gebhart/patrepeval huggingface dataset:
Lazy Revocation in Cryptographic File Systems (2006)

A crucial element of distributed cryptographic file systems are key management solutions that allow for flexible but secure data sharing. We consider efficient key management schemes for cryptographic file systems using lazy revocation. We give rigorous security definitions for three cryptographic schemes used in such systems, namely symmetric encryption, message-authentication codes and signature schemes. Additionally, we provide generic constructions for symmetric encryption and message-authentication codes with lazy revocation using key-updating schemes for lazy revocation, which have been introduced recently. We also give a construction of signature schemes with lazy revocation from identity-based signatures. Finally, we describe how our constructions improve the key rotation mechanism in the Plutus file system.
6.1: Photostability of Polymeric Cartesian Polarizing Beam Splitters (2004)

Abstract Polymeric Cartesian Polarizing Beam Splitters provide significant cost and performance advantages for LCOS RPTV engines. This paper describes work to demonstrate photo‐stability in these components. Film resins and adhesives both affect photostability, and must be selected carefully. Care must also be taken in constructing the tests and interpreting results.
Defects in DNA repair genes and sensitivity to cisplatin based neoadjuvant chemotherapy (NAC) for bladder cancer. (2015)

320 Background: Cisplatin based NAC prior to cystectomy is standard of care for MIBC, with 40-50% expected to respond with ≤pT1N0M0. Biomarkers predictive of response are lacking. Methods: MIBC pts who received 3 cycles of cisplatin based NAC on 1 of 2 prospective multicenter clinical trials were included. Pts treated with accelerated methotrexate, vinblastine, doxorubicin + cisplatin (AMVAC) provided the discovery set [n=34, 15/34 (44%) ≤pT1N0M0]. Pts treated with dose dense gemcitabine + cisplatin (DDGC) provided the validation set [n=24, 11/24 (46%) ≤pT1N0M0]. DNA from pre-treatment tumor tissue underwent sequencing for all coding exons of 287 cancer related genes and was analyzed for presence of base substitutions, indels, copy number alterations, and selected re-arrangements. The mean number of variants and variant status for each gene were correlated with response using two-sample t-test and Fisher’s exact tests. Variant data were used to create a classification tree to discriminate responders vs. non-responders in the AMVAC discovery cohort. The resulting decision rule was then tested in the independent DDGC validation set. Overall survival analysis was performed using Kaplan-Meier. Results: Pts with pT0 had significantly more alterations than those with residual tumor in both the AMVAC discovery (p=.024) and DDGC validation (p=0.018) set. In the AMVAC discovery set, alteration in ≥1 of the three DNA repair genes ATM, RB1 or FANCC predicted for ≤pT1N0M0 (p&lt;0.001, 87% sensitivity, 100% specificity) and improved overall survival (OS) (p=0.007). This test remained predictive for ≤pT1N0M0 in the DDGC validation set (p=0.033), with a trend towards improved OS (p=0.07) at short median follow up of 14.3 mo. Conclusions: Alterations in ≥1 of ATM, RB1 and FANCC predict response to cisplatin based chemotherapy defined as ≤pT1N0M0 in both our AMVAC discovery and DDGC validation sets. We hypothesize that defects in these genes, which are important for maintenance of chromatin structure and DNA repair, confer sensitivity to DNA damaging chemotherapy and explain the accumulation of alterations seen among pts with pT0. External validation in collaboration with the cooperative groups is planned.
An innate immune regulatory factor (IIRF) prevents tumorogenesis in a murine melanoma challenge model (2005)

Abstract Biological response modifiers (BRMs) are a family of compounds defined as agents or approaches that modify the host response to pathogens. A serum‐derived small peptide, termed Innate Immune Regulatory Factor (IIRF), stimulates the immune response through a natural killer cell–dependent pathway in mice. Ten days after administering a lethal dose of Salmonella typhimurium , 85% of control mice died. No difference was observed between control and mice depleted of natural killer cells and administered IIRF. However, only 30% of natural killer cell intact mice treated with IIRF died by day 10, indicating the critical role of natural killer cells in an IIRF‐induced immune response. The protective effects of IIRF were also examined in a natural killer cell–dependent melanoma model. Female B6C3F1 mice were injected with 8 × 10 5 B16F10 melanoma cells/mouse. Lung samples obtained from control and IIRF treated mice (5 mg on day −1) were analyzed using computerized imaging. Tumor morphometric analysis showed that 53±10% of the lung surface from control mice was cancerous. Prophylactic administration of IIRF lowered this value to 30±9%, a statistically significant decrease ( P =0.014). When this experiment was repeated with 1 × 10 5 cells, the number of melanoma nodules on the lung surface could be established through microscopic examination. Control mice (n=10) had an average of 88±7 tumor nodules, whereas IIRF‐treated mice (n=8) had 44±12 tumor nodules, a twofold reduction ( P =0.0036). These results suggest that IIRF is a BRM with therapeutic potential for cancer treatment. Drug Dev Res 64:213–219, 2005. © 2005 Wiley‐Liss, Inc.
Abstract 14178: Artificial Intelligence (AI)-ECG Derived Biological Age Identifies Accelerated Aging in the Lamin A/C Gene (LMNA) Mutations (2021)

Introduction: LMNA encodes the nuclear envelope proteins lamin A/C that are involved in ageing processes. Mutations in LMNA cause a spectrum of phenotypes which include muscular dystrophy, arrhythm...
Stimulating architectural thinking during requirements elicitation : an approach and tool support (2020)

Requirements engineering (RE) activities involve capturing both functional and non-functional requirements of the software system to be developed. The software requirements specifications (SRS) resulting from these activities often lack the details needed by software architects (SAs) to make informed architecture design decisions. In turn, if wrong architectural decisions are made, the intended but unstated requirements will not be satisfied. To cope with the lack of information, the SAs either make assumptions or go back to the business analysts (BAs) for clarifications or conduct additional stakeholder interviews. However, assumptions, if incorrect, can lead to costly and time-consuming refactoring efforts at later project stages, while additional unplanned interviews by BAs can slow down time-tomarket.
Acetate as a model for aspartate-based CXCR4 chemokine receptor binding of cobalt and nickel complexes of cross-bridged tetraazamacrocycles (2019)

A number of disease states including WHIM syndrome, HIV infection and cancer have been linked to the chemokine receptor CXCR4. High-affinity CXCR4 antagonist transition metal complexes of configurationally restricted bis-tetraazamacrocyclic ligands have been identified in previous studies. Recently synthesised and structurally characterised Co2+/Co3+ and Ni2+ acetate complexes of mono-macrocycle cross-bridged ligands have been used to mimic their known coordination interaction with the aspartate side chains on binding to CXCR4. Here, X-ray crystal structures for three Co2+/Co3+ acetate complexes and five Ni2+ acetate complexes are presented and demonstrate flexibility in the mode of binding to the acetate ligand concomitantly with the requisite cis-V-configured cross-bridged tetraazamacrocyle. Complexes of the smaller Co3+ metal ion exclusively bind acetate by chelating both oxygens of acetate. Larger Co2+ and Ni2+ metal ions in cross-bridged tetraazamacrocycles show a clear tendency to coordinate acetate in a monodentate fashion with a coordinated water molecule completing the octahedral coordination sphere. However, in unbridged tetraazamacrocycle acetate structures reported in the literature, the coordination preference is to chelate both acetate oxygens. We conclude that the short ethylene cross-bridge restricts the equatorial bulk of the macrocycle, prompting the metal ion to fill the equator with the larger monodentate acetate plus water ligand set. In unbridged ligand examples, the flexible macrocycle expands equatorially and generally only allows chelation of the sterically smaller acetate alone. These results provide insight for generation of optimised bis-macrocyclic CXCR4 antagonists utilising cobalt and nickel ions.
A coaxial test fixture for transmission/reflection measurements of metamaterials (2013)

Metamaterial structures exhibiting negative permittivity and/or negative permeability have been given considerable attention in recent years, but limited discussion has been given to a standard way of measuring these structures. Often, metamaterial measurements involve cumbersome fabrication and setup procedures making it very difficult in some cases to generate accurate data because of noise in the system or the complexity of the setup. This paper presents the design of a test fixture that overcomes much of the difficulty in metamaterial measurements to provide quick and accurate data. Furthermore, the data generated from this test fixture can be used directly with current extraction routines to determine the effective properties associated with the metamaterial structure.
Realizing High Sensitivity at 40 Gbit/s and 100 Gbit/s (2012)

We experimentally investigate modulation formats for realizing high data rate and high power sensitivity using coherent reception with low noise-figure optical preamplification. 40 Gbit/s PS-QPSK exhibits a sensitivity of 4.3 photons/bit while 100 Gbit/s PDM-QPSK exhibits a sensitivity of 5.3 photons/bit at 3.8 ⨉ 10-3 BER.
Installing Controlled Stereo-Defects Yields Semicrystalline and Biodegradable Poly(3-Hydroxybutyrate) with High Toughness and Optical Clarity (2023)

Stereo-defects present in stereo-regular polymers often diminish thermal and mechanical properties, and hence suppressing or eliminating them is a major aspirational goal for achieving polymers with optimal or enhanced properties. Here, we accomplish the opposite by introducing controlled stereo-defects to semicrystalline biodegradable poly(3-hydroxybutyrate) (P3HB), which offers an attractive biodegradable alternative to semicrystalline isotactic polypropylene but is brittle and opaque. We enhance the specific properties and mechanical performance of P3HB by drastically toughening it and also rendering it with the desired optical clarity while maintaining its biodegradability and crystallinity. This toughening strategy of stereo-microstructural engineering without changing the chemical compositions also departs from the conventional approach of toughening P3HB through copolymerization that increases chemical complexity, suppresses crystallization in the resulting copolymers, and is thus undesirable in the context of polymer recycling and performance. More specifically, syndio-rich P3HB (<i>sr</i>-P3HB), readily synthesized from the eight-membered <i>meso</i>-dimethyl diolide, has a unique set of stereo-microstructures comprising enriched syndiotactic [<i>rr</i>] and no isotactic [<i>mm</i>] triads but abundant stereo-defects randomly distributed along the chain. This <i>sr</i>-P3HB material is characterized by high toughness (<i>U</i><sub>T</sub> = 96 MJ/m<sup>3</sup>) as a result of its high elongation at break (>400%) and tensile strength (34 MPa), crystallinity (<i>T</i><sub>m</sub> = 114 °C), optical clarity (due to its submicron spherulites), and good barrier properties, while it still biodegrades in freshwater and soil.
Tag and Capture Flow Hydrogen Exchange Mass Spectrometry with a Fluorous-Immobilized Probe (2015)

Analysis of complex mixtures of proteins by hydrogen exchange (HX) mass spectrometry (MS) is limited by one's ability to resolve the protein(s) of interest from the proteins that are not of interest. One strategy for overcoming this problem is to tag the target protein(s) to allow for rapid removal from the mixture for subsequent analysis. Here we illustrate a new solution involving fluorous conjugation of a retrievable probe. The appended fluorous tag allows for facile immobilization on a fluorous surface. When a target protein is passed over the immobilized probe molecule, it can be efficiently captured and then exposed to a flowing stream of deuterated buffer for hydrogen exchange. The utility of this method is illustrated for a model system of the Elongin BC protein complex bound to a peptide from HIV Vif. Efficient capture is demonstrated, and deuteration when immobilized was identical to deuteration in conventional solution-phase hydrogen exchange MS. Protein captured from a crude bacterial cell lysate could also be deuterated without the need for separate purification steps before HX MS. The advantages and disadvantages of the method are discussed in light of miniaturization and automation.
Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide (2020)

Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) missense variant and proposed it as a founder allele in Puerto Rico segregating with Steel syndrome (STLS, MIM #615155); a rare osteochondrodysplasia characterized by short stature, congenital bilateral hip dysplasia, carpal coalitions, and scoliosis. We now report segregation of this variant in five probands from the initial clinical report defining the syndrome and an additional family of Puerto Rican descent with multiple affected adult individuals. We modeled the orthologous variant in murine Col27a1 and found it recapitulates some of the major Steel syndrome associated skeletal features including reduced body length, scoliosis, and a more rounded skull shape. Characterization of the in vivo murine model shows abnormal collagen deposition in the extracellular matrix and disorganization of the proliferative zone of the growth plate. We report additional COL27A1 pathogenic variant alleles identified in unrelated consanguineous Turkish kindreds suggesting Clan Genomics and identity-by-descent homozygosity contributing to disease in this population. The hypothesis that carrier states for this autosomal recessive osteochondrodysplasia may contribute to common complex traits is further explored in a large clinical population cohort. Our findings augment our understanding of COL27A1 biology and its role in skeletal development; and expand the functional allelic architecture in this gene underlying both rare and common disease phenotypes.
Dynamic mammalian cardiogenesis investigated by high-resolution ultrasound in guinea pigs. (1983)

Ultrasonic cardiac imaging of human fetuses has been feasible only after 12 to 14 weeks gestation when the heart is completely formed. Our purpose was to develop a method of examining dynamic mammalian cardiogenesis with a high-resolution 9 MHz ultrasound scanner. Fetal guinea pig hearts were imaged in utero over the course of 10 days. All images were obtained after blastocyst implantation estimated to occur 8 days after fertilization with cardiogenesis occurring over the next 14 days. After laparotomies were performed on the gravid guinea pigs, sterile transducers were placed on their uterine horns and ultrasonic images were obtained. Further optical magnification of videotaped images was required to visualize cardiac details. Ten gravid guinea pigs were examined and three of 10 underwent serial imaging. The earliest cardiac images, recorded approximately 10 days after implanta- tion, demonstrated a partially fused heart tube, ventricle, bulbus cordis, and first aortic arch. During the next 24 hr looping of the heart, a primitive atrium and an unfused endocardial cushion structure were observed. Midway through the first week of cardiac development, ventricular and atrial septation and development of primitive atrioventricular valve tissue were imaged. At the end of the first week of cardiac development, more distinct endocardial cushion structure and atrial and ventricular septation were noted. Additionally, a functioning foraminal flap was observed. Midway through the second week of cardiac development, spiraling and division of the bulbus cordis were complete. Scanning electron microscopic examination verified the size and configuration of ultrasonically imaged struc- tures. The high-frequency imaging allowed dynamic recording of events in mammalian cardiogenesis.
Extended molecular dynamics of ac-kitpromoter quadruplex (2015)

The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 μs long, ∼50 μs in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal μs-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex.
Reduced Complexity Digital Back-Propagation Methods for Optical Communication Systems (2014)

Next-generation optical communication systems will continue to push the ( bandwidth · distance) product towards its physical limit. To address this enormous demand, the usage of digital signal processing together with advanced modulation formats and coherent detection has been proposed to enable data-rates as high as 400 Gb/s per channel over distances in the order of 1000 km. These technological breakthroughs have been made possible by full compensation of linear fiber impairments using digital equalization algorithms. While linear equalization techniques have already matured over the last decade, the next logical focus is to explore solutions enabling the mitigation of the Kerr effect induced nonlinear channel impairments. One of the most promising methods to compensate for fiber nonlinearities is digital back-propagation (DBP), which has recently been acknowledged as a universal compensator for fiber propagation impairments, albeit with high computational requirements. In this paper, we discuss two proposals to reduce the hardware complexity required by DBP. The first confirms and extends published results for non-dispersion managed link, while the second introduces a novel method applicable to dispersion managed links, showing complexity reductions in the order of 50% and up to 85%, respectively. The proposed techniques are validated by comparing results obtained through post-processing of simulated and experimental data, employing single channel and WDM configurations, with advanced modulation formats, such as quadrature phase shift keying (QPSK) and 16-ary quadrature amplitude modulation (16-QAM). The considered net symbol rate for all cases is 25 GSymbol/s. Our post-processing results show that we can significantly reduce the hardware complexity without affecting the system performance. Finally, a detailed analysis of the obtained reduction is presented for the case of dispersion managed link in terms of number of required complex multiplications per transmitted bit.
The Age of Incorrect Information: A New Performance Metric for Status Updates (2020)

In this paper, we introduce a new performance metric in the framework of status updates that we will refer to as the Age of Incorrect Information (AoII). This new metric deals with the shortcomings of both the Age of Information (AoI) and the conventional error penalty functions as it neatly extends the notion of fresh updates to that of fresh “informative” updates. The word informative in this context refers to updates that bring new and correct information to the monitor side. After properly motivating the new metric, and with the aim of minimizing its average, we formulate a Markov Decision Process (MDP) in a transmitter-receiver pair scenario where packets are sent over an unreliable channel. We show that a simple “always update” policy minimizes the aforementioned average penalty along with the average age and prediction error. We then tackle the general, and more realistic case, where the transmitter cannot surpass a specific power budget. The problem is formulated as a Constrained Markov Decision Process (CMDP) for which we provide a Lagrangian approach to solve. After characterizing the optimal transmission policy of the Lagrangian problem, we provide a rigorous mathematical proof to showcase that a mixture of two Lagrange policies is optimal for the CMDP in question. Equipped with this, we provide a low complexity algorithm that finds the AoII-optimal operating point of the system in the constrained scenario. Lastly, simulation results are laid out to showcase the performance of the proposed policy and highlight the differences with the AoI framework.
Current Response and Determination of Traces of Coenzyme I At a Silver Microelectrode (1998)

Abstract A useful current response of nicotinamide coenzyme I at a silver microelectrode was obtained and, therefore, an electrochemical method has been developed for the determination of traces of the coenzyme by square wave adsorption stripping voltammetry. Under optimum conditions the proposed method provides a linear response over the coenzyme concentration in the range of 0.5∼7.5 μmol/L. The detection limit was 0.2 μmol/L. The relative standard deviation was 3.5% for 6 successive determinations of the coenzyme at 1.0 μmol/L. In view of the merits of the electrochemical techniques and this microelectrode, this method will be of great usefulness in the biochemical and clinical fields in the future.
Switching operation mode resonance ratio control for flexible robot system (2013)

Controlling robot with the mechanical resonance has been receiving increased attention. A new effective control method, a resonance ratio control, has been introduced as a new way to guarantee the robustness and suppress the oscillation during task executions for position and force control system. This work presents a new approach to the controlling of flexible robot system by a switching operation mode resonance ratio control. To calculate the optimal parameters of position/force servoing based on resonance ratio control, a Coefficient Diagram Method (CDM) is employed. In this paper, we introduce a novel approach that automatically adapt algorithm parameters conditional based on the operational tasks. Moreover, a multiencoder based disturbance observer (MEDOB) is shown to estimate the external force on the load side, rather than using a force sensor. The experiments with a linear motor and spring show the validity of the approach. From the experiments, it can reject vibration to improve controlling performance.