gebhart/patrepeval huggingface dataset:
Correction: Structural Basis for Rab1 De-AMPylation by the Legionella pneumophila Effector SidD (2013)

The covalent attachment of adenosine monophosphate (AMP) to proteins, a process called AMPylation (adenylylation), has recently emerged as a novel theme in microbial pathogenesis. Although several AMPylating enzymes have been characterized, the only known virulence protein with de-AMPylation activity is SidD from the human pathogen Legionella pneumophila. SidD de-AMPylates mammalian Rab1, a small GTPase involved in secretory vesicle transport, thereby targeting the host protein for inactivation. The molecular mechanisms underlying Rab1 recognition and de-AMPylation by SidD are unclear. Here, we report the crystal structure of the catalytic region of SidD at 1.6 A resolution. The structure reveals a phosphatase-like fold with additional structural elements not present in generic PP2C-type phosphatases. The catalytic pocket contains a binuclear metal-binding site characteristic of hydrolytic metalloenzymes, with strong dependency on magnesium ions. Subsequent docking and molecular dynamics simulations between SidD and Rab1 revealed the interface contacts and the energetic contribution of key residues to the interaction. In conjunction with an extensive structure-based mutational analysis, we provide in vivo and in vitro evidence for a remarkable adaptation of SidD to its host cell target Rab1 which explains how this effector confers specificity to the reaction it catalyses.
Biodegradation of Polyurethanes Derived from Polycaprolactonediols (1981)

Earlier studies on the biodegradation of synthetic polymers were initiated by the desire to avoid biodegradation, thereby obtaining long lasting materials. Disposing of nondegradable synthetic polymers after use is a problem that grows more serious every day. Designing the polymer to be biodegradable avoids the problem of accumulation of expended polymers. The disposal of biodegradable polymers, on the other hand, is less difficult. Moreover, the increasing uses of biodegradable polymers in medicine and agriculture as sutures, surgical inplants, and components of controlled release formulations of drugs and agricultural chemicals require knowledge concerning the biodegradabilities of synthetic polymers. Since natural macromolecules are generally degraded in biological systems by hydrolysis followed by oxidation, we have been studying biodegradable polymers containing hydrolyzable linkages (1). In addition to the semi quantitative method of following biodegradation recommended by ASTM (2) we have developed quantitative methods to study enzymic and microbial degradation (3). We report here
A Perovskite Containing Quadrivalent Iron as a Charge‐Disproportionated Ferrimagnet (2008)

Unter 15 GPa bei 1300 K entsteht CaCuII3FeIV4O12, das bei 210 K eine Ladungsdisproportionierung eingeht (2 FeIV→FeIII+FeV) und seine elektrischen und magnetischen Eigenschaften sowie seine Struktur verändert. Die FeIIIO6- und FeVO6-Oktaeder sind wie die Ionen einer Steinsalzstruktur angeordnet (siehe Bild; Ca grau, O blau, Cu rot); die Tieftemperaturphase CuII(S=1/2,↓)3FeIII(S=5/2,↑)2 FeV(S=3/2,↑)2 ist ferrimagnetisch.
Recombinant production of antimicrobial peptides in heterologous microbial systems (2007)

The emergence and rapid horizontal spread of antibiotic-resistant traits in bacteria of human and veterinary clinical significance has been a driving force in the search for new classes of antibiotics. Recent studies have shown that AMPs (antimicrobial peptides) potentially have a role in addressing this problem. These AMPs are produced naturally by a diverse array of organisms, including bacteria, plants, insects, fish and mammals. Given this diversity, researchers trying to perform comparative studies on AMPs are likely to encounter difficulties in obtaining workable quantities of peptide. Such studies are required for optimization of antimicrobial activity, product stability, mode of delivery and industrial-scale production, and are vital if these peptides are ever to be brought to the market. Recombinant expression of AMPs is one hope for producing suitable amounts of diverse peptides. Here we review the literature regarding microbial heterologous expression systems for the production of recombinant AMPs.
Which Predicts Incident Cardiovascular Disease Better: A Plant-Centered Diet or a Low-Saturated Fat Diet? The Coronary Artery Risk Development in Young Adults (CARDIA) Study (2021)

A low-saturated fat diet has been suggested to reduce serum cholesterol and thereby presumably lower the risk of atherosclerotic cardiovascular disease (CVD). We compared associations of a low-saturated fat diet vs a plant-centered diet with lower serum low-density lipoprotein cholesterol (LDL-C) concentration and risk of incident CVD, coronary heart disease (CHD), and stroke. We followed 4,887 Black and White men and women in the Coronary Artery Risk Development in Young Adults (CARDIA) cohort, ages 18–30 years and free of CVD at baseline from 1985–86 (exam year 0) to 2018 (year 32). The A Priori Diet Quality Score (APDQS), a measure of plant-centered diet quality, was assessed in an interviewer-administered diet history at years 0, 7, and 20. Higher APDQS implies higher intake of nutritionally-rich plant foods with less high-fat meats and unhealthy plant foods. Low-saturated fat diet was judged by lower the Keys score, based on saturated fat, polyunsaturated fat, and dietary cholesterol intake. Linear and proportional hazards regression models were used, the latter with time-varying average APDQS and CVD outcomes, both adjusted for age, sex, race, education, energy intake, physical activity, smoking, and parental history of CVD (CVD outcome only). Higher APDQS had higher dietary fiber and lower total and saturated fat. Keys score and APDQS 7-year changes correlated similarly with lower concurrent LDL-C change. During the 32 year follow-up, we documented 280,135, and 92 incident cases of CVD, CHD, and stroke, respectively. LDL-C predicted CVD and CHD, but not stroke. APDQS, but not Keys score, was associated with a lower risk of each CVD outcome. Multivariable-adjusted HRs per 1-SD increment for the APDQS were 0.81 (95% CI: 0.68 − 0.96) for CVD, 0.78 (95% CI: 0.61 − 1.00) for CHD, and 0.71 (95% CI: 0.52 − 0.98) for stroke. The primary results for APDQS and for LDL-C were not substantially altered in mutually adjusted models. Both a plant-centered and a low-saturated fat diet were associated with lower LDL-C. A plant-centered diet and LDL-C, but not a low-saturated fat diet, were associated with long-term CVD risk. Our findings imply that dietary strategies aimed solely to lower saturated fat may be less effective in reducing CVD burden than recommendations for a plant-centered diet. HFHL, MnDRIVE, NHLBI.
Understanding the Origin of Structure Sensitivity in Nano Crystalline Mixed Cu/Mg−Al Oxides Catalyst for Low‐Pressure Methanol Synthesis (2021)

Abstract Cu nanoparticles of size 5–10 nm supported on Mg−Al mixed oxide were prepared by the sol‐gel method. Cu loading was varied from 2.5 to 10 wt % on the support to investigate the effect on particle size and activity/selectivity of the catalyst. The Cu/Mg−Al catalysts containing small copper nanoparticles favor high selectivity of methanol, while the rate of CO formation was higher for larger copper particles. The high methanol selectivity (∼99 %) and methanol formation rate (0.016 mol g Cu −1 h −1 ) over the 4.8Cu/Mg−Al catalyst was due to the combined effect of the presence of high Cu dispersion, Cu surface area, and strong interaction between small Cu particles with Mg−Al support. The high stability of the catalyst was attributed to the strong binding of the Cu cluster (−179.7 kJ/mol) to the MgO/γ‐Al 2 O 3 support, as shown by the DFT study. Additionally, the adsorption energy calculated using DFT showed preferential adsorption of CO 2 and H 2 at the Cu/MgO(100) active site (−120.9 kJ/mol, −130.4 kJ/mol) compared to the Cu/γ‐Al 2 O 3 (100) (−64.2 kJ/mol, −85.7 kJ/mol)active site. The high selectivity of the catalyst towards methanol can be attributed to the higher stability of the formate (HCOO) intermediate (−257.2 kJ/mol) compared to the carboxylate (COOH) intermediate (−131.0 kJ/mol).
Ten‐year hard and soft tissue results of a pilot double‐blinded randomized controlled trial on immediately loaded post‐extractive implants using platform‐switching concept (2016)

With the limitations of this study, immediate single implant restorations rehabilitated with platform-switching protocol may provide peri-implant alveolar bone-level stability and avoid continuous soft tissue shrinkage after 10 years of prosthetic loading compared to a platform-matching restoration. Further studies involving larger sample sizes are required to confirm these preliminary results.
Molecular Pathophysiology of Cerebral Hemorrhage (2011)

Intracerebral hemorrhage (ICH) is an often fatal type of stroke that kills approximately 30,000 people annually in the United States. If the patient survives the ictus, then the resulting hematoma within brain parenchyma triggers a series of adverse events causing secondary insults and severe neurological deficits. This article discusses selected aspects of secondary brain injury after ICH and outlines key mechanisms associated with hematoma toxicity, oxidative stress, and inflammation. Finally, this review discusses the relevance of hematoma resolution processes as a target for ICH therapy and presents potential clinically relevant molecular targets that could be harnessed to treat secondary injury associated with ICH injury.
Physiological analyses of STX4 treatment confirm unique STX4 properties in foam cells. (2015)

&lt;p&gt;&lt;b&gt;A&lt;/b&gt;, Cholesterol content in foam cells after treatment for 48 h with DMSO (0.1%), T09 (10 µM) or STX4 (10 µM). Data are expressed as mean±SEM (n = 5–6). &lt;b&gt;B&lt;/b&gt;, Cholesterol content in macrophages after treatment for 48 h with DMSO (0.1%), T09 (10 µM) or STX4 (10 µM). Data are expressed as mean±SEM (n = 5–6). &lt;b&gt;C&lt;/b&gt;, Triglyceride content in foam cells after treatment for 48 h with DMSO (0.1%), T09 (10 µM) or STX4 (10 µM). &lt;b&gt;D&lt;/b&gt;, Triglyceride content in macrophages after treatment for 48 h with DMSO (0.1%), T09 (10 µM) or STX4 (10 µM). Data are expressed as mean±SEM (n = 5–6). ***P&lt;0.001 vs. DMSO; n.s., not significant.&lt;/p&gt;
Distributed transmit beamforming with one bit feedback revisited: How noise limits scaling (2015)

Distributed transmit beamforming with N cooperating nodes, each with fixed transmit power, provides a received power scaling with N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , corresponding to a “power pooling” gain of N and a beamforming gain of N. Prior work has shown that the optimal beamforming solution can be attained using a decentralized, iterative algorithm based on one bit (per iteration) feedback broadcast from the receiver to the transmitters. The algorithm is provably convergent in a noiseless setting, and is the basis for several successful prototypes. In this paper, we develop a framework for providing analytical insight into the effect of receiver noise, with the following key question in mind: can we bootstrap the algorithm from the incoherent power-pooled solution to operate in a regime in which the received SNR per node can be made arbitrarily small as we scale up the number of nodes N? Our analytical computations, validated by simulations, yield a somewhat negative answer: while the power-pooling gain guarantees a linear increase in received power with N, the per-node SNR cannot be scaled down with N if we wish to attain a quadratic increase in received power. Specifically, the fraction of the ideal beamforming gain attained using the one-bit algorithm is asymptotically independent of N, and depends only on the per-node SNR. However, the one-bit algorithm provides significant performance gains in practical regimes with a moderate number of cooperating nodes: the per-node SNR required for attaining a substantial fraction of the beamforming gain is low enough (e.g., - 5dB for 65% of the beamforming gain) to provide significant extension in operation regimes, while providing aggregate SNRs which permit reliable communication at high spectral efficiency: for example, starting from -5 dB per-node SNR, we obtain about 11 dB aggregate SNR with 10 cooperating nodes, and 17 dB SNR with 20 cooperating nodes.
Comparison of laboratory techniques for evaluating the fracture toughness of glassy polymers (1980)

Abstract Several test methods were employed to determine polymer fracture toughness (𝒢 Ic , the opening‐mode strain energy release rate) at room temperature. The materials used included DGEBA epoxies and those modified by the addition of CTBN elastomers. Double‐cantilever beam specimens were used to determine the fracture toughness both of bulk resins and of an adhesive layer bonded between two aluminum half‐beams. The adhesive fracture toughness of a 0.025‐cm bond was slightly less than the bulk 𝒢 Ic value, attributed to the bond thickness effect. Fracture toughness of bulk resins was also evaluated by using both rectangular and round compact tension specimens. The results, when compared with those obtained with the bulk double‐cantilever beams, are quite acceptable. The thickness of compact tension specimens, ranging from 0.64 to 1.0 cm, might not give pure plane‐strain conditions, and thus some plane‐stress contribution to 𝒢 Ic should be expected for the tougher materials. Izod impact tests were also carried out to determine sample fracture toughness at high loading rate.
TorontoCity: Seeing the World with a Million Eyes (2017)

In this paper we introduce the TorontoCity benchmark, which covers the full greater Toronto area (GTA) with 712.5km2 of land, 8439km of road and around 400, 000 buildings. Our benchmark provides different perspectives of the world captured from airplanes, drones and cars driving around the city. Manually labeling such a large scale dataset is infeasible. Instead, we propose to utilize different sources of high-precision maps to create our ground truth. Towards this goal, we develop algorithms that allow us to align all data sources with the maps while requiring minimal human supervision. We have designed a wide variety of tasks including building height estimation (reconstruction), road centerline and curb extraction, building instance segmentation, building contour extraction (reorganization), semantic labeling and scene type classification (recognition). Our pilot study shows that most of these tasks are still difficult for modern convolutional neural networks.
Contact Lenses: A Clinical Approach to Fitting, ed 2 (1983)

I have been part of several National Contact Lens courses for many years and have noticed a rather pronounced change in the makeup of the audiences attending these meetings. Formerly, these courses were attended by senior residents and ophthalmologists new in practice, with the older ophthalmologists staying away. In recent years, however, due to the rapid developments in the contact lens field (probably one of the most changeable fields in ophthalmology at present), the audience now consists mainly of older ophthalmologists who attend these meetings to keep up with names and materials to maintain a familiarity with the contact lens field. This popular book now in its second edition (the first was published in 1978) goes a long way toward answering the problems for both the resident and practicing ophthalmologist. The book serves well as both a reference and a fitting guide, and covers scleral lenses, corneal lenses, soft lenses,
Nanoscale true random bit generator based on magnetic state transitions in magnetic tunnel junctions (2019)

We present an investigation into the in-plane field induced free layer state transitions found in magnetic tunnel junctions. By applying an ac current into an integrated field antenna, the magnetisation of the free layer can be switched between the magnetic vortex state and the quasi-uniform anti-parallel state. When in the magnetic vortex state, the vortex core gyrates a discrete number of times, and at certain frequencies there is a 50% chance of the core gyrating n or n - 1 times, leading to the proposal of a novel nanoscale continuous digital true random bit generator.
Frequency-Zooming ARMA Modeling of Resonant and Reverberant Systems (2002)

Discrete-time analysis and modeling of reverberant and resonating systems has many applications in audio and acoustics. The methodology of ARMA modeling by pole ‐ zero filters for measured impulse responses was investigated. In addition to an overview of the standard AR and ARMA techniques, a spectral zooming technique is proposed, which is useful for resolving very closely positioned modes and high-density modal clusters. Application cases related to the analysis and modeling of room responses, loudspeaker ‐ room equalization, and the estimation of parameters for musical instrument modeling are studied.
NCL Method ITA-6.2 (2020)

Leukocyte Proliferation Assay
Soluble Poly(Bismethylene Hydroquinone): Synthesis and Properties (1988)

Soluble poly(bismethylene hydroquinone) (PBHQ) of two different intrinsic viscosities and degrees of ring closure were synthesized. The polymers were chemically oxidized using bromine. The oxidation process was studied by comparison of the unoxidized and oxidized polymers using Fourier transform infrared, 13C solid‐state CP/MAS NMR, elemental analysis, UV spectroscopy, and electron spin resonance. The oxidation‐reduction processes of the polymers were studied using cyclic voltammetry.
Classification-Driven Dynamic Image Enhancement (2018)

Convolutional neural networks rely on image texture and structure to serve as discriminative features to classify the image content. Image enhancement techniques can be used as preprocessing steps to help improve the overall image quality and in turn improve the overall effectiveness of a CNN. Existing image enhancement methods, however, are designed to improve the perceptual quality of an image for a human observer. In this paper, we are interested in learning CNNs that can emulate image enhancement and restoration, but with the overall goal to improve image classification and not necessarily human perception. To this end, we present a unified CNN architecture that uses a range of enhancement filters that can enhance image-specific details via end-to-end dynamic filter learning. We demonstrate the effectiveness of this strategy on four challenging benchmark datasets for fine-grained, object, scene, and texture classification: CUB-200-2011, PASCAL-VOC2007, MIT-Indoor, and DTD. Experiments using our proposed enhancement show promising results on all the datasets. In addition, our approach is capable of improving the performance of all generic CNN architectures.
Quasi-Optimal Channel Assignment for Real-Time Video in OFDM Wireless Systems (2008)

In this paper, real-time video transmission with quality of service (QoS) assurance over orthogonal frequency division multiplexing (OFDM) wireless systems is studied. Three quasi-optimal subcarrier allocation schemes, namely regular, delay tolerant and adaptive, are proposed. In the proposed schemes, effective throughput per subcarrier employing adaptive forward error correction (FEC) coding in a Rayleigh fading channel is evaluated, and a capacity matrix that governs all active users and all assignable subcarriers is formulated. The Munkres algorithm is used in the schemes to achieve optimal subcarrier assignment. Performance analyses in terms of spectral efficiency and packet loss probability are presented. Multi-user multichannel diversity is investigated to exploit the innate capacity gain in terms of fading variation and delay tolerance. The proposed schemes are scalable to both single-cell and multi-cell circumstances. Numerical results demonstrate that the proposed schemes can effectively achieve quasi-optimal spectral utilization and significantly improve system throughput.
Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer (2009)

microRNAs (miRNAs) play integral roles in diverse processes including tumorigenesis. miRNA gene loci are often found in close conjunction, and such clustered miRNA genes are transcribed from a common promoter to generate polycistronic primary transcript. The primary transcript (pri-miRNA) is then processed by two RNase III proteins to release the mature miRNAs. Although it has been speculated that the miRNAs in the same cluster may play related biological functions, this has not been experimentally addressed. Here we report that the miRNAs in two clusters (miR-106b approximately 93 approximately 25 and miR-222 approximately 221) suppress the Cip/Kip family members of Cdk inhibitors (p57(Kip2), p21(Cip1) and p27(Kip1)). We show that miR-25 targets p57 through the 3'-UTR. Furthermore, miR-106b and miR-93 control p21 while miR-222 and miR-221 regulate both p27 and p57. Ectopic expression of these miRNAs results in activation of Cdk2 and facilitation of G1/S phase transition. Consistent with these results, both clusters are abnormally upregulated in gastric cancer tissues compared to the corresponding normal tissues. Ectopic expression of miR-222 cluster enhanced tumor growth in the mouse xenograft model. Our study demonstrates the functional associations between clustered miRNAs and further implicates that effective cancer treatment may require a combinatorial approach to target multiple oncogenic miRNA clusters.
FACILE OXIDATION OF THIOPHENOL BY ISOALLOXAZINE(FLAVIN) BOUND TO A CATIONIC MICELLE (1977)

Abstract Oxidation of thiophenol by isoalloxazines(flavin analogs) was found to proceed readily in a cationic micelle solution. The observed rate enhancement was related to the activation of the thiophenol anion in the hydrophobic environment of the micelle.
Biosourced Foam‐Like Activated Carbon Materials as High‐Performance Supercapacitors (2018)

Abstract Bio‐inspired and cost‐effective development of highly porous foam‐like carbon structure originating from waste fig‐fruit raw materials using chemical activation is described. The as‐synthesized porous sample exhibits a specific surface area higher than 2000 m 2 g −1 and relatively high porosity with ultimately interconnected micro‐, meso‐, and macropores. Such sample displays superior specific capacitance in aqueous electrolyte of 340 and 217 F g −1 at current density of 0.5 A and 20 A g −1 , respectively, along with a high energy/power density performance compared to that developed in the literature and the commercial supercapacitors up to now. In addition, the sample also exhibits an extremely high stability as a function of cycling tests with more 99% capacitance retention after 10 000 cycles.