gebhart/patrepeval huggingface dataset:
ArabidopsisCONSTANS-LIKE3 Is a Positive Regulator of Red Light Signaling and Root Growth (2005)

Abstract CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) is an E3 ubiquitin ligase that represses photomorphogenesis in the dark. Therefore, proteins interacting with COP1 could be important regulators of light-dependent development. Here, we identify CONSTANS-LIKE3 (COL3) as a novel interaction partner of COP1. A green fluorescent protein–COL3 fusion protein colocalizes with COP1 to nuclear speckles when transiently expressed in plant cells. This localization requires the B-box domains in COL3, indicating a novel function of this domain. A loss-of-function col3 mutant has longer hypocotyls in red light and in short days. Unlike constans, the col3 mutant flowers early and shows a reduced number of lateral branches in short days. The mutant also exhibits reduced formation of lateral roots. The col3 mutation partially suppresses the cop1 and deetiolated1 (det1) mutations in the dark, suggesting that COL3 acts downstream of both of these repressors. However, the col3 mutation exerts opposing effects on cop1 and det1 in terms of lateral roots and anthocyanin accumulation, suggesting that COL3 also has activities that are independent of COP1 and DET1. In conclusion, we have identified COL3 as a positive regulator of photomorphogenesis that acts downstream of COP1 but can promote lateral root development independently of COP1 and also function as a daylength-sensitive regulator of shoot branching.
ORF17 from the Clavulanic Acid Biosynthesis Gene Cluster Catalyzes the ATP-dependent Formation of N-Glycyl-clavaminic Acid (2005)

(3R,5R)-Clavulanic acid, a clinically used inhibitor of serine beta-lactamases, is produced by fermentation of Streptomyces clavuligerus. The early steps in clavulanic acid biosynthesis leading to the bicyclic beta-lactam intermediate (3S,5S)-clavaminic acid have been defined. However, the mechanism by which (3S,5S)-clavaminic acid is converted to the penultimate intermediate (3R,5R)-clavaldehyde is unclear. Disruption of orf15 or orf16, of the clavulanic acid biosynthesis gene cluster, blocks clavulanic acid production and leads to the accumulation of N-acetyl-glycyl-clavaminic acid and N-glycyl-clavaminic acid, suggesting that these compounds are intermediates in the pathway. Two alternative start codons have been proposed for orf17 to encode for two possible polypeptides, one of which has 92 N-terminal residues less then the other. The shorter version of orf17 was successfully expressed in Escherichia coli and purified as a monomeric protein. Sequence analyses predicting the ORF17 protein to be a member of the ATP-grasp fold superfamily were supported by soft ionization mass spectrometric analyses that demonstrated binding of ATP to the ORF17 protein. Semisynthetic clavaminic acid, prepared by in vitro reconstitution of the biosynthetic pathway from the synthetically accessible intermediate proclavaminic acid, was shown by mass spectrometric analyses to be converted to N-glycyl-clavaminic acid in the presence of ORF17, ATP, and glycine. Under the same conditions N-acetyl-glycine and clavaminic acid were not converted to N-acetyl-glycyl-clavaminic acid. The specificity of ORF17 as an N-glycyl-clavaminic acid synthetase, together with the reported accumulation of N-glycyl-clavaminic acid in orf15 and orf16 disruption mutants, suggested that N-glycyl-clavaminic acid is an intermediate in clavulanic acid biosynthesis.
An internal thioester in a pathogen surface protein mediates covalent host binding (2015)

To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a 'chemical harpoon'. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions.
Effects of SNR-Dependent Beam Alignment Errors on Millimeter-Wave Cellular Networks (2022)

At millimeter-wave (mm-wave) frequencies, narrow beamwidth and inaccurate channel estimation result in beam alignment errors, which degrade the achievable signal-to-noise ratio (SNR) and rate. The extent of beam misalignment depends on the various link parameters, however, prior works ignored such a dependence and considered oversimplified array patterns. This paper formulates beam alignment errors for the uniform linear array at the base station as a function of the link parameters by using the Cramér Rao lower bound of angle-of-arrival estimates and proposes a tractable array pattern approximation to better reflect the effects of such alignment errors. Utilizing stochastic geometry and the statistics of the Student’s <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</i> -distribution, a novel and robust analytical technique is developed to obtain the downlink SNR and rate coverage probabilities due to beam misalignment, assuming a single antenna at the user. We show that beam alignment errors significantly affect the achievable SNR and rate for non line-of-sight (NLOS)/distant users whereas the effect is negligible for LOS/nearby users. It is also illustrated that the effects of alignment errors cannot be mitigated only by increasing the number of antennas. We also show that our proposed array pattern approximation better captures the effects of beam alignment errors as compared to the widely used flat-top pattern.
Encyclopaedias of the Ancient Near East (1997)

There have been various new encyclopaedias, which have been written to shed light on the history and archaeology related to the Ancient Near East. The article discusses the significance, advantages and relevance of the various encyclopaedias.
The Application and Research of the New Wave-absorbing Material (2013)

The mechanisms and operation principle of the wave-absorbing material were analyzed in different conditions.Structural characteristic and research conditions of the new inorganic absorbent such as carbon,iron,and chiral wave absorbent were explained.At the same time,research progress of the new wave-absorbing material which was composite with polymer and inoganic absorbent was introduced.In addition,the recent advances of the research of wave-absorbing material were reviewed and the trend of research and development was suggested.
Scalable Eventually Consistent Counters over Unreliable Networks (2013)

Counters are an important abstraction in distributed computing, and play a central role in large scale geo-replicated systems, counting events such as web page impressions or social network "likes". Classic distributed counters, strongly consistent, cannot be made both available and partition-tolerant, due to the CAP Theorem, being unsuitable to large scale scenarios. This paper defines Eventually Consistent Distributed Counters (ECDC) and presents an implementation of the concept, Handoff Counters, that is scalable and works over unreliable networks. By giving up the sequencer aspect of classic distributed counters, ECDC implementations can be made AP in the CAP design space, while retaining the essence of counting. Handoff Counters are the first CRDT (Conflict-free Replicated Data Type) based mechanism that overcomes the identity explosion problem in naive CRDTs, such as G-Counters (where state size is linear in the number of independent actors that ever incremented the counter), by managing identities towards avoiding global propagation and garbage collecting temporary entries. The approach used in Handoff Counters is not restricted to counters, being more generally applicable to other data types with associative and commutative operations.
Poly(β-Amino Ester)-Nanoparticle Mediated Transfection of Retinal Pigment Epithelial Cells In Vitro and In Vivo (2012)

A variety of genetic diseases in the retina, including retinitis pigmentosa and leber congenital amaurosis, might be excellent targets for gene delivery as treatment. A major challenge in non-viral gene delivery remains finding a safe and effective delivery system. Poly(beta-amino ester)s (PBAEs) have shown great potential as gene delivery reagents because they are easily synthesized and they transfect a wide variety of cell types with high efficacy in vitro. We synthesized a combinatorial library of PBAEs and evaluated them for transfection efficacy and toxicity in retinal pigment epithelial (ARPE-19) cells to identify lead polymer structures and transfection formulations. Our optimal polymer (B5-S5-E7 at 60 w/w polymer:DNA ratio) transfected ARPE-19 cells with 44±5% transfection efficacy, significantly higher than with optimized formulations of leading commercially available reagents Lipofectamine 2000 (26±7%) and X-tremeGENE HP DNA (22±6%); (p<0.001 for both). Ten formulations exceeded 30% transfection efficacy. This high non-viral efficacy was achieved with comparable cytotoxicity (23±6%) to controls; optimized formulations of Lipofectamine 2000 and X-tremeGENE HP DNA showed 15±3% and 32±9% toxicity respectively (p>0.05 for both). Our optimal polymer was also significantly better than a gold standard polymeric transfection reagent, branched 25 kDa polyethyleneimine (PEI), which achieved only 8±1% transfection efficacy with 25±6% cytotoxicity. Subretinal injections using lyophilized GFP-PBAE nanoparticles resulted in 1.1±1×10(3)-fold and 1.5±0.7×10(3)-fold increased GFP expression in the retinal pigment epithelium (RPE)/choroid and neural retina respectively, compared to injection of DNA alone (p = 0.003 for RPE/choroid, p<0.001 for neural retina). The successful transfection of the RPE in vivo suggests that these nanoparticles could be used to study a number of genetic diseases in the laboratory with the potential to treat debilitating eye diseases.
Graph-based rotation of the DCT basis for motion-adaptive transforms (2013)

In this paper, we consider motion-adaptive transforms that are based on vertex-weighted graphs. The graphs are constructed by motion vector information and the weights of the vertices are given by scale factors, where the scale factors are used to control the energy compaction of the transform. The vertex-weighted graph defines a one dimensional linear subspace. Thus, our transform basis is subspace constrained. To find a full transform matrix that satisfies our subspace constraint, we rotate the discrete cosine transform (DCT) basis such that the first basis vector matches the subspace constraint. Since rotation is not unique in high dimensions, we choose a simple rotation that only rotates the DCT basis in the plane which is spanned by the first basis vector of the DCT and the subspace constraint. Experimental results on energy compaction show that the motion-adaptive transform based on this rotation is better than the motion-compensated orthogonal transform based on hierarchical decomposition while sharing the same first basis vector.
Studies on starters (1928)

For a number of years the dairy section of the Iowa Agricultural Experiment Station has devoted considerable effort to an investigation of starters. This has seemed advisable because good starters have been shown to be very helpful in improving the quality of butter, which is the important dairy product of the state.
Continuous Semi-Solid Casting Process for Aluminum Alloy Billets (2002)

A new process for continuous semi-solid casting of billets of aluminum alloys was developed. Round aluminum alloy billets 75 mm and 150 mm in diameter are continuously cast in a semi-solid state by agitating the alloy in the agitating vessel with a mechanical screw and/or an electromagnetic stirrer. The solidification structure of the billets obtained by this process is a mixed structure of granular particles and a fine eutectic structure, except in a thin chill layer about 2 mm in thickness, which shows a dendrite structure. It was possible to use billets of AC4C alloy obtained by this process in the thixoforming process without surface conditioning.
Selective Preservation and Degeneration Within the Prefrontal Cortex in Aging and Alzheimer Disease (2001)

Orbital PFC is selectively preserved in OHE subjects. In contrast, degeneration within the PFC with AD is most prominent in the inferior PFC region. Thus, degeneration within the PFC has a regionally distinct pattern in healthy aging and AD.
Ku‐Band satellite data networks using very small aperture terminals—part II: System design (1987)

Abstract In this part of the paper on Ku‐band VSAT networks, the issue of overall system design is considered. After discussing possible system architectures, primary attention is given to the star network configuration in which customer‐premise VSATs communicate with a central hub station, co‐located with, or terrestrially connected to a host computer. The component elements of a Ku‐band star network for interactive data applications are discussed and the critical items from the point‐of‐view of performance, capacity and cost are identified. An analytical model for the network, which combines delay‐throughput characterization of the multi‐access inbound and TDM outbound channels with satellite link analysis is described. The analytical model is exercised over a range of typical system component, traffic model and performance objective scenarios to provide a set of general design guidelines. These guidelines are useful for evaluating the trade‐offs between key system elements (channel access unit, modem, VSAT antenna and satellite), VSAT traffic message length parameters and the performance objectives (average and peak network response time and availability). The results are used to address the issue of multi‐access protocol selection over a range of scenarios typical of 1.2 or 1.8m VSAT‐based interactive networks using current commercial Ku‐band satellites. The results show that interactive star networks are often limited by satellite power rather than bandwidth, so that the use of simple contention access for VSATs may not imply a significant system capacity penalty.
Fabrication of Ti Porous body with Improved Specific Surface Area by Synthesis of CNTs (2016)

이 논문은 2015년도 정부 (미래창조과학부)의 재원으로 한국 연구 재단의 지원을 받아 수행된 연구임(No.2012R1A2A2A02046179).
본 연구는 2015년도 산업통상자원부의 재원으로 한국에너지기술평가원(KETEP)의 지원을 받아 수행한 연구 과제입니다(No. 20154030200900).
Vascular smooth muscle cell growth kinetics in vivo in aged rats. (1982)

Age is a risk factor in the development of atherosclerosis. In this study we investigated the hypothesis that proliferation of vascular smooth muscle cells (SMCs), an integral part of atherosclerotic plaque formation, changes with age. SMC growth kinetics of old rats (21-24 months) were compared to those of young adult rats (3-4 months). Rat aortas were denuded of their endothelium and the animals were killed after [3H]thymidine and Evans blue injections at 0-28 days after denudation. Incorporation of [3H]thymidine into SMC peaked in the young animals by day 2, whereas the older animals responded to endothelial removal with greater incorporation at day 2 and a more sustained rate of incorporation peaking at day 4. The [3H]thymidine incorporation curves decreased sharply from their peaks at 2 and 4 days, respectively, and paralleled each other after day 7. [3H]Thymidine uptake reflected the subsequent SMC intimal growth as measured morphometrically, with old animals showing greater numbers of intimal SMC than did the younger animals. The difference in response of SMC to injury with age suggests that aging produces a change in the vascular SMC that enhances proliferation. This change in response implies that the more pronounced atherosclerotic plaque growth seen with aging may be a result of an age-related increase in response to injury rather than merely the accumulation of time-related intimal change.
A Commutation Overlap Period Reduction Method Expanding the Buck Operating Range for a Bidirectional Isolated DC–DC Converter (2015)

SUMMARY This paper proposes a bidirectional isolated DC–DC converter with an active clamp circuit and two novel control methods in the buck mode. A circulating current reduction method decreases the conduction loss. A commutation overlap period reduction method maintains the output power by expanding the maximum actual duty cycle even if the input voltage decreases. The experimental results show that the proposed method increased the maximum output 1.5 times, without increasing the voltage applied to the low‐voltage side MOSFETs under the minimum input voltage condition. A 2‐kW class prototype showed a higher than 90% efficiency over a wide operating range for a greater than 20 input–output voltage ratio at 100‐kHz switching frequency.
Image reconstruction: a unifying model for resolution enhancement and data extrapolation Tutorial (2006)

In reconstructing an object function F(r) from finitely many noisy linear-functional values integral of F(r)Gn(r)dr we face the problem that finite data, noisy or not, are insufficient to specify F(r) uniquely. Estimates based on the finite data may succeed in recovering broad features of F(r), but may fail to resolve important detail. Linear and nonlinear, model-based data extrapolation procedures can be used to improve resolution, but at the cost of sensitivity to noise. To estimate linear-functional values of F(r) that have not been measured from those that have been, we need to employ prior information about the object F(r), such as support information or, more generally, estimates of the overall profile of F(r). One way to do this is through minimum-weighted-norm (MWN) estimation, with the prior information used to determine the weights. The MWN approach extends the Gerchberg-Papoulis band-limited extrapolation method and is closely related to matched-filter linear detection, the approximation of the Wiener filter, and to iterative Shannon-entropy-maximization algorithms. Non-linear versions of the MWN method extend the noniterative, Burg, maximum-entropy spectral-estimation procedure.
Proton pump inhibitors act synergistically with fluconazole against resistant Candida albicans (2020)

The incidence of resistant Candida isolates, especially Candida albicans, has increased continuously. To overcome the resistance, research on antifungal agent sensitizers has attracted considerable attention. Omeprazole and lansoprazole were found to inhibit the growth of sensitive C. albicans and hyphae formation in a high dose, respectively. This study aimed to determine the interactions of common clinically proton pump inhibitors (PPIs) and fluconazole both in vitro and in vivo and to further explore the possible mechanisms. In vitro, the tested PPIs all acted synergistically with fluconazole against both resistant C. albicans planktonic cells and biofilms preformed for ≤12 h with the minimum inhibitory concentration of fluconazole decreased from >512 μg/mL to 1-4 μg/mL. In vivo, PPIs plus fluconazole prolonged the survival rate of infected Galleria mellonella larvae by two-fold compared with that for the fluconazole monotherapy group and significantly reduced the tissue damage of infected larvae. Mechanism studies showed that PPIs significantly suppressed efflux pump activity, which is the common resistance mechanism of C. albicans, and significantly inhibited the virulence factors: phospholipase activity and morphology switching. These findings will provide new insights into antifungal agent discovery and potential approaches for the treatment of candidiasis caused by resistant C. albicans.
Vapor-liquid equilibrium thermodynamics of N2 + CH4: Model and Titan applications (1992)

Calculations of the vapor-liquid equilibrium thermodynamics of the N2 + CH4 system show that the tropospheric clouds of Titan are not pure CH4, but solutions of CH4 containing substantial quantities of N2. The conditions for saturation, latent heat of condensation, and droplet composition all depend on this equilibrium. We present a thermodynamic model for vapor-liquid equilibrium in the N2 + CH4 system which, by its structure, places strong constraints on the consistency of experimental equilibrium data, and confidently embodies temperature effects by also including enthalpy (heat of mixing) data. Selected equilibrium and enthalpy data are used in a maximum likehood determination of model parameters. The model can be readily evaluated to compute the saturation criteria, composition of condensate, and latent heat in Titan's atmosphere for a given pressure-temperature (p-T) profile. For a nominal p-T profile, the partial pressure of CH4 required for formation of CH4 + N2 condensate is ∼20% lower than that required to saturate pure CH4, and ∼25% higher than that which would be computed by Raoult's law. N2 constitutes 16–30% of the cloud condensate, and higher altitude clouds are generally more N2-rich. The N2 content of condensate is ∼1/2 of that computed from Raoult's law and about 30% greater than that computed from Henry's law. Heats of condensation are ∼10% lower than for pure CH4. Above 14 km altitude, the liquid solution becomes metastable with respect to a solid solution containing less N2: freezing of liquid droplets will be accompanied by the exsolution of about 30% of the dissolved N2, probably leading to an underdense, porous texture. The refractive index, single-scattering albedo, and density of CH4 + N2 cloud droplets of the appropriate composition and phase should be used in modeling and spacecraft planning studies for Titan. Cassini investigations with sufficient altitude resolution (primarily Huygens probe experiments) can potentially detect vertical motion of particles by determining whether condensate and gas are in local thermodynamic equilibrium.