gebhart/patrepeval huggingface dataset:
Strategies to Develop Allergy Immunotherapeutics with Applications of Directed Molecular Evolution (2003)

Allergic immune responses result from complex cascades of events mediated by multiple effector cells and their signaling molecules. The multiplicity of mediators involved in allergic reactions also provides numerous potential targets for intervention. In recent years, a number of approaches have been undertaken to inhibit the synthesis and function of allergen-specific IgE antibodies, induce blocking anti-allergen IgG antibodies, prevent the differentiation of Th2 cells, or eliminate the cells or mediators causing allergic symptoms. Directed molecular evolution using DNA shuffling and appropriate screening technologies provides a means to generate improved vaccines and therapeutics with the potential for short-term and long-term therapeutic effects. DNA shuffling enables the generation of large libraries of chimeric genes from which improved variants can be selected based on functional properties. Structural information obtained from shuffled molecules will also help in the understanding of receptor-ligand interactions and may assist in the design of small molecules that specifically interact with given targets. Here we review strategies to generate novel allergy vaccines and anti-allergic therapeutics, with particular emphasis on approaches utilizing directed molecular evolution.
Peripheral nerve stimulation characteristics of an asymmetric head‐only gradient coil compatible with a high‐channel‐count receiver array (2015)

Measured PNS characteristics of asymmetric head-only gradient coil prototypes indicate that such coils, especially in the A/P direction, can be used for fast EPI readout in high-performance neuroimaging scans with substantially reduced PNS concerns compared with conventional whole body gradient coils. Magn Reson Med 76:1939-1950, 2016. © 2015 International Society for Magnetic Resonance in Medicine.
IN-SILICO PHARMACOKINETICS PREDICTION OF MAJOR COUMARINS PRESENT IN AEGLE MARMELOS L. (2023)

Natural coumarins has enormous power as natural magical remedy for wide range of diseases, they are present in high concentrations in several dietary plant species like cinnamon, lemon, dill, soy oil, peanut oil, olive oil etc. In the larger category of nutraceuticals natural coumarins contribute for various activities, their pharmacotherapeutic aspects have been already published. A large amount of coumarin intake may have negative impact on health as the safety profile of coumarins was not thoroughly reviewed to present date [1-3]. The subtropical fruit Aegle marmelos L (A.M.) commonly known as Bael, a plant of Indian origin belongs to the Rutaceae family. Bael has been used as a medicine for diarrhea and dysentery treatment since 5000 B.C. [4]. Selective coumarins present in A.M. like umbelliferone, scopoletin, scoparone, xanthotoxol, marmesin, psoralen, imperatorin, alloimperatorin, and marmin [5-6] was taken for in silico ADME screening using SwissADME software [7]. In silico methods have the advantage that they can make fast predictions for a large set of compounds in a highthroughput mode. The earlier detection of PK/PD properties along with drug likeness and ADME profiling can save both money and time. It is also ensuring the safety and stability of the candidate-drugs or designed-drugs In Lipophilicity property, the rule says, “The larger the log P value greater the lipophilicity&quot; [8]. XLOGP3 value of coumarins is in the range of -0.7 to + 5.0 size which indicates that they are lipophilic compounds, Log S (ESOL), Log S (ali), and Log S (SILICOS-IT) values of umbelliferone, scopoletin, scoparone, xanthotoxol, and marmesin shows good water solubility whereas psoralen, imperatorin, alloimperatorin, and marmin are moderately soluble in water [9]. According to pharmacokinetic properties, all other coumarins showed good GI absorption and penetration at BBB whereas marmin showed no penetration at BBB [10-13]. All coumarins showed no inhibition of the isoenzymes like CYP2D6, CYP3A4 as well as they are not good P-gp substrates which is clear indication of their low toxicity and no drug-drug interactions. The isoenzyme CYP1A2 found to be inhibited by all coumarins other than marmin whereas imperatoin, and alloimperatorin are inhibiting the isoenzymes like CYP2C19, CYP2C9 which leads to increase in bioavailability of drug. All selected coumarin were in the limit of Lipinski, Veber, and Egan filters which make them to have promising drug likeness properties. In the BOILED egg model, all coumarins found in yellow regions (i.e., regions of high BBB absorption and high GI absorption) except marmin which is located on the boundary of white and yellow region that means it has good GI absorption, and no BBB permeation property. This data supports to conduct pre-clinical and clinical trials of bael fruit-based products such as squash, jelly, candy, etc. which will increase their value as food and nutraceutical products by a huge margin.
Metal Assembly in Novel Dendrimers with Porphyrin Cores (2002)

A series of phenylazozmethine (DPA) dendrimers with a porphyrin core (PnH2) were synthesized by dehydration using TiCl4 from meso-tetrakis(4-aminophenyl)porphyrin and the DPA dendrons. The addition of SnCl2 to a dichloromethane/acetonitrile solution of dendritic cobalt porphyrin resulted in a stepwise spectral change. By using UV-vis spectroscopy to monitor the complexation of the P4CoIIICl until an equimolar amount of SnCl2 has been added, four changes in the position of the isosbestic point were observed during the addition of SnCl2. Titration results suggest that four different complexes are successively formed upon the SnCl2 addition and that the complexation proceeds in, not a random, but a stepwise fashion from the core imines to the terminal imines of P4CoIIICl. The electrochemical study reveals that their dendrimers with Tb ion act as a multielectron mediator in CO2 reduction at high applied potential on the electrode.
Doubly Robust and Efficient Estimation of Marginal Structural Models for the Hazard Function (2016)

In social and health sciences, many research questions involve understanding the causal effect of a longitudinal treatment on mortality (or time-to-event outcomes in general). Often, treatment status may change in response to past covariates that are risk factors for mortality, and in turn, treatment status may also affect such subsequent covariates. In these situations, Marginal Structural Models (MSMs), introduced by Robins (1997. Marginal structural models Proceedings of the American Statistical Association. Section on Bayesian Statistical Science, 1-10), are well-established and widely used tools to account for time-varying confounding. In particular, a MSM can be used to specify the intervention-specific counterfactual hazard function, i. e. the hazard for the outcome of a subject in an ideal experiment where he/she was assigned to follow a given intervention on their treatment variables. The parameters of this hazard MSM are traditionally estimated using the Inverse Probability Weighted estimation Robins (1999. Marginal structural models versus structural nested models as tools for causal inference. In: Statistical models in epidemiology: the environment and clinical trials. Springer-Verlag, 1999:95-134), Robins et al. (2000), (IPTW, van der Laan and Petersen (2007. Causal effect models for realistic individualized treatment and intention to treat rules. Int J Biostat 2007;3:Article 3), Robins et al. (2008. Estimaton and extrapolation of optimal treatment and testing strategies. Statistics in Medicine 2008;27(23):4678-721)). This estimator is easy to implement and admits Wald-type confidence intervals. However, its consistency hinges on the correct specification of the treatment allocation probabilities, and the estimates are generally sensitive to large treatment weights (especially in the presence of strong confounding), which are difficult to stabilize for dynamic treatment regimes. In this paper, we present a pooled targeted maximum likelihood estimator (TMLE, van der Laan and Rubin (2006. Targeted maximum likelihood learning. The International Journal of Biostatistics 2006;2:1-40)) for MSM for the hazard function under longitudinal dynamic treatment regimes. The proposed estimator is semiparametric efficient and doubly robust, offering bias reduction over the incumbent IPTW estimator when treatment probabilities may be misspecified. Moreover, the substitution principle rooted in the TMLE potentially mitigates the sensitivity to large treatment weights in IPTW. We compare the performance of the proposed estimator with the IPTW and a on-targeted substitution estimator in a simulation study.
Ultrabroadband nonlinear optics in nanophotonic periodically poled lithium niobate waveguides (2020)

Quasi-phase-matched interactions in waveguides with quadratic nonlinearities enable highly efficient nonlinear frequency conversion. In this paper, we demonstrate the first generation of devices that combine the dispersion engineering available in nanophotonic waveguides with quasi-phase-matched nonlinear interactions available in periodically poled lithium niobate (PPLN). This combination enables quasi-static interactions of femtosecond pulses, reducing the pulse energy requirements by several orders of magnitude compared to conventional devices, from picojoules to femtojoules. We experimentally demonstrate two effects associated with second harmonic generation (SHG). First, we observe efficient quasi-phase-matched SHG with <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mo>&lt;</mml:mo> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>100</mml:mn> </mml:mrow> <mml:mspace width="thickmathspace"/> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">f</mml:mi> <mml:mi mathvariant="normal">J</mml:mi> </mml:mrow> </mml:math> of pulse energy. Second, in the limit of strong phase-mismatch, we observe spectral broadening of both harmonics with as little as 2 pJ of pulse energy. These results lay a foundation for a new class of nonlinear devices, in which coengineering of dispersion with quasi-phase-matching enables efficient nonlinear optics at the femtojoule level.
FY09 Advanced Instrumentation and Active Interrogation Research for Safeguards (2009)

Multiple small-scale projects have been undertaken to investigate advanced instrumentation solutions for safeguard measurement challenges associated with advanced fuel cycle facilities and next-generation fuel reprocessing installations. These activities are in support of the U.S. Department of Energy's Fuel Cycle Research and Development program and its Materials Protection, Accounting, and Control for Transmutation (MPACT) campaign. 1) Work was performed in a collaboration with the University of Michigan (Prof. Sara Pozzi, co-PI) to investigate the use of liquid-scintillator radiation detectors for assaying mixed-oxide (MOX) fuel, to characterize its composition and to develop advanced digital pulse-shape discrimination algorithms for performing time-correlation measurements in the MOX fuel environment. This work included both simulations and experiments and has shown that these techniques may provide a valuable approach for use within advanced safeguard measurement scenarios. 2) Work was conducted in a collaboration with Oak Ridge National Laboratory (Dr. Paul Hausladen, co-PI) to evaluate the strengths and weaknesses of the fast-neutron coded-aperture imaging technique for locating and characterizing fissile material, and as a tool for performing hold-up measurements in fissile material handling facilities. This work involved experiments at Idaho National Laboratory, using MOX fuel and uranium metal, in both passive and active interrogation configurations. A complete analysis has not yet been completed but preliminary results suggest several potential uses for the fast neutron imaging technique. 3) Work was carried out to identify measurement approaches for determining nitric acid concentration in the range of 1 – 4 M and beyond. This work included laboratory measurements to investigate the suitability of prompt-gamma neutron activation analysis for this measurement and product reviews of other commercial solutions. Ultrasonic density analysis appears to be the best candidate technology for determining nitric acid concentrations but the PGNAA approach may also be applicable. 4) Work was also carried out to begin investigating the use of remote UV imaging to detect air-ionization induced by alpha particle emission from plutonium. This approach has been shown elsewhere as a useful tool for detecting and quantifying plutonium contamination and has the potential of providing a unique and powerful approach for quantifying hold-up in reprocessing facilities. Based on these simple scoping experiments the potential far-reaching capabilities of the measurement are clear.
Max-Min Power Control in Downlink Massive MIMO With Distributed Antenna Arrays (2020)

In this paper, we investigate optimal downlink power allocation in massive multiple-input multiple-output (MIMO) networks with distributed antenna arrays (DAAs) under correlated and uncorrelated channel fading. In DAA massive MIMO, a base station (BS) consists of multiple antenna sub-arrays. Notably, the antenna sub-arrays are deployed in arbitrary locations within a DAA massive MIMO cell. Consequently, the distance-dependent large-scale propagation coefficients are different from a user to these different antenna sub-arrays, which makes power control a challenging problem. We assume that the network operates in time-division duplex mode, where each BS obtains the channel estimates via uplink pilots. Based on the channel estimates, the BSs perform maximum-ratio transmission in the downlink. We then derive a closed-form signal-to-interference-plus-noise ratio (SINR) expression, where the channels are subject to correlated fading. Based on the SINR expression, we propose a network-wide max-min power control algorithm to ensure that each user in the network receives a uniform quality of service. Numerical results demonstrate the performance advantages offered by DAA massive MIMO. For some specific scenarios, DAA massive MIMO can improve the average per-user throughput up to 55%. Furthermore, we demonstrate that channel fading covariance is an important factor in determining the performance of DAA massive MIMO.
Subaperture decoding to enhance performance of coded excitation (2004)

Coded excitation requires long code to improve signal to noise ratio (SNR). However, in order to achieve a high lateral resolution, the beam forming is normally performed based on a low f-number and real-time dynamic focusing, which limits the maximum length of coded waves. Individual decoding before beamforming can solve this problem, but it demands an enormous size of hardware. In this study, a subaperture decoding technique is proposed to achieve a high SNR based on coded excitation without compromising lateral resolution. In this technique, the receiving aperture is divided into N subapertures, beamforming is performed for each subaperture, and each output is decoded, delayed and summed together to complete beamforming in whole aperture. Computer simulations were used to demonstrate this technique. When the transmission waveform was encoded by the 13-chip Barker code and decoded with a mismatched filter, and the reception f-number was 1, the proposed technique, with the number of subaperture of 16, lowered the range sidelobe level from -25 dB to -45 dB.
Amphiphilic Porphinatoirons Having Steroid Groups and Their Oxygen-Adduct Formation in an Aqueous Medium (1990)

Abstract Amphiphilic heme derivatives having four steroid groups (steroid-heme), 5,10,15,20-tetrakis[α,α,α,α-o-[2,2-dimethyl-8-(3α-hydroxycholan-24-oyloxy)octanamido]phenyl]porphinatoiron (1b) and 5,10,15,20-tetrakis[α,α,α,α-o-(3-acetoxycholan-24-oylamino)phenyl]porphinatoiron (2b), were synthesized as a model of an oxygen carrier. They were efficiently embedded in the bilayer of a phospholipid liposome based on their high compatibility with the lipid. The oxygen-binding ability of 1b was compared with those of hemoglobin (Hb) and myoglobin (Mb). The dioxygen adduct of 1b was also characterized by Mössbauer and infrared spectroscopy.
Herman F. Mark: The Geheimrat (1981)

The years Mark worked in Berlin in retrospect set the stage for his rocket like rise to eminence in polymer science. Postwar inflation placed many of Berlin's bolder attractions out of the reach of the young scientist and his new bride, Mimi. In place of the expensive frolics, the Mark's entertained and exchanged ideas with an international set of coworkers in his Lichterfelde-West apartment. Besides his fellow Austrians, Mark's close friends included Hungarians and Poles, as well as Germans. This broad mesh of backgrounds and styles of thinking was catalyzed by the unexcelled and readily available music, art, and architecture, and stimulated by such scientists as Schroedinger, Haber, Hahn, V. Laue, Einstein, Planck, Nerst, and Schlenk. The result was it expanded his perspective, taught him how to communicate and lead a diverse group of scientists despite problems of differing nationality and proclivity, and enhanced his natural sagacity as only a
Reproductive toxicological effects of gossypol on male rabbits: semen characteristics and hormonal levels (2006)

Abstract The objective of this study was to evaluate the effects of two sublethal doses (4 and 20 mg/kg live weight (LW); every other day) of gossypol on semen and hormonal characteristics of male rabbits. The experiment lasted 16 weeks and included two periods: a treatment period (first 8 weeks) where the animals were given the test materials, and a recovery period (second 8 weeks) where drugs were withdrawn. Results showed that LW and respiration rate (RR) decreased ( P &lt;0·05) among animals that received gossypol, while rectal temperature increased ( P &lt;0·05). Animals in gossypol treatment groups had decreased ( P &lt;0·05) blood plasma levels of tri-iodothyronine (T 3 ) and testosterone. This was accompanied by reductions ( P &lt;0·05) in sperm concentration, total sperm output, percentage incidence of forward motility, total functional sperm fraction and semen initial fructose concentration. Gossypol however increased ( P &lt;0·05) reaction time (i.e. decreased libido), percentages of dead sperm and abnormal sperm (AbSp) and altered acrosomes. Estimated weights of testes and semen ejaculate volume increased ( P &lt;0·05) possibly due to increased water retention. Values of LW, RR, AbSp, and blood plasma T 3 and testosterone returned to control levels after withdrawal of gossypol, while the effect of this drug on other parameters continued during the recovery period.
Coupling-induced oscillations in overdamped bistable systems (2003)

It is well known that overdamped and unforced dynamical systems do not oscillate. However, well-designed coupling schemes, together with the appropriate choice of initial conditions, can induce oscillations when a control parameter exceeds a threshold value. We demonstrate this effect in a specific system, a soft-potential mean-field description of the dynamics in a (hysteretic) single-domain ferromagnetic sample. Using a specific (unidirectional, with cyclic boundary conditions) coupling scheme, together with nonidentical initial conditions, one can cause the coupled system of N elements (N odd) to oscillate when the coupling coefficient is swept through a critical value. The ensuing oscillations could find utility in the detection of very weak "target" signals, via their effect on the oscillation characteristics.
The OSMOSIS Optical Packet Switch for Supercomputers (2009)

We describe the OSMOSIS project from requirements through realization, in which IBM research and Corning Inc. completed the 64 port at 40 Gbps/port demonstrator hardware for what we believe is the world’s first true optical packet switch.
Anatomical and Functional Connectivity of Cytoarchitectonic Areas within the Human Parietal Operculum (2010)

In monkeys, the somatosensory cortex on the parietal operculum can be differentiated into several distinct cortical fields. Potential human homologues for these areas have already been defined by cytoarchitectonic mapping and functional imaging experiments. Differences between the two most widely studied areas [operculum parietale (OP) 1 and OP 4] within this region particularly pertain to their connection with either the perceptive parietal network or the frontal motor areas. In the present study, we investigated differences in anatomical connection patterns probed by probabilistic tractography on diffusion tensor imaging data. Functional connectivity was then mapped by coordinate-based meta-analysis of imaging studies. Comparison between these two aspects of connectivity showed a good congruency and hence converging evidence for an involvement of these areas in matching brain networks. There were, however, also several instances in which anatomical and functional connectivity diverged, underlining the independence of these measures and the need for multimodal characterization of brain connectivity. The connectivity analyses performed showed that the two largest areas within the human parietal operculum region display considerable differences in their connectivity to frontoparietal brain regions. In particular, relative to OP 1, area OP 4 is more closely integrated with areas responsible for basic sensorimotor processing and action control, while OP 1 is more closely connected to the parietal networks for higher order somatosensory processing. These results are largely congruent with data on nonhuman primates. Differences between anatomical and functional connectivity as well as between species, however, highlight the need for an integrative view on connectivity, including comparison and cross-validation of results from different approaches.
High data rate silicon optical modulator with self-aligned fabrication process (2012)

In this work we present optical modulation at both 40Gbit/s and 50Gbit/s from a carrier depletion based device in silicon. The modulator can be fabricated using a self-aligned process aiding performance reliability and device yield.
Pathological and Molecular Characteristics of Colorectal Cancer with Brain Metastases (2018)

<i>Background:</i> Colorectal cancers (CRC) with brain metastases (BM) are scarcely described. The main objective of this study was to determine the molecular profile of CRC with BM. <i>Methods:</i> We included 82 CRC patients with BM. <i>KRAS</i>, <i>NRAS</i>, <i>BRAF</i> and mismatch repair (MMR) status were investigated on primary tumors (<i>n</i> = 82) and BM (<i>n</i> = 38). ALK, ROS1, cMET, HER-2, PD-1, PD-L1, CD3 and CD8 status were evaluated by immunohistochemistry, and when recommended, by fluorescence in situ hybridization. <i>Results:</i> In primary tumors, <i>KRAS</i>, <i>NRAS</i> and <i>BRAF</i> mutations were observed in 56%, 6%, and 6% of cases, respectively. No <i>ROS1</i>, <i>ALK</i> and <i>cMET</i> rearrangement was detected. Only one tumor presented <i>HER-2</i> amplification. Molecular profiles were mostly concordant between BM and paired primary tumors, except for 9% of discordances for <i>RAS</i> mutation. CD3, CD8, PD-1 and PD-L1 expressions presented some discordance between primary tumors and BM. In multivariate analysis, multiple BM, lung metastases and PD-L1+ tumor were predictive of poor overall survival. <i>Conclusions:</i> CRCs with BM are associated with high frequency of <i>RAS</i> mutations and significant discordance for <i>RAS</i> mutational status between BM and paired primary tumors. Multiple BM, lung metastases and PD-L1+ have been identified as prognostic factors and can guide therapeutic decisions for CRC patients with BM.
Nanocellulose/clay thin films and foams : Biobased nanocomposites with superior flame retardant properties (2016)

Nanocellulose/clay thin films and foams : Biobased nanocomposites with superior flame retardant properties