gebhart/patrepeval huggingface dataset:
Toward error-free scaled spin torque majority gates (2016)

The functionality of a cross-shaped Spin Torque Majority Gate is explored by means of micromagnetic simulations. The different input combinations are simulated varying material parameters, current density and size. The main failure mode is identified: above a critical size, a domain wall can be pinned at the center of the cross, preventing further propagation of the information. By simulating several phase diagrams, the key parameters are obtained and the operating condition is deduced. A simple relation between the domain wall width and the size of the Spin Torque Majority Gate determines the working range. Finally, a correlation is found between the energy landscape and the main failure mode. We demonstrate that a macrospin behavior ensures a reliable majority gate operation.
Engineering Escherichia coli for the utilization of ethylene glycol (2021)

Overall, our work suggests that EG could provide a renewable starting material for commercial biosynthesis of fuels and chemicals that may achieve economic parity with petrochemical feedstocks while sequestering carbon dioxide.
<title>Recording of an achromatic holographic doublet for focusing laser diodes</title> (1993)

A method for designing and recording a holographic achromat, composed of two holographic optical elements (HOEs), is presented. The method is demonstrated with a doublet recorded at 488 nm for application at a central frequency of 820 nm. A near-diffraction-limited focus and high diffraction efficiency are achieved over a comparatively wide spectral range.
Anonymization of location data does not work (2011)

We examine a very large-scale data set of more than 30 billion call records made by 25 million cell phone users across all 50 states of the US and attempt to determine to what extent anonymized location data can reveal private user information. Our approach is to infer, from the call records, the "top N" locations for each user and correlate this information with publicly-available side information such as census data. For example, the measured "top 2" locations likely correspond to home and work locations, the "top 3" to home, work, and shopping/school/commute path locations. We consider the cases where those "top N" locations are measured with different levels of granularity, ranging from a cell sector to whole cell, zip code, city, county and state. We then compute the anonymity set, namely the number of users uniquely identified by a given set of "top N" locations at different granularity levels. We find that the "top 1" location does not typically yield small anonymity sets. However, the top 2 and top 3 locations do, certainly at the sector or cell-level granularity. We consider a variety of different factors that might impact the size of the anonymity set, for example the distance between the "top N" locations or the geographic environment (rural vs urban). We also examine to what extent specific side information, in particular the size of the user's social network, decrease the anonymity set and therefore increase risks to privacy. Our study shows that sharing anonymized location data will likely lead to privacy risks and that, at a minimum, the data needs to be coarse in either the time domain (meaning the data is collected over short periods of time, in which case inferring the top N locations reliably is difficult) or the space domain (meaning the data granularity is strictly higher than the cell level). In both cases, the utility of the anonymized location data will be decreased, potentially by a significant amount.
Lipidized prolactin-releasing peptide improved glucose tolerance in metabolic syndrome: Koletsky and spontaneously hypertensive rat study (2018)

We demonstrated that our new lipidized PrRP analog is capable of improving glucose tolerance in obese SHROB rats after peripheral application, suggesting that its effect on glucose metabolism is independent of leptin signaling and body weight lowering. These data suggest that this analog has the potential to be a compound with both anti-obesity and glucose-lowering properties.
A two-sample method for assessing growth hormone response to growth hormone-releasing hormone challenge: use as a predictor of gain in beef bulls. (2000)

In two experiments, Black Angus bulls were challenged at weaning with GHRH analog and evaluated for their GH response to determine whether GH response can predict subsequent growth characteristics. The GH response was determined by measuring GH in blood serum collected 0 and 10 min after GHRH injection (Exp. 1: 1.5 μg/100 kg BW human GHRH, n = 34; Exp. 2: 1.5 and 4.5 μg/100 kg BW bovine GHRH [treatments LGHRH and HGHRH, respectively] administered 3 h after a 4.5 μg/100 kg BW “clearance dose” of GHRH, n = 38]. In Exp. 1, GH response did not predict growth or carcass measurements. In Exp. 2, GH response to LGHRH was positively related to ADG (R2 = .18; P = .007) during a 112-d controlled feeding trial. In addition, there was a tendency for bulls with a greater GH response to HGHRH to exhibit greater ADG than animals with a low response. However, GH response to GHRH was not related to changes in hip height (HH) or carcass ultrasound measurements at d 112 of the growth performance trial. Response of GH to repeated GHRH challenges was consistent within animal over time (r = .47; P = .003). The use of a clearance dose 3 h prior to GHRH challenge improved the relationship between GH response and ADG. Results of this study suggest that GH response to GHRH challenge is a useful tool for identifying beef bulls with superior growth potential.
Assessing Cloud Network Performance (2018)

Performance and scalability of cloud applications are heavily dependent on those same characteristics in the underlying network. Several factors complicate cloud network evaluation. Most notable are 1) large scale, 2) a practically infinite set of application workloads, 3) a large set of potential metrics, 4) a large variety of available configurations within and across clouds and 5) a lack of visibility into the underlying network. There is a tremendous need for a cloud network evaluation methodology that overcomes these challenges, that is practical to apply and provides predictive results. We describe our work to develop such a methodology for cloud network evaluation and a tool (Euclid) that automates its application. Euclid leverages a set of widely used traffic generators to evaluate throughput and latency across a cloud network between endpoint pairs. Evaluation of these micro benchmarks between and among different sets of endpoints is coordinated to reflect several well-known application traffic patterns. Large sets of results are distilled into a tractable set of metrics and associated graphs that facilitate consumption of the results by cloud operators and users. We report results from applying Euclid to seventeen cloud configurations that span three public and one private cloud. The results demonstrate the practicality of our approach and highlight some interesting differences across clouds.
Improved monolithic tandem solar cell (1991)

A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surf ace of the InP substrate, (c) a second photoactive subcell on the first subcell; and (d) an optically transparent prismatic cover layer over the second subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched.
Power-Dependent Bandstop Filters for Wide-Bandwidth, High-Speed Interference Suppression (2018)

Power-dependent switchable bandstop filters are discussed in this paper. The co-design of a switchable bandstop filter, a sensing bandpass filter, a sensing analog circuit, and a switch driving circuit enable all-pass-to-bandstop switchable filters that automatically activate when power above a designable threshold is present within the bandwidth of the filter. A third-order suspended-stripline power-activated switchable all-pass-to-bandstop filter with a second-order resonant power sensor was fabricated and measured to test the technique at 2.15 GHz. The measured all-pass state has less than 1.7 dB insertion loss while the automatically-switched bandstop state provides more than 18 dB attenuation.
Fabrication and characterization of photonic-crystal surface-emitting lasers with triangular double-hole lattice points (2017)

Recently, W-class photonic-crystal surface-emitting lasers (PCSELs) with both a single spectrum and narrow spot beam pattern are reported. These highly coherent PCSEL properties cause a highly bright laser light that is useful for various applications. To improve the PCSEL output power, it is important to enlarge the emitting area to reduce the heat generation effect. However, multi-mode oscillation occurs in a broad emitting area because the difference in the threshold gain between the fundamental and higher modes becomes narrower as the emitting area is broadened. In this work, we fabricate PCSELs with double-hole lattice points that decrease the optical confinement to prevent multi-mode oscillation. The fabricated device, consisting of an AlGaAs/InGaAs material system designed to be oscillated at a wavelength of 940nm, has an emitting area of 300 × 300 μm<sup>2</sup>. In a square lattice photonic crystal whose lattice period equals the lasing wavelength embedded in PCSELs, the distance between the centers of the double hole is set to one quarter of the lasing wavelength to decrease in-plane coupling caused by interference. We confirm that this device is oscillated at the Γ point of band edge A in the photonic band structure. The peak power is more than 5 W under pulse operation at 10 A. The device has a narrow beam divergence of less than 1° and single lobe spectrum in spite of the broad emitting area, so these double-hole lattice points are an effective structure to improve the PCSEL output power.
Structural basis for Zika envelope domain III recognition by a germline version of a recurrent neutralizing antibody (2020)

Recent epidemics demonstrate the global threat of Zika virus (ZIKV), a flavivirus transmitted by mosquitoes. Although infection is usually asymptomatic or mild, newborns of infected mothers can display severe symptoms, including neurodevelopmental abnormalities and microcephaly. Given the large-scale spread, symptom severity, and lack of treatment or prophylaxis, a safe and effective ZIKV vaccine is urgently needed. However, vaccine design is complicated by concern that elicited antibodies (Abs) may cross-react with other flaviviruses that share a similar envelope protein, such as dengue virus, West Nile virus, and yellow fever virus. This cross-reactivity may worsen symptoms of a subsequent infection through Ab-dependent enhancement. To better understand the neutralizing Ab response and risk of Ab-dependent enhancement, further information on germline Ab binding to ZIKV and the maturation process that gives rise to potently neutralizing Abs is needed. Here we use binding and structural studies to compare mature and inferred-germline Ab binding to envelope protein domain III of ZIKV and other flaviviruses. We show that affinity maturation of the light-chain variable domain is important for strong binding of the recurrent VH3-23/VK1-5 neutralizing Abs to ZIKV envelope protein domain III, and identify interacting residues that contribute to weak, cross-reactive binding to West Nile virus. These findings provide insight into the affinity maturation process and potential cross-reactivity of VH3-23/VK1-5 neutralizing Abs, informing precautions for protein-based vaccines designed to elicit germline versions of neutralizing Abs.
Diffusion MRI quality control and functional diffusion map results in ACRIN 6677/RTOG 0625: A multicenter, randomized, phase II trial of bevacizumab and chemotherapy in recurrent glioblastoma (2015)

Functional diffusion mapping (fDM) is a cancer imaging technique that quantifies voxelwise changes in apparent diffusion coefficient (ADC). Previous studies have shown value of fDMs in bevacizumab therapy for recurrent glioblastoma multiforme (GBM). The aim of the present study was to implement explicit criteria for diffusion MRI quality control and independently evaluate fDM performance in a multicenter clinical trial (RTOG 0625/ACRIN 6677). A total of 123 patients were enrolled in the current multicenter trial and signed institutional review board-approved informed consent at their respective institutions. MRI was acquired prior to and 8 weeks following therapy. A 5-point QC scoring system was used to evaluate DWI quality. fDM performance was evaluated according to the correlation of these metrics with PFS and OS at the first follow-up time-point. Results showed ADC variability of 7.3% in NAWM and 10.5% in CSF. A total of 68% of patients had usable DWI data and 47% of patients had high quality DWI data when also excluding patients that progressed before the first follow-up. fDM performance was improved by using only the highest quality DWI. High pre-treatment contrast enhancing tumor volume was associated with shorter PFS and OS. A high volume fraction of increasing ADC after therapy was associated with shorter PFS, while a high volume fraction of decreasing ADC was associated with shorter OS. In summary, DWI in multicenter trials are currently of limited value due to image quality. Improvements in consistency of image quality in multicenter trials are necessary for further advancement of DWI biomarkers.
Lovastatin decreases coenzyme Q levels in humans. (1990)

Lovastatin is clinically used to treat patients with hypercholesterolemia and successfully lowers cholesterol levels. The mechanism of action of lovastatin is inhibition of 3-hydroxy-3-methylglutaryl-coenzyme A reductase, an enzyme involved in the biosynthesis of cholesterol from acetyl-CoA. Inhibition of this enzyme could also inhibit the intrinsic biosynthesis of coenzyme Q10 (CoQ10), but there have not been definitive data on whether lovastatin reduces levels of CoQ10 as it does cholesterol. The clinical use of lovastatin is to reduce a risk of cardiac disease, and if lovastatin were to reduce levels of CoQ10, this reduction would constitute a new risk of cardiac disease, since it is established that CoQ10 is indispensable for cardiac function. We have conducted three related protocols to determine whether lovastatin does indeed inhibit the biosynthesis of CoQ10. One protocol was done on rats, and is reported in the preceding paper [Willis, R. A., Folkers, K., Tucker, J. L., Ye, C.-Q., Xia, L.-J. & Tamagawa, H. (1990) Proc. Natl. Acad. Sci. USA 87, 8928-8930]. The other two protocols are reported here. One involved patients in a hospital, and the other involved a volunteer who permitted extraordinary monitoring of CoQ10 and cholesterol levels and cardiac function. All data from the three protocols revealed that lovastatin does indeed lower levels of CoQ10. The five hospitalized patients, 43-72 years old, revealed increased cardiac disease from lovastatin, which was life-threatening for patients having class IV cardiomyopathy before lovastatin or after taking lovastatin. Oral administration of CoQ10 increased blood levels of CoQ10 and was generally accompanied by an improvement in cardiac function. Although a successful drug, lovastatin does have side effects, particularly including liver dysfunction, which presumably can be caused by the lovastatin-induced deficiency of CoQ10.
Sustained drug delivery systems. I. The permeability of poly(ϵ‐caprolactone), poly(<scp>DL</scp>‐lactic acid), and their copolymers (1979)

The maximum steady state flux, diffusion coefficients, and solubilities of five contraceptive steroids in homopolymers and copolymers of epsilon-caprolactone and DL-lactic acid were determined. The permeabilities of polymers of epsilon-caprolactone were comparable to silicone rubber and, by inference, are suitable for the construction of drug delivery devices. Poly(DL-lactic acid) was 10(4) times less permeable, although its permeability was significantly enhanced by additives.
An Efficient Amination Method for Manufacturing Cytidines (2004)

A novel method for amination of uridine derivatives was developed and applied to the syntheses of cytidines. The method consists of an activation step with 1-methylpiperidine at the C4-position of a uracil base. Large-scale preparation of 2‘-deoxycytidine was performed using this method.
In-Silico Skin Model: A Multiscale Simulation Study of Drug Transport (2017)

Accurate in-silico models are required to predict the release of drug molecules through skin in order to supplement the in-vivo experiments for faster development/testing of drugs. The upper most layer of the skin, stratum corneum (SC), offers the main resistance for permeation of actives. Most of the SC's molecular level models comprise cholesterol and phospholipids only, which is far from reality. In this study we have implemented a multiscale modeling framework to obtain the release profile of three drugs, namely, caffeine, fentanyl, and naphthol, through skin SC. We report for the first time diffusion of drugs through a realistic skin molecular model comprised of ceramides, cholesterol, and free fatty acid. The diffusion coefficients of drugs in the SC lipid matrix were determined from multiple constrained molecular dynamics simulations. The calculated diffusion coefficients were then used in the macroscopic models to predict the release profiles of drugs through the SC. The obtained release profiles were in good agreement with available experimental data. The partition coefficient exhibits a greater effect on the release profiles. The reported multiscale modeling framework would provide insight into the delivery mechanisms of the drugs through the skin and shall act as a guiding tool in performing targeted experiments to come up with a suitable delivery system.
Moving-object detection method for moving cameras by merging background subtraction and optical flow methods (2017)

This paper presents a novel moving-object detection method for moving cameras. The proposed method merges two scores to detect moving objects more accurately in quasi-real time. We designed two scores, anomaly and motion, for real-time application. The anomaly score is calculated based on a background subtraction and depends on the difference in pixel intensities between the current image and the background model. The anomaly score extract the moving objects pixels with high precision rate, however it tends to result in under-detection (low recall rate) in the object pixels whose intensities are close to the background. The motion score is calculated from a sparse optical-flow, which is based on the short-term tracking results of sparsely sampled points. The motion score can extract the moving object's pixels with high recall rate, even if those pixel intensities are close to the background. However, it tends to result in over-detection (low precision rate) around the object boundaries due to the sparse optical flow. We propose to merge these two complementary scores to compensate for each other, thus it can detect moving objects with robustness and high resolution. Experimental results showed that our proposed method outperforms the conventional methods in terms of F-measure.
Methylene blue is a potent and broad-spectrum inhibitor against Zika virus <i>in vitro</i> and <i>in vivo</i> (2020)

Many flaviviruses including the Dengue virus (DENV), Zika virus (ZIKV), West Nile virus, Yellow Fever virus, and Japanese encephalitis virus are significant human pathogens, unfortunately without any specific therapy. Here, we demonstrate that methylene blue, an FDA-approved drug, is a broad-spectrum and potent antiviral against Zika virus and Dengue virus both <i>in vitro</i> and <i>in vivo</i>. We found that methylene blue can considerably inhibit the interactions between viral protease NS3 and its NS2B co-factor, inhibit viral protease activity, inhibit viral growth, protect 3D mini-brain organoids from ZIKV infection, and reduce viremia in a mouse model. Mechanistic studies confirmed that methylene blue works in both entry and post entry steps, reduces virus production in replicon cells and inhibited production of processed NS3 protein. Overall, we have shown that methylene blue is a potent antiviral for management of flavivirus infections, particularly for Zika virus. As an FDA-approved drug, methylene blue is well-tolerated for human use. Therefore, methylene blue represents a promising and easily developed therapy for management of infections by ZIKV and other flaviviruses.
Plasmodium falciparum DHODH inhibitor complexes reveal flexible binding site (2014)

Malaria is a preventable and treatable disease, yet annually there are still hundreds of thousands of malaria-related deaths. The disease is caused by infection with mosquito-borne Plasmodium parasites. With hundreds of millions of cases each year there is a very high potential for drug resistance and this has compromised many existing therapies. One target under investigation is the enzyme dihydroorotate dehydrogenase (DHODH) which catalyses the rate-limiting step of pyrimidine biosynthesis and is an essential enzyme in the malaria parasite. There are currently several Plasmodium-selective DHODH inhibitors under development. To investigate the potential for drug resistance against DHODH inhibitors in vitro resistance selections were carried out using known inhibitors from different structural classes [1]. These studies identified point mutations in the drug binding site which lead to reduced sensitivity to the inhibitors, and in some cases increased sensitivity to a different inhibitor, suggesting a novel combination therapy approach to combat resistance. To help understand the significance of the inhibitor binding site mutations we determined the crystal structures of P. falciparum DHODH in complex with the inhibitors Genz-669178, IDI-6253 and IDI-6273. Co-crystallisation experiments led to a new crystal form in each case. Here we describe the crystal structures, the binding modes of the inhibitors and the great flexibility of the binding site, which is able to adjust to accommodate different inhibitor series. The structural role of the resistance mutations is also discussed.
Blood Clotting by Low-Temperature Air Plasma (2009)

In this paper, the feasibility and effectiveness of using an air-plasma torch to clot blood are studied. The emission spectroscopy and temperature measurement of the torch show that the torch produces abundant atomic oxygen in the plasma effluent. Anticoagulated whole-blood samples (10 mulscr ) were tested for two cases: 1) sample exposed to the plasma effluent and 2) sample exposed to a heated airflow; in both cases, the increase of the sample temperature was controlled to be about the same. No indication of blood coagulation was observed in the second case; on the other hand, in the first case when the blood sample was exposed directly to the plasma effluent, a shell was formed on the surface of the blood sample. The experimental results demonstrated that this plasma torch could clot a blood sample via a nonthermal mechanism. The dependence of the degree of blood clotting on the atomic-oxygen flux was demonstrated by varying the exposure distance. Experimental results also showed that blood coagulation was seen in the treated platelet-rich plasma sample but not in the treated platelet-poor plasma sample. Moreover, plasma treatment with multiple short exposures was shown as more effective in clotting blood than that of applying a continuous exposure with the same total exposure time.