gebhart/patrepeval huggingface dataset:
Attack Resilience of Cache Replacement Policies: A Study Based on TTL Approximation (2022)

Caches are pervasively used in communication networks to speed up content access by reusing previous communications, where various replacement policies are used to manage the cached contents. The replacement policy of a cache plays a key role in its performance, and is thus extensively engineered to achieve a high hit ratio in benign environments. However, some studies showed that a policy with a higher hit ratio in benign environments may be more vulnerable to cache pollution attacks that intentionally send requests for unpopular contents. To understand the cache performance under such attacks, we analyze a suite of representative replacement policies under the framework of TTL approximation in how well they preserve the hit ratios for legitimate users, while incorporating the delay for the cache to obtain a missing content. We further develop a scheme to adapt the cache replacement policy based on the perceived level of attack. Our analysis and validation on real traces show that although no single policy is resilient to all the attack strategies, suitably adapting the replacement policy can notably improve the attack resilience of the cache. Motivated by these results, we implement selected policies as well as policy adaptation in an open-source SDN switch to manage flow rule replacement, which is shown to notably improve its resilience to pollution attacks.
TLR7/8 agonists impair monocyte-derived dendritic cell differentiation and maturation (2006)

Pathogen recognition by TLR activates the innate immune response and is typically followed by the development of an adaptive immune response initiated by antigen presentation. Dendritic cells (DC) are the most efficient APC and express diverse TLRs, including TLR7 and -8, which have been recently identified as targets for ssRNA recognition during viral infection. We have studied the effect of TLR7/8 agonists on DC differentiation and maturation from human monocytes. The synthetic agonist Resiquimod (R-848) or the physiological agonist ssRNA impaired monocyte differentiation to DC phenotypically and functionally. Induced expression of the nonclassical MHC molecules of the CD1 family in DC was inhibited at the protein and mRNA levels, and antigen acquisition was inhibited. Proinflammatory cytokine (including IL-6, IL-8, TNF-alpha, IL-1beta) and IL-10 production were induced during DC differentiation. Cross-talk between TLR4 and TLR7/8 was revealed as immature DC, which had been differentiated in the presence of R-848 were insensitive to LPS-mediated maturation and cytokine production but still induced allostimulation. These data lead us to suggest that ongoing viral activation of TLR7/8 could alter the adaptive immune response by modifying DC differentiation and by down-regulating DC responsiveness to a subsequent bacterial TLR4-mediated signal.
The Mitochondriotropic Effects of L-carnitine and its Esters in the Central Nervous System (2003)

Mitochondrial defects have been linked to such devastating neurodegenerative diseases as Parkinsons, Huntingtons, amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS) and Alzheimers as well as senile dementias. Mitochondrial metabolic defects could affect the electron transport, the tricarboxylic acid cycle (TCA), and substrate transport. However, it is the escape of oxygen free radicals (superoxide formation) as a result of a disturbed electron transfer within the respiratory chain that is thought to underlie many of the deleterious effects of mitochondrial dysfunction. A therapeutic strategy aimed at ameliorating these effects with supplementation of antioxidants, cofactors, and substrates is becoming prevalent. L-carnitine (LC), a biologically active stereoisomer of trimethylammonium hydroxide, is a highly polar, small zwitterion (inner salt). Ingested, LC is incorporated into the total body carnitine pool that includes unchanged LC, acetyl-L-carnitine (ALC), and other carnitine esters. LC optimises cell energy production by transporting medium and long chain fatty acids into the mitochondria for utilization in metabolism through β-oxidation. Free LC serves then two important intra-mitochondrial functions. It maintains the acetyl-CoA / CoA ratio and scavenges excess potentially toxic, free acyl groups to transport them out of the mitochondria. A lower acetyl-CoA / CoA ratio favors the action of pyruvate dehydrogenase that increases the formation of acetyl-CoA from pyruvate. The increased formation of acetyl-CoA from pyruvate significantly impacts glucose oxidative metabolism by limiting access to the TCA cycle. LC is also important in maintaining cell membrane stability through its involvement in acetylation of membrane phospholipids and amphiphilic actions. The carnitine system plays a role in the mitochondrial elongation-desaturation of the ω-3-polyunsaturated fatty acids to docosahexaenoic acid (DHA). Thus, LC is an endogenous mitochondriotropic substance and its use in therapy is to replace depleted carnitine levels, resulting in restoration of normal cellular and, hence body functions. LC and its acetylated form, acetyl-L-carnitine (ALC), may have antioxidative properties, protecting cells against lipid peroxidation and membrane breakdown. The carnitine system prevents loss of mitochondrial function in isolated liver mitochondria, prevents lipid peroxidation damage associated with energy loss due to hypobaric hypoxia in rat brain cells, and protects against mitochondrial inhibitor-induced toxicity in neurons. Consequently, LC protects against the neurotoxicity induced by mitochondrial inhibitors such as 3-nitropropionic acid (3-NPA) as well as methamphetamine. Supportive findings indicating a protective ability of LC and some of its esters at the mitochondrial level in the CNS have been reported by various groups and are discussed in further detail in this review.
Use of the lambda Red recombinase system to rapidly generate mutants in Pseudomonas aeruginosa (2008)

The lambda Red-based technique can be used efficiently to generate mutants in P. aeruginosa. The main advantage of this procedure is its rapidity as mutants can be easily obtained in less than a week if the 3-step PCR procedure is used, or in less than three days if the mutation needs to be transferred from one strain to another.
The Relationship Between Vitamin D and Postoperative Atrial Fibrillation: A Prospective Cohort Study (2022)

In our contemporary mid-European cohort, higher 25(OH)D concentration did not show a benefit for POAF in CABG patients and may even be harmful, though with borderline statistical significance. Our data are in line with a recent randomised study in community-based adults and call for further research to determine both, the clinical impact of elevated 25(OH)D concentration and vitamin D supplementation as well as the possible underlying pathophysiological mechanisms.
Reply to Ramos-Silva et al.: Regarding coral skeletal proteome (2013)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Fundamental statistical properties of reconstruction methodology for TDDB with variability in BEOL/MOL/FEOL applications (2016)

In this work, we investigate the validity of the so-called big-data deconvolution approach with its use of sampling-based reconstruction methodology for general applications to BEOL and MOL dielectrics with substantial non-uniformity and multiple variability sources. Unlike conventional statistical sampling, we have found that all parameters (β and T <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">63</inf> ) and area scaling characteristics of reconstructed Weibull distributions along with T <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">63</inf> variation (σT <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">63</inf> ) across the sampling units (chips or dies) show a strong dependence on sampling number per unit (chip). We developed the statistical theory to correctly characterize the sampling number dependence of reconstructed Weibull slope and σT <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">63</inf> , including a criterion for the general applicability of the sampling-based reconstruction methodology. We have examined why the big-data deconvolution approach cannot be used for BEOL/MOL dielectrics with multiple variability sources. The sampling-number dependence of reconstructed T <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">63</inf> fundamentally nullifies the feasibility of this approach while sampling-number dependence of area scaling should be always demonstrated prior to the use this methodology. Finally, we show that V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">BD</inf> results can provide misleading conclusions due to the different scaling property of variance in Vbd and Tbd in use of reconstruction methodology.
Adaptive Optical Scanning Holography (2016)

Optical Scanning Holography (OSH) is a powerful technique that employs a single-pixel sensor and a row-by-row scanning mechanism to capture the hologram of a wide-view, three-dimensional object. However, the time required to acquire a hologram with OSH is rather lengthy. In this paper, we propose an enhanced framework, which is referred to as Adaptive OSH (AOSH), to shorten the holographic recording process. We have demonstrated that the AOSH method is capable of decreasing the acquisition time by up to an order of magnitude, while preserving the content of the hologram favorably.
711. A Unique Breath Secondary Metabolite Volatile Signature for the Diagnosis of Histoplasmosis (2021)

Abstract Background Histoplasmosis is a common endemic fungal infection in the Americas, causing significant morbidity and mortality, particularly in immunocompromised patients. Existing diagnostic methods are limited in their sensitivity (especially in pulmonary histoplasmosis) and turnaround time. Methods We examined prospectively collected breath samples from 84 patients with suspected histoplasmosis 3/2019 - 2/2020 at Hospital Roosevelt (HR; Guatemala City, Guatemala, n = 56) and suspected invasive fungal disease 1/2018 - 10/2019 at Brigham and Women’s Hospital (BWH; Boston, MA, USA, n = 28) using thermal desorption gas chromatography-tandem mass spectrometry (TDU-GC-MS/MS). Patients were evaluated for histoplasmosis and other infections according to the local standard of care – of note, 18/56 patients at HR did not have Histoplasma urine antigen testing. Results Median age was 44 years, 60 (71%) were male, 23 (27%) had HIV, 15 (18%) had hematologic malignancy. 7 patients were diagnosed with histoplasmosis over the study period (4 at HR, 5 at BWH), with a clinical syndrome + positive Histoplasma urine or serum antigen test, with some patients also having yeast forms on tissue biopsy. 3 patients had disseminated and 4 pulmonary histoplasmosis. 4 patients with histoplasmosis had co-infections – 2 tuberculosis (TB), 1 influenza, and 1 Pneumocystis jirovecii (PJP) pneumonia. 4 patients were receiving antifungal therapy active against Histoplasma at the time of their first breath sample. We found 3 sesquiterpenes: (A) cyperene, (B) 1R,4aR,8aR)-2,5,5,8a-Tetramethyl-4,5,6,7,8,8a-hexahydro-1H-1,4a-methanonaphthalene, and (C) viridiflorol in patients with histoplasmosis, that distinguished these patients from those with other pneumonia (TB, coccidioidomycosis, invasive aspergillosis, mucormycosis, PJP, bacterial pneumonia) with 100% sensitivity and 70% (95% CI 59, 80) specificity. Figure 1. TDU GC-MS/MS spectral comparison in histoplasmosis vs. the other invasive mycoses aspergillosis or mucormycosis. A: Cyperene; B: (1R,4aR,8aR)-2,5,5,8a Tetramethyl-4,5,6,7,8,8a-hexahydro-1H-1,4a-methanonaphthalene; C: viridiflorol; D: 1H-Indene, 2,3,3a,4-tetrahydro-3,3a,6-trimethyl-1-(1-methylethyl)-; E: β-funebrene; F: trans-α-bergamotene; G: eremophilene; H: spathulenol; I: cedrene; J: cedranoxide, 8,14- Conclusion Conclusion: Patients with histoplasmosis have a unique secondary metabolite breath signature that can be used for the noninvasive diagnosis of pulmonary and disseminated histoplasmosis. Many patients in this cohort did not undergo urine antigen testing or other diagnostic workup for histoplasmosis, which may have affected our specificity estimates. Disclosures Francisco M. Marty, MD, SCYNEXIS, Inc. (Scientific Research Study Investigator)
What Sports Activity Levels Are Achieved in Patients With Modular Tumor Endoprostheses of Osteosarcoma About the Knee? (2014)

Level IV, therapeutic study. See Guidelines for Authors for a complete description of levels of evidence.
Abstract 2985: Predicting the impact of mutations in cancer using an integrated pathway approach (2012)

Abstract The major mechanism by which cancer arises is through somatic mutations. These mutations can lead to alterations in gene regulation as well as changes in protein structure and function. Individual tumors can contain hundreds to thousands of mutations. It is critical to distinguish mutations that have an important role defining the cancer - driver mutations - from mutations that are unimportant to the tumor - passenger mutations. Differentiating driver and passenger events is essential for understanding cancer disease mechanisms, which can help guide treatment decisions as well as identify novel targets for treatment. Genomic probing with technologies such as expression arrays and high-throughput RNA sequencing provide insight into changes in gene regulation in cancer, but determining the tumorigenic role of a coding mutation is less clear. Genomic data coupled with pathway information may provide insight into the functional impact of a mutation to particular genes. We are developing a mutation prediction method based on integrated pathway analysis to discriminate loss-of-function, neutral, and gain-of-function mutations. Utilizing the set of regulatory interactions annotated for a given gene, we can detect a discrepancy in the downstream effects of an altered gene compared to what is expected from its upstream influences. We show that a score based on this discrepancy is highly predictive of the presence of a mutation and that the directionality of this discrepancy also reflects the gain- or loss-of-function in a gene. Application of our method to a set of known driver mutations reveals that there is a significantly strong signal for loss- and gain- of functional mutations in the surrounding network, demonstrating the sensitivity of this approach. In addition, when applied to the negative control of passenger mutations, the method predicts little pathway impact, indicating this approach also has high specificity. Application of this approach to all recurrent mutations in ovarian and glioblastoma multiforme cancers from the TCGA project identifies several important driver mutations across these cohorts. We also highlight the novel utility of this specific approach by comparison to earlier published approaches including MutSig, CHASM, and MutPred. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2985. doi:1538-7445.AM2012-2985
Xylem vessel radii comparison between soybean genotypes differing in tolerance to drought (2020)

Xylem element radius can be a key factor in determining plant hydraulic conductance and vulnerability to cavitation. Most studies of xylem element radius have been on woody species with a focus on plant survival under severe water-deficit stress. However, xylem element radius, particularly the largest radius elements, can potentially have an influence on hydraulic flow at more moderate water-deficits. Few studies have offered a detailed distribution of xylem element radii, and even fewer on the distribution in crop species. In this study, the xylem element radii of two genotypes of soybean (Glycine max L. Merr.) were compared because these two genotypes had been documented to react differently to drying soil. The stems of young plants were harvested from three positions, and in stem cross-sections, the number of xylem elements and the radius of each element were determined. While the number of xylem elements did not differ significantly between the two genotypes, the distribution of the radii was skewed to smaller radii in drought-tolerant PI 4719386 as compared to Hutcheson. This contrast extended to a difference between the genotypes in the radii of the largest elements, which are considered most vulnerable to cavitation.
Growth of<i>c</i>-axis-oriented aluminum nitride thin films onto different substrates and buffer layers (2014)

The growth of aluminum nitride thin films onto various substrates (glass, flexible polyimide, or silicon) and onto different buffer layers (Au, Nb, Cu, Ag, Co, Fe, NiFe, or IrMn) is reported. Samples grown on IrMn, Co, NiFe, Nb, or Au show smooth surfaces. This same smooth quality is observed in samples grown at a lower 200 °C temperature directly on glass, Si, or flexible polyimide. In applications where thin and smooth piezoelectric films are necessary, c-axis-oriented AlN can be grown onto a wide range of different surfaces: conducting, insulating, ferromagnetic, antiferromagnetic, or flexible. Copyright © 2014 John Wiley & Sons, Ltd.
Sensors, sunscreens, and shirts (2019)

As the largest segment of the global skincare market, facial care products are designed and marketed as commodities that cleanse, protect, and moisturize skin. Over the past decade, these products have diversified into multi-functional formulations with claims to also renew, rejuvenate, and restore skin function. This trend has not only stimulated the creation of new biomaterials that provide both aesthetic and therapeutic benefits but has also prompted alternative platforms to evaluate their effects such as color, texture, and function. In alignment with these growing trends, this thesis describes the design of multifunctional biomimetic materials that can be used for future skincare products. Originally inspired by the adaptive coloration exhibited by marine animals like cephalopods, I describe the design of materials that absorb and dissipate solar radiation, enhance natural color, and offer a stimuli responsive color-changing platform. First, I discuss methods for characterizing the cephalopod-derived chromophore, Xanthommatin (Xa), from both natural and synthetic origins by employing a suite of chromatographic, spectrophotometric, and spectroscopic analytical techniques. Applications of these chromophores were then explored in two contexts: (1) biohybrid colorants and (2) alternative ultraviolet (UV)-filters. In the first, I describe the design and fabrication of colorants containing Xa encased within silica-based nanostructures. I employed a biomimetic approach to encapsulate Xa with amine-terminal polyamidoamine (PAMAM) dendrimer templates which helped stabilize the pigment. Depending on the concentration of Xa used in the reaction, the resultant biohybrid nanomaterials generated a range of neutral colors of differing hues. When applied as coatings, these colorants could be triggered to change color from yellow/gold to red in the presence of a chemical reducing agent. Altogether, these capabilities demonstrated the ability to process biochromes like Xa as nanomaterials that can be applied as coatings with a tunable, dynamic range. In the second context, I explored the utility of Xa as a sunscreening agent. This is important because commercially available suncare products, containing traditional chemical and physical UV-filters, have recently been reported to elicit systemic toxicities prompting a reevaluation of their safety for humans. As part of a collaborative effort, I demonstrated the application of Xa as an alternative chemical UV-filter with a tunable sun protection factor (SPF) range. The photoprotective properties and cytocompatibility of Xa-based materials were investigated in vitro, where we found over 95% cell viability when incubated directly with fibroblasts. An added, unexpected feature is that Xa behaves as a free radical scavenger, making it among one of the first UV-filters that can not only protect against solar irradiation but can also be used in preventative skin care. Altogether, our work supports the use of this cephalopod-inspired platform towards the development of next-generation consumer healthcare products.
Desarrollo y validación de un método por CG para la determinación de D004 en emulsiones (2008)

Resumen es: El D004 es un nuevo ingrediente activo compuesto por una mezcla de acidos grasos entre 8 y 18 atomos de carbono, que ha mostrado eficacia en modelos expe...
ChemInform Abstract: SYNTHESIS OF A 1,3‐DIOXA‐2,4‐DIBORETANE, AN OXOBORANE PRECURSOR (1985)

Abstract Das 1,3‐Dioxadiboretan (III) wird wie aufgezeichnet synthetisiert.
Design, Fabrication, and Characterization of Single Crystal Silicon Latching Snap Fasteners for Micro Assembly (1995)

Abstract A snap fastener is a deformable device consisting of a pair of mating surfaces that “snap” together during assembly. Because of the simple, linear assembly motion, such latching micro fasteners have a wide range of applications in micro assembly tasks, e.g. for devices with multiple or layered components, or micro opto-mechanical plugs. At the micro scale, conventional types of fasteners like screws and hinges are unlikely to work due to present fabrication constraints and large friction forces. Micro snap fasteners also have great potential to be used as sensors with memory. We present a detailed theoretical analysis of design and function of micro snap fasteners, and describe the fabrication in single crystal silicon (SCS) technology. We perform experiments on snap fasteners with 1 – 2 μm wide latches. Independent comb drive actuators generating micro-Newton forces were used for actuation of the fasteners to verify the theoretically obtained design rules. Our experimental results are in close accordance with the theoretical predictions.
<i>In Situ</i> Optical Quantification of Extracellular Electron Transfer Using Plasmonic Metal Oxide Nanocrystals** (2021)

Abstract Extracellular electron transfer (EET) is a critical form of microbial metabolism that enables respiration on a variety of inorganic substrates, including metal oxides. However, quantifying current generated by electroactive bacteria has been predominately limited to biofilms formed on electrodes. To address this, we developed a platform for quantifying EET flux from cell suspensions using aqueous dispersions of infrared plasmonic tin‐doped indium oxide nanocrystals. Tracking the change in optical extinction during electron transfer enabled quantification of current generated by planktonic Shewanella oneidensis cultures. Using this method, we differentiated between starved and actively respiring cells, cells of varying genotype, and cells engineered to differentially express a key EET gene using an inducible genetic circuit. Overall, our results validate the utility of colloidally stable plasmonic metal oxide nanocrystals as quantitative biosensors in aqueous environments and contribute to a fundamental understanding of planktonic S. oneidensis electrophysiology using simple in situ spectroscopy.