gebhart/patrepeval huggingface dataset:
Mechanisms Associated with HIV-1 Resistance to Acyclovir by the V75I Mutation in Reverse Transcriptase (2009)

It has recently been demonstrated that the anti-herpetic drug acyclovir (ACV) also displays antiviral activity against the human immunodeficiency virus type 1 (HIV-1). The triphosphate form of ACV is accepted by HIV-1 reverse transcriptase (RT), and subsequent incorporation leads to classical chain termination. Like all approved nucleoside analogue RT inhibitors (NRTIs), the selective pressure of ACV is associated with the emergence of resistance. The V75I mutation in HIV-1 RT appears to be dominant in this regard. By itself, this mutation is usually not associated with resistance to currently approved NRTIs. Here we studied the underlying biochemical mechanism. We demonstrate that V75I is also selected under the selective pressure of a monophosphorylated prodrug that was designed to bypass the bottleneck in drug activation to the triphosphate form (ACV-TP). Pre-steady-state kinetics reveal that V75I discriminates against the inhibitor at the level of catalysis, whereas binding of the inhibitor remains largely unaffected. The incorporated ACV-monophosphate (ACV-MP) is vulnerable to excision in the presence of the pyrophosphate donor ATP. V75I compromises binding of the next nucleotide that can otherwise provide a certain degree of protection from excision. Collectively, the results of this study suggest that ACV is sensitive to two different resistance pathways, which warrants further investigation regarding the detailed resistance profile of ACV. Such studies will be crucial in assessing the potential clinical utility of ACV and its derivatives in combination with established NRTIs.
Optical Efficiency Enhancement of Nanojet-Based Dielectric Double-Material Color Splitters for Image Sensor Applications (2021)

We propose a new type of color splitter, which guides a selected bandwidth of incident light towards the proper photosensitive area of the image sensor by exploiting the nanojet (NJ) beam phenomenon. Such splitting can be performed as an alternative to filtering out part of the received light on each color subpixel. We propose to split the incoming light thanks to a new type of NJ-based near-field focusing double-material element with an insert. To suppress crosstalk, we use a Deep-Trench Isolation (DTI) structure. We demonstrate that the use of a dielectric insert block allows for reduction in the size of the color splitting element. By changing the position of the DTI, the functionality of separating blue, green and red light can be improved.
Texture Illumination Separation for Single-Shot Structured Light Reconstruction (2015)

Active illumination based methods have a trade-off between acquisition time and resolution of the estimated 3D shapes. Multi-shot approaches can generate dense reconstructions but require stationary scenes. Single-shot methods are applicable to dynamic objects but can only estimate sparse reconstructions and are sensitive to surface texture. We present a single-shot approach to produce dense shape reconstructions of highly textured objects illuminated by one or more projectors. The key to our approach is an image decomposition scheme that can recover the illumination image of different projectors and the texture images of the scene from their mixed appearances. We focus on three cases of mixed appearances: the illumination from one projector onto textured surface, illumination from multiple projectors onto a textureless surface, or their combined effect. Our method can accurately compute per-pixel warps from the illumination patterns and the texture template to the observed image. The texture template is obtained by interleaving the projection sequence with an all-white pattern. The estimated warps are reliable even with infrequent interleaved projection and strong object deformation. Thus, we obtain detailed shape reconstruction and dense motion tracking of the textured surfaces. The proposed method, implemented using a one camera and two projectors system, is validated on synthetic and real data containing subtle non-rigid surface deformations.
Total synthesis of the Amaryllidaceae alkaloid clivonine (2011)

Two syntheses of the Amaryllidaceae alkaloid clivonine (1) are described. Both employ previously reported 7-arylhydrindane 6 as an intermediate but differ in the method employed for subsequent introduction of what becomes the ring-B lactone carbonyl carbon (C7). The synthesis featuring a Bischler-Napieralski reaction for this transformation constitutes the first asymmetric synthesis of natural (+)-clivonine. Crystal structures for compounds (±)-13, (±)-16, (-)-20 and (±)-28 are also reported.
Consensus transcriptional states describe human mononuclear phagocyte diversity in the lung across health and disease (2020)

SUMMARY Monocytes, dendritic cells, and macrophages, commonly referred to as mononuclear phagocytes (MNPs), are innate immune cells capable of adopting diverse homeostatic and pathogenic phenotypes. Recent single-cell RNA-sequencing studies across many diseases in the lung have profiled this diversity transcriptionally, defining new cellular states and their association with disease. Despite these massive cellular profiling efforts, many studies have focused on defining myeloid dysfunction in specific diseases without identifying common pan-disease trends in the mononuclear phagocyte compartment within the lung. To address these gaps in our knowledge, we collate, process, and analyze 561,390 cellular transcriptomes from 12 studies of the human lung across multiple human diseases. We develop a computational framework to identify and compare dominant gene markers and gene expression programs and characterize MNP diversity in the lung, proposing a conserved dictionary of gene sets. Utilizing this reference, we efficiently identify disease-associated and rare MNP populations across multiple diseases and cohorts. Furthermore, we demonstrate the utility of this dictionary in characterizing a recently published dataset of bronchoalveolar lavage cells from COVID-19 patients and healthy controls which further reveal novel transcriptional shifts directly relatable to other diseases in the lung. These results underline conserved MNP transcriptional programs in lung disease, provide an immediate reference for characterizing the landscape of lung MNPs and establish a roadmap to dissecting MNP transcriptional complexity across tissues.
Síntesis de nano-Au soportados en óxidos metálicos y su actividad catalítica en reacciones de oxidación de CO (2013)

Gold nanoparticles, Nano-Au, were prepared on different supports and used as CO oxidation catalysts. Synthesis of Nano-Au, supported on TiO 2, CeO 2 and �-Al 2O3 was done by precipitation in non-aqueous HAuCl 4/ethylene-glycol in a Li 2S/oxide/ethylene-glycol suspension in a minimum HClO 4 volume. All the nano-structured systems were characterized by TEM, XPS, XRD, AE, ICP and UVVisible methods. The TEM images confirm Nano-Au/ oxide formation on all the supports. Particle size distribution analysis suggest different dispersions, being Au/Al 2O3 (~3,45 nm) the least dispersed system. XRD analysis shows the presence of Au/oxide, compared with the XRD standard, and crystal size was estimated using the Debye-Scherrer equation. UV-visible spectra shows a characteristic band near 520 nm, due to plasmon resonance in all the synthetized systems and there was no clear tendency between particle size and the absorption band displacement. XPS analysis shows two peaks with a slight displacement in bonding energy, assigned to the Au4 f7/2 y Au4 f5/2 transitions due to Au(0) and Au 3+ from Au 2S3. The CO oxidation catalytic activity of Nano-Au was done in a static bed reactor at low temperature, obtaining a 36% conversion with Au/TiO 2.
Strain characterization of CoSi2/n-Si0.9Ge0.1/p-Si heterostructures (1994)

We report on the structural characterization of CoSi2/n-Si0.9Ge0.1/p-Si heterostructures. Silicon molecular beam epitaxy is combined with Co sputtering to obtain these structures. The strain in the Si1−xGex is investigated after the formation of the CoSi2 by using high-resolution x-ray diffraction mapping in reciprocal space and cross-sectional transmission electron microscopy. The results show that in order to keep the strain in Si1−xGex unaffected, a sacrificial Si layer is needed. It was possible to obtain transistor action, but with low-current gain (β).
Parameterized framework for the analysis of visual quality assessments using crowdsourcing (2015)

The ability to assess the quality of new multimedia tools and applications relies heavily on the perception of the end user. In order to quantify the perception, subjective tests are required to evaluate the effectiveness of new technologies. However, the standard for subjective user studies requires a highly controlled test environment and is costly in terms of both money and time. To circumvent these issues we are utilizing crowdsourcing platforms such as CrowdFlower and Amazon's Mechanical Turk. The reliability of the results relies on factors that are not controlled and can be considered “hidden”. We are using pre-test survey to collect responses from subjects that reveal some of the hidden factors. Using statistical analysis we build parameterized model allowing for proper adjustments to collected test scores.
Hydrophobicity variations on plasma treated silicone rubber surfaces (2002)

Studies of the loss and recovery of hydrophobicity on silicone rubber surfaces during different plasma treatments and following storage at ambient atmosphere are presented. The plasma gases were oxygen, air, nitrogen and argon. Attempts were made to understand correlation between the chemical state of surface, its hydrophobicity and plasma nature. The changes in the chemical state were investigated by means of chemiluminescence, infrared and differential scanning spectroscopic methods.
Towards practical and robust DNA-based data archiving using the yin–yang codec system (2022)

DNA is a promising data storage medium due to its remarkable durability and space-efficient storage. Early bit-to-base transcoding schemes have primarily pursued information density, at the expense of introducing biocompatibility challenges or decoding failure. Here we propose a robust transcoding algorithm named the yin-yang codec, using two rules to encode two binary bits into one nucleotide, to generate DNA sequences that are highly compatible with synthesis and sequencing technologies. We encoded two representative file formats and stored them in vitro as 200 nt oligo pools and in vivo as a ~54 kbps DNA fragment in yeast cells. Sequencing results show that the yin-yang codec exhibits high robustness and reliability for a wide variety of data types, with an average recovery rate of 99.9% above 10<sup>4</sup> molecule copies and an achieved recovery rate of 87.53% at ≤10<sup>2</sup> copies. Additionally, the in vivo storage demonstration achieved an experimentally measured physical density close to the theoretical maximum.
Dose-Dependent Effects of Alcohol on Insulin Signaling: Partial Explanation for Biphasic Alcohol Impact on Human Health (2007)

Routine consumption of alcohol at low doses is associated with decreased risk of acquiring type 2 diabetes, whereas chronic and excessive alcohol consumption increases the risk. Although there is good epidemiologic evidence for these biphasic effects, careful validation of these effects on insulin signaling has not been reported, nor have biological mechanisms underlying these biphasic effects been proposed. In this study, we provide evidence in rats that low-dose alcohol intake (4 g/kg x d) enhances hepatic insulin signaling by suppressing p55gamma (a phosphatidylinositol 3-kinase regulatory subunit isoform) at the posttranscriptional level, leading to the increased association of the phosphatidylinositol 3-kinase catalytic subunit (p110) with insulin receptor substrate-1 (P < 0.05) and subsequent activation of downstream effectors such as Akt, glycogen synthase kinase 3beta, and nuclear sterol regulatory element binding protein (SREBP)-1. These results, combined with our previous data (confirmed in the present study) demonstrating that ethanol intake at high doses (13 g/kg x d) disrupts hepatic insulin signaling by inducing TRB3, a mammalian homolog of Drosophila (tribbles-related protein 3) that prevented activation of downstream effectors (such as Akt, GSK3beta, and nSREBP-1), provide clear mechanistic validation of the biphasic effects of ethanol on insulin signaling. We also report that ethanol induction of TRB3 can be partially blocked (P < 0.01) by compounds (4-phenyl butyric acid and taurine-ursodeoxycholic acid) known to reduce endoplasmic reticulum stress. Thus, alcohol exerts biphasic actions on hepatic insulin signaling, such that low doses activate insulin signaling pathways associated with reduced p55gamma to increase nSREBP-1, whereas high doses of ethanol elevate TRB3 and suppress insulin signaling to decrease SREBP-1.
A dielectric electroactive polymer generator-actuator model: modeling, identification, and dynamic simulation (2008)

Dielectric electroactive polymer membranes have been shown to have capabilities both as actuators and generators. Recent models of actuators have shown input to output dynamics that link the electrical energy input to the acceleration of a mass. Models such as these are useful for implementing closed loop control systems and will be necessary in the future for the construction of robust and fault tolerant controls. On the other hand, explanations of the generator behavior of dielectric EAP devices tend to ignore full dynamics. In this paper it is demonstrated that an EAP actuator model with full electrical-mechanical dynamics can be used as a generator model with the generator input force equivalent to the actuator disturbance force. Since the generator and actuator models are equivalent, it can be shown how disturbance inputs can cause energy surges back toward the electrical input. Simulations and experimental results are provided of a device model that describes generation and actuation.
Theoretical research on new concepts for the remote sensing of hydrometeors (2002)

There is an interest for climatology and meteorology to map hydrometeors, and in particular precipitation, both over the entire globe and across large defined regions. To achieve this goal at the proper spatial and temporal resolution which are required to satisfy the end users needs it has been proposed to use satellite based observations. This paper presents the results of a theoretical study aiming to the research of new concepts for the remote sensing of hydrometeors with emphasis on precipitation. The concept proposed is a Focused Wide band millimeter wave INTERferometer (WINTER-F) comprising a constellation of two small satellites, flying close to each other. The two satellites, which are phase synchronized by the GNSS (Global Navigation Satellite System) signals, perform near field interferometry by passive (radiometer) and active (radar) means. The study comprises the realization of laboratory experiments to check the validity of the theoretical models.
Direct growth of a‐plane GaN on r‐plane sapphire substrate by metalorganic vapor phase epitaxy (2007)

Abstract We have investigated a direct growth of non‐polar a ‐plane GaN on r ‐plane sapphire substrate by metalorganic vapor‐phase epitaxy (MOVPE). We found that high‐density nucleation of GaN islands was grown on r ‐plane sapphire substrate at an initial stage of high temperature growth without a buffer layer, which resulted in a flat surface of the a ‐plane GaN. We also studied an effect of growth conditions on surface morphologies and the growth features of the a ‐plane GaN. The results showed that inverse‐triangular pits surrounded with facets were formed at a relatively high V/III ratio, and the lateral growth rate along the c ‐axis direction was enhanced at a relatively low V/III ratio. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Disulfide oxidoreductase activity of Shigella flexneri is required for release of Ipa proteins and invasion of epithelial cells. (1995)

Secretion of IpaB, IpaC, and IpaD proteins of Shigella flexneri, essential for the invasion of epithelial cells, requires a number of proteins encoded by the spa and mxi loci on the large plasmid. Introduction of dsbA::Tn5 into S.flexneri from Escherichia coli K-12 reduced invasiveness, which resulted from a decrease in the capacity to release IpaB, IpaC, and IpaD proteins into the external medium. Examination of the surface-presented Ipa proteins of the dsbA mutant, however, revealed Ipa proteins at levels similar to those on wild-type cells. Since the defective phenotype was similar to that of the spa32 mutant of S. flexneri and the Spa32 sequence possessed two Cys residues, the effect of dsbA mutation of the folding structure of Spa32 under reducing conditions and on the surface expression of Spa32 was investigated. The results indicated that Spa32 was a disulfide-containing protein whose correctly folded structure was required for its presentation on the outer membrane. Indeed, replacing either one of the two Cys residues in Spa32 with Ser by site-directed mutagenesis reduced its capacity to release Ipa proteins into the external medium and led to the accumulation of Spa32 protein in the periplasm. These results indicated that the DsbA protein performs an essential function during the invasion of mammalian cells, by facilitating transport of the Spa32 protein across the outer membrane.
Contrasting HIV phylogenetic relationships and V3 loop protein similarities (1992)

At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant bymore » cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.« less
The mechanism of resistance in Escherichia coli to ridinilazole and other antibacterial head-to-head bis-benzimidazole compounds (2022)

Abstract The appY gene has been characterised as conferring resistance to a novel series of antimicrobial benzimidazole derivatives in E. coli MC1061 cells when expressed in high copy-number. A microarray approach was used to identify genes involved in the mechanism of appY-mediated antibacterial resistance, that were up- or down-regulated following induction of the gene in the appY knockout strain JW0553. In total, expression of 90 genes was induced and 48 repressed greater than 2.5-fold ( P &lt; 0.05), 45 min after appY induction. Over half the genes up-regulated following appY expression had confirmed or putative roles in acid resistance (AR) and response to oxidative and antibiotic stresses. These included the genes for MdtE and MdtF, which form a multi-drug transporter with TolC and have been implicated in resistance to several antibiotics including erythromycin. Amongst the acid resistance genes were gadAB and adiAC encoding the glutamate-dependant (AR2) and arginine-dependant (AR3) acid resistance systems respectively, in addition to the transcriptional activators of these systems gadE and gadX. In agreement with earlier studies, appA, appCB and hyaA-F were also up-regulated following induction of appY. This study has also confirmed that over-expression of mdtEF confers resistance to these antibacterial benzimidazoles, indicating that the observation of appY conferring resistance to these compounds, proceeds through an appY-mediated up-regulation of this efflux transporter. To assess the importance of the AppY enzyme to acid stress responses, the percentage survival of bacteria in acidified media (pH ≤ 2) was measured. From an initial input of 1 × 10 6 CFU/ml, the wild-type strain MG1655 showed 7.29% and 0.46% survival after 2 and 4 h, respectively. In contrast, strain JW0553 in which appY is deleted was completely killed by the treatment. Transformation of JW0553 with a plasmid carrying appY returned survival to wild-type levels (7.85% and 1.03% survival at 2 and 4 h). Further dissection of the response by prior induction of each of the three AR systems has revealed that AR1 and AR3 were most affected by the absence of appY. This work highlights an important and previously unidentified role for the AppY enzyme in mediating the responses to several stress conditions. It is likely that the appY gene fits into a complex transcriptional regulatory network involving σ S and gadE and gadX. Further work to pinpoint its position in such a hierarchy and to assess the contribution of appY to oxidative stress responses should help determine its full significance. This work is also consistent with recent studies in C. difficile showing that the mechanism of action of ridinilazole involves AT-rich DNA minor groove binding.
Oscillatory multiphase flow strategy for chemistry and biology (2016)

Continuous multiphase flow strategies are commonly employed for high-throughput parameter screening of physical, chemical, and biological processes as well as continuous preparation of a wide range of fine chemicals and micro/nano particles with processing times up to 10 min. The inter-dependency of mixing and residence times, and their direct correlation with reactor length have limited the adaptation of multiphase flow strategies for studies of processes with relatively long processing times (0.5-24 h). In this frontier article, we describe an oscillatory multiphase flow strategy to decouple mixing and residence times and enable investigation of longer timescale experiments than typically feasible with conventional continuous multiphase flow approaches. We review current oscillatory multiphase flow technologies, provide an overview of the advancements of this relatively new strategy in chemistry and biology, and close with a perspective on future opportunities.
Multi-Constrained Anypath Routing in Wireless Mesh Networks (2010)

Anypath routing has been proposed to improve the performance of unreliable wireless networks by exploiting the spatial diversity and broadcast nature of the wireless medium. In this paper, we focus on anypath routing subject to K constraints, and present a polynomial time K-approximation algorithm. When K = 1, our algorithm is the optimal polynomial time algorithm for the corresponding problem. When K ≥ 2, the corresponding problem is NP-hard. We are the first to present an O(1)-approximation algorithm. Furthermore, our algorithm is as simple as Dijkstra's shortest path algorithm, and is therefore suitable for implementation in actual wireless routing protocols.