 18S rDNA sequences of 12 species of Meloidogyne and 4 outgroup taxa (Globodera pallida, Nacobbus abberans, Subanguina radicicola, and Zygotylenchus guevarai). Alignments were generated manually from a secondary structure model, and computationally using ClustalX and Treealign. Trees were constructed using distance, parsimony, and likelihood algorithms in PAUP* 4.0b4a. Obtained tree topologies were stable across algorithms and alignments, supporting 3 clades: clade I = [M. incognita (M. javanica, M. arenaria)]; clade II = M. duytsi and M. maritima in an unresolved trichotomy with (M. hapla, M. microtyla); and clade III = (M. exigua (M. graminicola, M. chitwoodi)). Monophyly of [(clade I, clade II) clade III] was given maximal bootstrap support (mbs). M. artiellia was always a sister taxon to this joint clade, while M. ichinohei was consistently placed with mbs as a basal taxon within the genus. Affinities with the outgroup taxa remain unclear, although G. pallida and S. radicicola were never placed as closest relatives of Meloidogyne. Our results show that SSU sequence data are useful in addressing deeper phylogeny within Meloidogyne, and that both M. ichinohei and M. artiellia are credible outgroups for phylogenetic analysis of speciations among the major species.
INFERENCE OF LETTER-PHONEME CORRESPONDENCES USING GENERALISED STOCHASTIC TRANSDUCERS (2024)

This paper describes a Ipeclal hlealy machine called a generaliaed stochastic transducer (GST) used to infer letterphonetne correspondence from a large act of word spelling and their associated phonemic fortut. T'he maiu idea it to use the transducer to de ne the most likely alignment tor each word and based on the alignment, eorrupondencen are obtained according to the {our neighbourhood connecttivity. We compared the performance at the inferred correspondencewith the mutually-derived corrapondencel, with theinlet'xed correspondences uling the delimiting and dynamic programming (DP) ledtttiquen and with the GST used directly for translation.
Investigation of Differential Twisted-Pairs Implemented on Silicon IPD and High Performance Multilayer Organic Platforms (2016)

In this paper, results of twisted pairs implemented in silicon IPD and low loss MLO up to 20 GHz is reported. First, origin of differential lines is explained, followed by explanation of differential twisted pairs' natural ability to suppress noise. Issues related to differential twisted pairs (DTPs) are also discussed. In this paper, differential lines with and without (i.e., the coupled lines) twists were focused. Their transmission properties, including Common Mode Rejection Ratio (CMRR), were obtained. An aggressor line (single-ended transmission line terminated with Zc by a probe head, or a 50 W resistor) and victim differential lines were created on silicon IPD and Rogers MLO. The victim differential lines include coupled and twisted pairs, and they were terminated at open, short, and matched load. In analyzing cross-talk noise (Near and Far ends -- NEXT and FEXT), S-parameter measurements for the aggressor-victim configurations were conducted, and they agreed well with HFSS simulated results. Moreover, Hx and Hy fields were obtained using EMI/EMC Near field measurement tool EM-ISight-4 (10 kHz - 6 GHz) by APREL. The near field results can be used to obtain the current distributions on the victim differential twisted pairs. The current distributions are in good agreement with HFSS simulated results.
MVPN/EVPN C-Multicast Routes Enhancements (2019)

[RFC6513] and [RFC6514] specify procedures for originating,
propagating, and processing C-multicast routes. However, there are a
number of MVPN use cases that are not properly or optimally handled by
those procedures. This document describes those use cases, and
specifies the additional procedures needed to handle them. Some of the
additional procedures are also applicable to EVPN SMET routes [I- D
.ietf-bess-evpn-igmp-mld-proxy].
Les actionneurs électromagnétiques : quels choix pour la robotique ? (2007)

National audience
Performance Parameter Optimization of Graphene Enhanced Surface Plasmon Resonance Biosensors (2019)

In this paper, we perform a theoretical study in order to optimize the sensitivity S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> and detection accuracy DA performance parameters of a proposed Silver-based and Graphene enhanced Fiber Optic Surface Plasmon Resonance (FO-SPR) biosensor. Upon simulation utilizing the 4-layer model, it was found that the physical and geometrical parameters of this biosensor such as the metal layer type, addition of a Graphene coating, sensing region length L, core diameter D and thickness of the metal layer d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> have an effect on the sensor performance parameters and thus need to be optimized. The optimal design was found to be a Silver-based and Graphene enhanced FO-SPR biosensor with L = 10 mm, D = 100 mm and d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> = 40 nm.
Synthesis of Naphtho[2,3-b]indolizine-6,11-dione Derivatives by Iodine Oxidation of 2-Alkyl-1,4-naphthoquinones in the Presence of Substituted Pyridines (1998)

Iodine oxidation of 2-alkyl-1,4-naphthoquinones (1) in the presence of substituted pyridines (2) afforded naphtho[2,3-b]indolizine-6,11-dione derivatives (3). Other oxidant systems (MnO2/I- or Fe(ClO4)3/I2) can be used and 2-alkylbenzoquinones reacted in lower yield. Iodination of 3 by I2 and dibenzoyl peroxide occurred seelctively at position 12
Preliminary investigation of unconstrained person identification for tabletops using soft biometrics (2016)

This paper tries to realize unconstrained person identification for tabletop systems using a ceiling-mounted depth camera that overlooks a table. We extract a user's soft biometrics from a depth image, such as the shoulder width and shape of the head that can be captured from the ceiling. We then try to achieve robust person identification by combining each of the soft biometric. Person identification from a ceiling has several advantages: a ceiling-mounted camera hardly suffers from the occlusion problem, does not interfere users' activities and can capture multiple users in one shot. In the preliminary experiment, proposed method has achieved 83% accuracy identifying 19 participants.
Optomagnetically Controlled Microparticles Manufactured with Glancing Angle Deposition (2015)

Optical trapping and magnetic trapping are common micro-manipulation techniques for controlling colloids including micro- and nano-particles. Combining these two manipulation strategies allows for a larger range of applied forces and decoupled control of rotation and translation; each of which are beneficial properties for many applications including force spectroscopy and advanced manufacturing. However, optical trapping and magnetic trapping have conflicting material requirements inhibiting the combination of these methodologies. In this paper, anisotropic micron scaled particles capable of being simultaneously controlled by optical and magnetic trapping are synthesized using a glancing angle deposition (GLAD) technique. The anisotropic alignment of dielectric and ferromagnetic materials limits the optical scattering from the metallic components which typically prevents stable optical trapping in three dimensions. Compared to the current state of the art, the benefits of this approach are two-fold. First, the composite structure allows for larger volumes of ferromagnetic material so that larger magnetic moments may be applied without inhibiting the stability of optical trapping. Secondly, the robustness of the synthesis process is greatly improved. The dual optical and magnetic functionality of the synthesized colloids is demonstrated by simultaneously optically translating and magnetically rotating a magnetic GLAD particle using a custom designed opto-magnetic trapping system.
The performance of two-dimensional media scaling for Internet videoconferencing (2002)

Until mechanisms for true real-time network communications are deployed and pervasive, one must rely on adaptive, best-effort congestion control methods to provide acceptable levels of service for interactive, real-time multimedia applications. Here we report on our experiences with a novel media-scaling congestion control scheme that was implemented in an experimental version of the Intel ProShare videoconferencing system and tested over the Internet. The media scaling scheme is unique in that it employs two-dimensional media scaling-the bit-rate and packet-rate of media streams are independently scaled. The goals of our study were (1) to empirically assess the performance improvement of two-dimensional media scaling over the simpler, and more commonly employed, one-dimensional scaling approaches and (2) to determine if it was possible to sustain ProShare conferences for a significant enough fraction of the time that two-dimensional scaling could be considered effective. We observed that systems using one-dimensional and two-dimensional scaling were both able to sustain conferences and that the two-dimensional scaling system always produced conferences with greater effective throughput. Our study provides empirical evidence that two-dimensional media scaling can be used effectively to ameliorate the effects of congestion in the Internet and can significantly extend the usability of an interactive multimedia application on the Internet.
703-P: Randomized Crossover Comparison of Automated Insulin Delivery vs. Conventional Therapy with Scheduled Stress Challenges (2021)

Automated Insulin Delivery (AID) hybrid closed-loop systems have not been well studied in the context of psychological and physiological stress. We evaluated our interoperable artificial pancreas system with in-clinic stress challenges in a randomized crossover trial. Fourteen adults with type 1 diabetes were randomized to 2 weeks of AID-based control and two weeks of sensor augmented pump (SAP)l therapy at home in random order. The AID system used the Zone-Model Predictive Control algorithm with a continuous function of glucose velocity and insulin-on-board to gradually increase insulin infusion under conditions of sustained hyperglycemia. During each two-week period, in-clinic stress assessments for psychological stress (TSST and SECPT) and pharmacological stress (hydrocortisone 40-20-20 mg) were performed. Ten subjects completed the study per protocol, with 48 stress sessions completed in 12 subjects. AID increased time 70-180mg/dL from 63.1 to 74.4% (p=0.001), decreased time <70mg/dL from 1.5 to 0.8% (p=0.04) and decreased time >180mg/dL from 35.4 to 24.8% (p=0.001) during the 2 weeks outpatient use. AID decreased glycemic variability as measured by CV (p=0.037) and time <70mg/dL (p=0.014) during psychological stress (Table 1) AID improved glucose control during outpatient use and improved CV and % time <70mg/dL during in-clinic psychologic stress compared to SAP.View largeDownload slideView largeDownload slide DisclosureR. Kaur: None. Y. C. Kudva: Research Support; Self; Dexcom, Inc. S. Deshpande: None. J. E. Pinsker: Advisory Panel; Self; Medtronic, Consultant; Self; Eli Lilly and Company, Tandem Diabetes Care, Research Support; Self; Dexcom, Inc., Insulet Corporation, Medtronic, Tandem Diabetes Care. S. K. Mccrady-spitzer: None. D. Desjardins: None. M. Church: None. W. K. Kremers: Research Support; Self; AstraZeneca, Biogen, Roche Pharma. F. J. Doyle: Advisory Panel; Self; Mode AGC, Other Relationship; Self; Dexcom, Inc., Insulet Corporation, Roche Diabetes Care. E. Dassau: Consultant; Self; Eli Lilly and Company, Employee; Self; Eli Lilly and Company, Research Support; Self; Dexcom, Inc., Tandem Diabetes Care, Speaker’s Bureau; Self; Dexcom, Inc., Roche Diabetes Care, Stock/Shareholder; Self; Eli Lilly and Company.FundingJDRF (2-SRA-2017-503-M-B); The Leona M. and Harry B. Helmsley Charitable Trust; Dexcom, Inc. (IIS-2019-017)
Memory abstractions for parallel programming (2012)

A memory abstraction is an abstraction layer between the program execution and the memory that provides a different view of a memory location depending on the execution context in which the memory access is made. Properly designed memory abstractions help ease the task of parallel programming by mitigating the complexity of synchronization or admitting more efficient use of resources. This dissertation describes five memory abstractions for parallel programming: (i) cactus stacks that interoperate with linear stacks, (ii) efficient reducers, (iii) reducer arrays, (iv) ownership-aware transactions, and (v) location-based memory fences. To demonstrate the utility of memory abstractions, my collaborators and I developed Cilk-M, a dynamically multithreaded concurrency platform which embodies the first three memory abstractions. 
Many dynamic multithreaded concurrency platforms incorporate cactus stacks to support multiple stack views for all the active children simultaneously. The use of cactus stacks, albeit essential, forces concurrency platforms to trade off between performance, memory consumption, and interoperability with serial code due to its incompatibility with linear stacks. This dissertation proposes a new strategy to build a cactus stack using thread-local memory mapping (or TLMM), which enables Cilk-M to satisfy all three criteria simultaneously.
A reducer hyperobject allows different branches of a dynamic multithreaded program to maintain coordinated local views of the same nonlocal variable. With reducers, one can use nonlocal variables in a parallel computation without restructuring the code or introducing races. This dissertation introduces memory-mapped reducers, which admits a much more efficient access compared to existing implementations. 
When used in large quantity, reducers incur unnecessarily high overhead in execution time and space consumption. This dissertation describes support for reducer arrays, which offers the same functionality as an array of reducers with significantly less overhead. 
Transactional memory is a high-level synchronization mechanism, designed to be easier to use and more composable than fine-grain locking. This dissertation presents ownership-aware transactions , the first transactional memory design that provides provable safety guarantees for open-nested transactions. 
On architectures that implement memory models weaker than sequential consistency, programs communicating via shared memory must employ memory fences to ensure correct execution. This dissertation examines the concept of location-based memory fences, which unlike traditional memory fences, incurs latency only when synchronization is necessary. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Boron-Containing Red Light-Emitting Phosphors And Light Sources Incorporating The Same (2023)

A boron-containing phosphor comprises a material having a formula of AD1-xEuxB9O16, wherein A is an element selected from the group consisting of Ba, Sr, Ca, Mg, and combinations thereof; D is at least an element selected from the group consisting of rare-earth metals other than europium; and x is in the range from about 0.005 to about 0.5. The phosphor is used in a blend with other phosphors in a light source for generating visible light with a high color rendering index.
Abstract P3-05-12: Combination of anti-progranulin (GP88/PGRN) antibody and letrozole inhibits tumor formation of letrozole resistant breast cancer cell lines (2016)

Abstract The 88 kDa glycoprotein GP88 (Progranulin, PCDGF, acrogranin) is the largest member of the granulin/epithelin family of growth modulators identified as a driver of tumorigenesis. GP88 (PGRN) was also shown to be overexpressed in invasive ductal carcinoma (IDC)whereas it was negative in benign tumors and normal mammry epithelial tissue, thereby establishing GP88 as a therapeutic and diagnostic target in breast cancer (BC). Our laboratory has developed validated tools to measure GP88 in tumor biopsies and biological fluids as well as blocking its action. WE showed that GP88 was secreted and detected in the serum of BC patients at an increased level when compared to healthy subjects. Pathological studies with 530 cases of ER+ IDC with clinical outcomes showed that GP88 tumor expression was an independent prognostic indicator of recurrence in early stage BC patients. Training study followed by an independent validation study demonstrated that high GP88 tissue expression (GP88 3+) was associated with a 4-fold increase in risk of recurrence at 5 years. A neutralizing anti-GP88 antibody AG1 was expressed in a high yield CHO cell line was developed. The present study examined the effect of AG1 in letrozole resistant cell line AGLetR developed by long term selection in letrozole supplemented medium. This cell line showed decreased letrozole responsiveness in vivo and therefore constituted an excellent model for investigating letrozole resistance in vitro as well as in vivo. Here we report the results of studies investigating the effect of various doses of AG1 on LetR tumor development in combination with letrozole for AGLetR. We show that treatment with AG1 (10 mg/kg i.p.) in combination with letrozole was efficient to maintain long term responsiveness and inhibit tumor growth. Letrozole alone (5mg/kg) was unable to inhibit tumor growth and showed a doubling of tumor volume. Interestingly, long term combination treatment lead to tumor regression and inhibited tumor growth. These data suggest that inhibiting GP88 could provide a novel and alternative therapeutic strategy for patients with resistance to anti-estrogen therapy, being tamoxifen or letrozole. This works is supported by 2R44CA124179, HHSN 261201200060C, and HHSN2612014400C from NCI. Citation Format: Serrero G, Dong J, Yue B, Hicks D, Hayashi J. Combination of anti-progranulin (GP88/PGRN) antibody and letrozole inhibits tumor formation of letrozole resistant breast cancer cell lines. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-05-12.
Response of cigarette smoke particles to change in humidity. (1982)

In Eq. ( 5), vB and k's are invariable while pB takes distinct values for different mixtures.Hence, according to Eq. ( 5), surface rate constant ks should vary corresponding to the molar density of B in each particle.With insertion ofEq.(5), Eq. ( 4) is therefore rewritten asThis is now independent of the particle molar density of B, as is seen in experimental observations.Consequently, one mayunderstand that the rate constant ki based on the effective surface area given by Eq.