gebhart/patrepeval huggingface dataset:
Joint Wireless Information and Energy Transfer in a Two-User MIMO\n Interference Channel (2013)

This paper investigates joint wireless information and energy transfer in a\ntwo-user MIMO interference channel, in which each receiver either decodes the\nincoming information data (information decoding, ID) or harvests the RF energy\n(energy harvesting, EH) to operate with a potentially perpetual energy supply.\nIn the two-user interference channel, we have four different scenarios\naccording to the receiver mode -- ($ID_1$, $ID_2$), ($EH_1$, $EH_2$), ($EH_1$,\n$ID_2$), and ($ID_1$, $EH_2$). While the maximum information bit rate is\nunknown and finding the optimal transmission strategy is still open for\n($ID_1$, $ID_2$), we have derived the optimal transmission strategy achieving\nthe maximum harvested energy for ($EH_1$, $EH_2$). For ($EH_1$, $ID_2$), and\n($ID_1$, $EH_2$), we find a necessary condition of the optimal transmission\nstrategy and, accordingly, identify the achievable rate-energy (R-E) tradeoff\nregion for two transmission strategies that satisfy the necessary condition -\nmaximum energy beamforming (MEB) and minimum leakage beamforming (MLB).\nFurthermore, a new transmission strategy satisfying the necessary condition -\nsignal-to-leakage-and-energy ratio (SLER) maximization beamforming - is\nproposed and shown to exhibit a better R-E region than the MEB and the MLB\nstrategies. Finally, we propose a mode scheduling method to switch between\n($EH_1$, $ID_2$) and ($ID_1$, $EH_2$) based on the SLER.\n
Needle-free delivery of macromolecules across the skin by nanoliter-volume pulsed microjets (2007)

Needle-free liquid jet injectors were invented >50 years ago for the delivery of proteins and vaccines. Despite their long history, needle-free liquid jet injectors are not commonly used as a result of frequent pain and bruising. We hypothesized that pain and bruising originate from the deep penetration of the jets and can potentially be addressed by minimizing the penetration depth of jets into the skin. However, current jet injectors are not designed to maintain shallow dermal penetration depths. Using a new strategy of jet injection, pulsed microjets, we report on delivery of protein drugs into the skin without deep penetration. The high velocity (v >100 m/s) of microjets allows their entry into the skin, whereas the small jet diameters (50-100 mum) and extremely small volumes (2-15 nanoliters) limit the penetration depth ( approximately 200 mum). In vitro experiments confirmed quantitative delivery of molecules into human skin and in vivo experiments with rats confirmed the ability of pulsed microjets to deliver therapeutic doses of insulin across the skin. Pulsed microjet injectors could be used to deliver drugs for local as well as systemic applications without using needles.
Vaccine-Mediated Induction of an Ebolavirus Cross-Species Antibody Binding to Conserved Epitopes on the Glycoprotein Heptad Repeat 2/Membrane-Proximal External Junction (2018)

The membrane-proximal external regions (MPER) of the human immunodeficiency virus envelope glycoprotein (GP) generate broadly reactive antibody responses and are the focus of vaccine development efforts. The conservation of amino acids within filovirus GP heptad repeat region (HR)2/MPER suggests that it may also represent a target for a pan-filovirus vaccine. We immunized a cynomolgus macaque against Ebola virus (EBOV) using a deoxyribonucleic acid/adenovirus 5 prime/boost strategy, sequenced memory B-cell receptors, and tested the antibodies for functional activity against EBOV GP. Antibody ma-C10 bound to GP with an affinity of 48 nM and was capable of inducing antibody-dependent cellular cytotoxicity. Three-dimensional reconstruction of single-particle, negative-stained, electron microscopy showed that ma-C10 bound to the HR2/MPER, and enzyme-linked immunosorbent assay reveals it binds to residues 621-631. More importantly, ma-C10 was found to bind to the GP of the 3 most clinically relevant Ebolavirus species, suggesting that a cross-species immunogen strategy targeting the residues in this region may be a feasible approach for producing a pan-filovirus vaccine.
Immunisation antitumorale : du transfert de genes codant pour une cytokine regulatrice (il-12) et pour une molecule de costimulation (b7-1). a l'utilisation de cellules dendritiques autologues pulsees par des peptides tumoraux (1995)

L'immunotherapie active specifique (ias), chez un hote porteur d'une tumeur, a pour but l'elaboration d'une reponse immunitaire, surtout cellulaire, specifique de tumeur, permanente et protectrice, capable de reconnaitre une ou plusieurs composante(s) immunogenique(s) exprimees par les cellules tumorales autologues. A cette fin, plusieurs approches ont ete envisagees et testees dans des modeles tumoraux murins precliniques. 1) vaccins tumoraux modifies genetiquement par des genes codant pour des immunomodulateurs (il-12, cytokine regulatrice et b7-1, molecule de costimulation lymphocytaire) developpant une immunite cellulaire t antitumorale dont les cibles sont non definies, 2) cellules dendritiques pulsees par des peptides: 2a) synthetiques dont les nonameres peptidiques sont des epitopes prealablement definis par des lymphocytes t cytotoxiques (ltc), restreints par les molecules de classe i du cmh ; ces peptides tumoraux peuvent etre pulses sur des cellules presentatrices d'antigene (cpa: cellules dendritiques (cd)) qui servent de vehicules pour le priming de cellules t naives ; les animaux peuvent ainsi prevenir (prophylaxie) l'etablissement de la tumeur autologue porteuse des epitopes specifiquement caracterises par les ltc ou eradiquer (curatif) une tumeur deja etablie. 2b) naturels ; lorsque les epitopes tumoraux ne sont pas disponibles, l'extraction non fractionnee par elution acidique des peptides presentes par les molecules du cmh (classe i et/ou ii) a la surface d'une tumeur non immunogenique permet de pulser les cellules dendritiques autologues. Ces cpa peuvent initier une reponse antitumorale specifique, dependante des cellules t, cd4+ et cd8+, du systeme de costimulation lymphocytaire b7/cd28-ctla4 et des cytokines de la differentiation t helper 1(th1). La therapie genique antitumorale utilisant l'il-12+b7-1 et dendritique utilisant des peptides isoles ou non encore caracterises pourraient offrir une option therapeutique nouvelle, adjuvante surtout, a nos patients cancereux porteurs de tumeurs non immunogeniques
Preparation of CRISPR/Cas9 and gRNA plasmids (2017)

Human genome engineering has been transformed by the introduction of the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) system found in most bacteria and archaea. Type II CRISPR/Cas systems have been engineered to induce RNA-guided genome editing in human cells, where small RNAs function together with Cas9 nucleases for sequence-specific cleavage of target sequences. Here we describe the protocol for Cas9-mediated human genome engineering, including construct building and transfection methods necessary for delivering Cas9 and guide RNA (gRNA) into human-induced pluripotent stem cells (hiPSCs) and HEK293 cells. Following genome editing, we also describe methods to assess genome editing effi- ciency using next-generation sequencing and isolate monoclonal hiPSCs with the desired modifications for downstream applications. Keywords: genome engineering • CRISPR • human stem cells
Chiral enrichment of serine via formation, dissociation, and soft-landing of octameric cluster ions (2004)

Chiral enrichment of serine is achieved in experiments that involve formation of serine octamers starting from non-racemic serine solutions. Serine octamers were generated by means of electrospray and sonic spray ionization of aqueous solutions of d(3)-L-serine (108 Da) and D-serine (105 Da) having different molar ratios of enantiomers. A cyclic process involving the formation of chirally-enriched octameric cluster ions and their dissociation, viz. Ser(1) --> Ser(8) --> Ser(1), allows serine monomers to be regenerated with increased enantiomeric excess as shown in two types of experiments: (1) Chiral enrichment in serine was observed in MS/MS/MS experiments in a quadrupole ion trap in which the entire distribution of serine octamers formed from non-racemic solutions was isolated, collisionally activated, and fragmented. Monomeric serine was regenerated with increased enantiomeric excess upon dissociation of octamers when compared with the enantiomeric composition of the original solution. (2) Chiral enrichment was observed in the products of soft-landing of mass-selected protonated serine octamers. These ions were generated by means of electrospray or sonic spray ionization, mass selected, and collected on a gold surface using ion soft-landing. Chiral enrichment of the soft-landed serine was established by redissolving the recovered material and comparing the intensities of protonated molecular ions of d(3)-L-serine and D-serine after APCI-MS analysis. Both of these experiments showed comparable results, suggesting that formation of serine octamers depends only on the enantiomeric composition of the serine solution and that the magnitude of the chiral preference is intrinsic to octamers formed from solutions of given chiral composition.
Surface-modified protein nanospheres as potential antiviral agents (2012)

A novel application of surface-modified protein nanospheres as potential antiviral agents is illustrated. By using a single-step sonochemical process, bovine serum albumin nanospheres were generated, whose surface was covalently conjugated with mercaptoethane sulfonate to chemically and electrostatically mimic cellular heparan sulfate. The nanospheres effectively inhibited HSV-1 infection.
Development and Verification of a High-Fidelity Computational Fluid Dynamics Model of Canine Nasal Airflow (2009)

The canine nasal cavity contains a complex airway labyrinth, dedicated to respiratory air conditioning, filtering of inspired contaminants, and olfaction. The small and contorted anatomical structure of the nasal turbinates has, to date, precluded a proper study of nasal airflow in the dog. This study describes the development of a high-fidelity computational fluid dynamics (CFD) model of the canine nasal airway from a three-dimensional reconstruction of high-resolution magnetic resonance imaging scans of the canine anatomy. Unstructured hexahedral grids are generated, with large grid sizes ((10-100) x 10(6) computational cells) required to capture the details of the nasal airways. High-fidelity CFD solutions of the nasal airflow for steady inspiration and expiration are computed over a range of physiological airflow rates. A rigorous grid refinement study is performed, which also illustrates a methodology for verification of CFD calculations on complex unstructured grids in tortuous airways. In general, the qualitative characteristics of the computed solutions for the different grid resolutions are fairly well preserved. However, quantitative results such as the overall pressure drop and even the regional distribution of airflow in the nasal cavity are moderately grid dependent. These quantities tend to converge monotonically with grid refinement. Lastly, transient computations of canine sniffing were carried out as part of a time-step study, demonstrating that high temporal accuracy is achievable using small time steps consisting of 160 steps per sniff period. Here we demonstrate that acceptable numerical accuracy (between approximately 1% and 15%) is achievable with practical levels of grid resolution (approximately 100 x 10(6) computational cells). Given the popularity of CFD as a tool for studying flow in the upper airways of humans and animals, based on this work we recommend the necessity of a grid dependence study and quantification of numerical error when presenting CFD results in complicated airways.
A Solver for a Theory of Strings and Bit-Vectors (2017)

We present the Z3strBV solver for a many-sorted first-order quantifier-free theory Tw, bv of string equations, string length represented as bit-vectors, and bit-vector arithmetic aimed at formal verification, automated testing, and security analysis of C/C++ applications. Our key motivation for building such a solver is the observation that existing string solvers are not efficient at modeling the combined theory over strings and bit-vectors. We demonstrate experimentally that Z3strBV is significantly more efficient than a reduction of string/bit-vector constraints to strings/natural numbers followed by a solver for strings/natural numbers or modeling strings as bit-vectors. We also propose two optimizations. First, we explore the concept of library-aware SMT solving, which fixes summaries in the SMT solver for string library functions such as strlen in C/C++. Z3strBV is able to consume these functions directly instead of re-analyzing the functions from scratch each time. Second, we experiment with a binary search heuristic that accelerates convergence on a consistent assignment of string lengths. We also show that Z3strBV is able to detect nontrivial overflows in real-world system-level code, as confirmed against seven security vulnerabilities from the CVE and Mozilla databases.
Abstract 15520: A Multiscale Model of Cardiac Remodeling Under Pulmonary Arterial Hypertension: From Organ to Titin (2019)

Introduction: Right ventricular (RV) function is the primary determinant of pulmonary arterial hypertension (PAH) patients survival. Our recent studies suggested that, in response to pressure overl...
Nonlinear phase and polarization rotation noise in fully loaded WDM systems (2015)

We show that nonlinear interference noise (NLIN) produced by faraway WDM channels is dominated by nonlinear phase-noise and polarization-rotations, whereas NLIN produced by nearest channels tends to be more circular. We discuss the impact of these results on nonlinear mitigation.
Measuring functional status in patients with systemic lupus erythematosus (2003)

Abstract With improvements in mortality in systemic lupus erythematosus (SLE), the functional status of these patients, assessed using health‐related quality‐of‐life (HRQoL) measures, is increasingly being recognized as an important outcome measure in clinical research. Domains of HRQoL of particular importance to SLE patients include fatigue, ability to work, good health, independence and social and family life. The SF‐36 currently appears to be the best available measure for assessment of HRQoL in SLE. It measures some of the domains of importance to SLE patients, has good psychometric properties, patient acceptability, construct validity and has been validated for use in many languages. Using HRQoL measures, it has been shown that SLE patients have poorer functional status than the general population, and that specific manifestations of SLE (e.g. fibromyalgia and renal failure) may influence HRQoL in these patients. Prospective and cross‐sectional studies have identified a variety of factors – some potentially modifiable – which influence HRQoL in SLE. Additional research is needed to identify strategies which can improve HRQoL in SLE patients.
Long Spin Coherence and Relaxation Times in Nanodiamonds Milled from Polycrystalline $^{12}$C Diamond (2023)

The negatively charged nitrogen-vacancy centre (NV$^-$) in diamond has been utilized in a wide variety of sensing applications. The centre's long spin coherence and relaxation times ($T_2^*$, $T_2$ and $T_1$) at room temperature are crucial to this, as they often limit sensitivity. Using NV$^-$ centres in nanodiamonds allows for operations in environments inaccessible to bulk diamond, such as intracellular sensing. We report long spin coherence and relaxation times at room temperature for single NV$^-$ centres in isotopically-purified polycrystalline ball-milled nanodiamonds. Using a spin-locking pulse sequence, we observe spin coherence times, $T_2$, up 786 $\pm$ 200 $μ$s. We also measure $T_2^*$ times up to 2.06 $\pm$ 0.24 $μ$s and $T_1$ times up to 4.32 $\pm$ 0.60 ms. Scanning electron microscopy and atomic force microscopy measurements show that the diamond containing the NV$^{-}$ centre with the longest $T_1$ time is smaller than 100 nm. EPR measurements give an N$_{s}$$^{0}$ concentration of 0.15 $\pm$ 0.02 ppm for the nanodiamond sample.
First-in-human trial of ONC201 in patients with refractory solid tumors. (2016)

2514 Background: ONC201 is an orally active, first-in-class small molecule activator of the integrated stress response that selectively upregulates ATF4 to trigger tumor cell death. Preclinical studies have established the compelling antitumor efficacy of the small molecule in a range of advanced solid tumors as well as its excellent safety profile in animals. A first-in-human phase I study of ONC201 was conducted to determine its recommended phase II dose (RP2D) in patients with advanced solid tumors. Methods: This open-label study treated 10 patients during the single-patient cohort dose escalation portion of the trial. The human starting dose was 125mg, which represents 1/10th of the no-adverse-adverse-effect-level in animal toxicology studies using standard allometric conversion. Results: The RP2D was defined as 625 mg and no Grade > 1 drug-related adverse events occurred on this trial, which enrolled patients at increasing dose levels of 125mg, 250mg, 375mg, 500mg, and finally 625mg. Pharmacokinetic analysis revealed saturation of absorption at 375mg, suggesting dose escalation above 625mg was not warranted. The terminal half-life was 9.6 hours, Cmax values ranged from 1.5 - 7.5 ug/mL (~3.9-19.4 uM), and the AUC was 25 hr ug/L. Prolonged induction of caspase-cleaved keratin 18 and induction of TRAIL was observed in serum samples. Eight of 10 patients had stable disease and one patient with endometrial cancer underwent a mixed response. 17 of 25 additional patients have been accrued in an ongoing expansion phase. The available results from the expansion cohort confirm the excellent safety, and the pharmacokinetic and pharmacodynamic profiles of ONC201 at the recommended phase II dose of 625mg every three weeks. Conclusions: This study demonstrates that ONC201 is well tolerated and active at an oral dose of 625mg, warranting further evaluation in lead indications. Clinical trial information: NCT02250781.
supplementary video 2 from Visualization of Breast Cancer Metabolism Using Multimodal Nonlinear Optical Microscopy of Cellular Lipids and Redox State (2023)

&lt;p&gt;The 3D reconstruction of T47D cancer acinus treated with E2.&lt;/p&gt;
Securing mobile code. (2004)

If software is designed so that the software can issue functions that will move that software from one computing platform to another, then the software is said to be 'mobile'. There are two general areas of security problems associated with mobile code. The 'secure host' problem involves protecting the host from malicious mobile code. The 'secure mobile code' problem, on the other hand, involves protecting the code from malicious hosts. This report focuses on the latter problem. We have found three distinct camps of opinions regarding how to secure mobile code. There are those who believe special distributed hardware is necessary, those who believe special distributed software is necessary, and those who believe neither is necessary. We examine all three camps, with a focus on the third. In the distributed software camp we examine some commonly proposed techniques including Java, D'Agents and Flask. For the specialized hardware camp, we propose a cryptographic technique for 'tamper-proofing' code over a large portion of the software/hardware life cycle by careful modification of current architectures. This method culminates by decrypting/authenticating each instruction within a physically protected CPU, thereby protecting against subversion by malicious code. Our main focus is on the camp that believes that neither specialized software nor hardware is necessary. We concentrate on methods of code obfuscation to render an entire program or a data segment on which a program depends incomprehensible. The hope is to prevent or at least slow down reverse engineering efforts and to prevent goal-oriented attacks on the software and execution. The field of obfuscation is still in a state of development with the central problem being the lack of a basis for evaluating the protection schemes. We give a brief introduction to some of the main ideas in the field, followed by an in depth analysis of a technique called 'white-boxing'. We put forth some new attacks and improvements on this method as well as demonstrating its implementation for various algorithms. We also examine cryptographic techniques to achieve obfuscation including encrypted functions and offer a new application to digital signature algorithms. To better understand the lack of security proofs for obfuscation techniques, we examine in detail general theoretical models of obfuscation. We explain the need for formal models in order to obtain provable security and the progress made in this direction thus far. Finally we tackle the problem of verifying remote execution. We introduce some methods of verifying remote exponentiation computations and some insight into generic computation checking.
Chimeric enzymes for conversion of lignin-derived chemicals (2023)

Disclosed herein are enzymes useful for the dealkylation of aromatic substrates, including the conversion of guaiacol or guaethol to catechol. Methods of converting aromatic substrates found in lignin-based feedstocks such as pyrolysis oil into products such as catechol are also disclosed. Also presented herein are methods for rapidly evolving and optimizing genetic regions.
Temperature‐ and pH‐Responsive Polymeric Photocatalysts for Enhanced Control and Recovery (2022)

The emergence of heterogeneous photocatalysis has facilitated redox reactions with high efficiency, without compromising the recyclability of the photocatalyst. Recently, stimuli-responsive heterogeneous photocatalytic materials have emerged as a powerful synthetic tool, with simple and rapid recovery, as well as an enhanced dynamic control over reactions. Stimuli-responsive polymers are often inexpensive and easy to produce. They can be switched from an active "on" state to an inert "off" state in response to external stimuli, allowing the production of photocatalyst with adaptability, recyclability, and orthogonal control on different chemical reactions. Despite this versatility, the application of artificial smart material in the field of heterogeneous photocatalysis has not yet been maximized. In this Minireview, we will examine the recent developments of this emerging class of stimuli-responsive heterogeneous photocatalytic systems. We will discuss the synthesis route of appending photoactive components into different triggerable systems and, in particular, the controlled activation and recovery of the materials.
Secure Autonomous Mobile Agents for Web Services (2018)

Autonomous Mobile agents can be extremely useful in dynamic environments that require a continuous network connection. Network bandwidth reduction, protocol encapsulation, software automation and intelligence gathering can significantly affect Web Services. Integrating mobile agents with Web Services enables software adaptation to cope with a dynamic environment, automated system configuration and application requirement changes that are frequent in today''s ever fast-evolving technology. In this paper, we use a lightweight and efficient composition for mobile agents based Web services complying with Representational State Transfer (REST) principles for agent creation, migration, and control. The paper presents the overall concept and architecture of RESTful agents for web services. A security scheme is proposed for mobile agent security based on an infrastructure-less Identity Based Encryption (IBE) scheme integrated with Broadcast based Secure Mobile Agent Protocol (BROSMAP). A proof- of-concept implementation is provided.