gebhart/patrepeval huggingface dataset:
Open-Source Chromatographic Data Analysis for Reaction Optimization and Screening (2023)

Automation and digitalization solutions in the field of small molecule synthesis face new challenges for chemical reaction analysis, especially in the field of high-performance liquid chromatography (HPLC). Chromatographic data remains locked in vendors' hardware and software components, limiting their potential in automated workflows and data science applications. In this work, we present an open-source Python project called MOCCA for the analysis of HPLC-DAD (photodiode array detector) raw data. MOCCA provides a comprehensive set of data analysis features, including an automated peak deconvolution routine of known signals, even if overlapped with signals of unexpected impurities or side products. We highlight the broad applicability of MOCCA in four studies: (i) a simulation study to validate MOCCA's data analysis features; (ii) a reaction kinetics study on a Knoevenagel condensation reaction demonstrating MOCCA's peak deconvolution feature; (iii) a closed-loop optimization study for the alkylation of 2-pyridone without human control during data analysis; (iv) a well plate screening of categorical reaction parameters for a novel palladium-catalyzed cyanation of aryl halides employing <i>O</i>-protected cyanohydrins. By publishing MOCCA as a Python package with this work, we envision an open-source community project for chromatographic data analysis with the potential of further advancing its scope and capabilities.
Topical application of human-derived Ig isotypes for the control of acute respiratory infection evaluated in a human CD89-expressing mouse model (2019)

Recurrent and persistent airway infections remain prevalent in patients with primary immunodeficiency (PID), despite restoration of serum immunoglobulin levels by intravenous or subcutaneous plasma-derived IgG. We investigated the effectiveness of different human Ig isotype preparations to protect mice against influenza when delivered directly to the respiratory mucosa. Four polyvalent Ig preparations from pooled plasma were compared: IgG, monomeric IgA (mIgA), polymeric IgA-containing IgM (IgAM) and IgAM associated with the secretory component (SIgAM). To evaluate these preparations, a transgenic mouse expressing human FcαRI/CD89 within the myeloid lineage was created. CD89 was expressed on all myeloid cells in the lung and blood except eosinophils, reflecting human CD89 expression. Intranasal administration of IgA-containing preparations was less effective than IgG in reducing pulmonary viral titres after infection of mice with A/California/7/09 (Cal7) or the antigenically distant A/Puerto Rico/8/34 (PR8) viruses. However, IgA reduced weight loss and inflammatory mediator expression. Both IgG and IgA protected mice from a lethal dose of PR8 virus and for mIgA, this effect was partially CD89 dependent. Our data support the beneficial effect of topically applied Ig purified from pooled human plasma for controlling circulating and non-circulating influenza virus infections. This may be important for reducing morbidity in PID patients.
Energy partition in collisions of C60+ ions with diamond (111) and graphite (0001) surfaces (1993)

Velocity distributions and fragmentation of C60 molecules after collision with type IAa diamond (111) and graphite (0001) surfaces are studied for primary energies up to 500 eV at a scattering angle of 140° using time-of-flight mass spectrometry. The absolute scattering yield is much lower for diamond due to polishing induced surface corrugation. However, the final velocity distribution of C60+ and its rate of metastable fragmentation after collision are similar for scattering off the two targets, and is interpreted by their similar lateral atomic structure. At a particular impact energy, the final internal energy of C60+, as monitored by the rate of metastable fragmentation, increases with final kinetic energy, but the energy transferred to the target decreases. These results are understood when considering the collision as a two-step mechanism, in which the impact energy is transformed into thermal and deformational energy of the target and C60. This latter energy is subsequently transformed to final kinetic and further thermal energy.
Real-Time Software Receiver for GPS Controlled Reception Pattern Antenna Array Processing (2010)

This paper demonstrates a real-time software receiver supporting GPS L1 C/A controlled reception pattern antenna (CRPA) processing. The software receiver is implemented on a widely-available recent generation multi-core processor and is capable of processing array signals from either radio frequency (RF) front-end modules or collected datasets. Most importantly, the receiver allocates dedicated satellite-tracking antenna patterns for each baseband receiver channel. The architecture of such a software receiver needs to be carefully developed so that it can process signals from each individual antenna, calculate the appropriate beam formed composite signals (one for each satellite/receiver channel) and then process those signals. Multitasking and synchronization mechanisms were developed to support the tracking of multiple channels in real time. To achieve real-time capability, parallel operations are necessary to reduce computation complexity. Bit-wise operations are exploited and implemented in the correlator. Additionally, Single Instruction Multiple Data (SIMD) instructions are used to efficiently calculate the covariance matrix for the beam steering algorithm. The architecture supports at least eighty tracking channels (ten channels from each of seven antennas plus ten composite beam formed signals) in real time. The CRPA software receiver was architected to operate without extensive set up and pre-calibration enhancing its suitability for commercial users. The algorithm design was architected to aid ease of set up. While conventional antenna array system receivers are used with the geometry of antennas and cable lengths known in advance, the algorithm implemented allows for operation without such a priori knowledge. Two beam steering techniques were tested. First is deterministic beam steering. An adaptive algorithm, Minimum Variance Distortion Response (MVDR) algorithm, was implemented to adaptively maximize signal power. The architecture determines of the carrier phase difference between signals from different antennas for a single satellite in order to build the steering vector. An experiment was conducted to show the enhanced C/No and controlled reception patterns through directing the CRPA toward the direction of satellite of interest. For evaluating interference rejection, a LI GPS simulator is used to build an environment with CDMA and CW interferences. The result shows that the MVDR algorithm has reliable performance than non beam steered and deterministic beam steering under the both type of interferences.
A Noncoherent Incremental Learning Demodulator (2020)

Incremental learning after deployment is one of several attractive capabilities that motivate the use of neural network demodulators. This paper presents a complex noncoherent neural network suitable for on-off key (OOK) demodulation. When trained in an AWGN channel, the demodulator learns a solution that outperforms the traditional noncoherent matched filter demodulator. The paper also explores incremental learning techniques that enable continued learning in the field. Training in the field with known labels provides maximum adaptability to new conditions, but the availability of known symbols maybe limited. As an alternative, we considered the effectiveness of entropy regularization and pseudo-labels to adapt a lab-trained reference network to new field conditions. Simulation of these techniques in an example multipath channel demonstrates successful unsupervised adaptation with initial symbol error rates up to 20% and successful semi-supervised adaptation with a small fraction of known symbols per packet and initial symbol error rates as high as 40%. In both cases, symbol error rates after adaptation are below 0.3%.
OXIDATION OF ALKYLCYANOHYDRAZINES TO AZO- BIS NITRILES USING OXONE®–POTASSIUM BROMIDE IN AQUEOUS MEDIUM (2002)

ABSTRACT Azo-bis nitriles were prepared in good yields and high purity by oxidation of corresponding 1,2-bis-dialkylcyano hydrazines using oxone-potassium bromide in aqueous medium. ACKNOWLEDGMENTS BVT thanks UGC, New Delhi for the award of fellowship under Faculty Improvement programme.
IRS-Aided SWIPT: Joint Waveform, Active and Passive Beamforming Design Under Nonlinear Harvester Model (2021)

The performance of Simultaneous Wireless Information and Power Transfer (SWIPT) is mainly constrained by the received Radio-Frequency (RF) signal strength. To tackle this problem, we introduce an Intelligent Reflecting Surface (IRS) to compensate the propagation loss and boost the transmission efficiency. This paper proposes a novel IRS-aided SWIPT system where a multi-carrier multi-antenna Access Point (AP) transmits information and power simultaneously, with the assist of an IRS, to a single-antenna User Equipment (UE) employing practical receiving schemes. Considering harvester nonlinearity, we characterize the achievable Rate-Energy (R-E) region through a joint optimization of waveform, active and passive beamforming based on the Channel State Information at the Transmitter (CSIT). This problem is solved by the Block Coordinate Descent (BCD) method, where we obtain the active precoder in closed form, the passive beamforming by the Successive Convex Approximation (SCA) approach, and the waveform amplitude by the Geometric Programming (GP) technique. To facilitate practical implementation, we also propose a low-complexity design based on closed-form adaptive waveform schemes. Simulation results demonstrate the proposed algorithms bring considerable R-E gains with robustness to CSIT inaccuracy and finite IRS states, and emphasize the importance of modeling harvester nonlinearity in the IRS-aided SWIPT design.
Development of continuous on‐line purge and trap analysis (2006)

An on-line purge and trap system for continuous monitoring of Volatile Organic Compounds (VOC) is presented. The purge chamber was designed for continuous extraction of VOC from water with nitrogen. The analytes were preconcentrated on a microtrap prior to analysis by GC with flame ionization detection. The microtrap served as a fast injection device for carrying out analysis at high frequency. Continuous monitoring was accomplished by performing injections at fixed intervals. This system showed high sensitivity, high precision, detection limits at the ppb level, and stable response over long periods of continuous operation. Factors affecting system performance were studied. A predictive model based on gas-liquid partitioning is also presented.
Enzymatic Characterization of a Human Acyltransferase Activity (2009)

In conclusion, our data demonstrate the presence of a zinc-stimulated acyltransferase activity concentrated in the endoplasmic reticulum in HEL cells which is likely to contribute to medium-chain protein lipidation.
A community effort to protect genomic data sharing, collaboration and outsourcing (2017)

The human genome can reveal sensitive information and is potentially re-identifiable, which raises privacy and security concerns about sharing such data on wide scales. In 2016, we organized the third Critical Assessment of Data Privacy and Protection competition as a community effort to bring together biomedical informaticists, computer privacy and security researchers, and scholars in ethical, legal, and social implications (ELSI) to assess the latest advances on privacy-preserving techniques for protecting human genomic data. Teams were asked to develop novel protection methods for emerging genome privacy challenges in three scenarios: Track (1) data sharing through the Beacon service of the Global Alliance for Genomics and Health. Track (2) collaborative discovery of similar genomes between two institutions; and Track (3) data outsourcing to public cloud services. The latter two tracks represent continuing themes from our 2015 competition, while the former was new and a response to a recently established vulnerability. The winning strategy for Track 1 mitigated the privacy risk by hiding approximately 11% of the variation in the database while permitting around 160,000 queries, a significant improvement over the baseline. The winning strategies in Tracks 2 and 3 showed significant progress over the previous competition by achieving multiple orders of magnitude performance improvement in terms of computational runtime and memory requirements. The outcomes suggest that applying highly optimized privacy-preserving and secure computation techniques to safeguard genomic data sharing and analysis is useful. However, the results also indicate that further efforts are needed to refine these techniques into practical solutions.
Mercury removal from combustion flue gas by activated carbon injection: Mass transfer effects (1996)

The Clean Air Act Amendments of 1990 listed 189 substances as hazardous air pollutants, of which 37 substances have been detected in power plant emissions. Of the 37 hazardous air pollutants, 11 are trace metal species. Mercury is trace metal species of greatest concern because of perceived risks from its environmental release and because it is present mainly in the vapor form and is not captured effectively by existing particulate removal systems. Carbon-based processes (both direct injection and fixed-bed) have been developed for control of mercury emission from municipal- and hazardous-waste incinerators. Existing data from the incinerators provide some insight on mercury control, but these data cannot be used directly for coal-fired utilities because mercury concentration, species, and process conditions differ greatly. This paper describes the results of phase I of a program to develop a sorbent for the removal of mercury from flue gas.
Subnanometer Imaging of Adsorbate-Induced Electronic Structure Perturbation on Silicon Surfaces (2008)

Room-temperature scanning tunneling microscopy is utilized to explore the consequences of a single covalent bond formed between an organic molecule, 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO), and the Si(111)-7 × 7 surface at the atomic scale. Upon binding, both topographic imaging and spectroscopic techniques reveal significant charge rearrangement within the substrate that is delocalized from the organic adsorbate. With scanning tunneling spectroscopy, the spatial extent of this charge transfer is directly visualized and determined to extend up to 2 nm from the molecule predominately within half of the Si(111)-7 × 7 unit cell. Analysis of individual differential tunneling conductance spectra suggests that the charge transfer is mediated by the back-bonds of the silicon substrate.
Joint Radar and Communications With Multicarrier Chirp-Based Waveform (2022)

We consider a multicarrier chirp-based waveform for joint radar and communication (JRC) systems and derive its time discrete periodic ambiguity function (AF). A set of waveform parameters (e.g., chirp rate) can together with the transmit sequence be selected to shape the AF to be thumbtack-like, or to be ridge-like, either along the delay axis or the Doppler axis. We demonstrate how these shapes are applicable for different use cases, e.g., radar target detection or time-and frequency synchronization. The results show that better signal detection performance than OFDM and DFT-s-OFDM can be achieved on channels with large Doppler shift. Furthermore, it is shown how transmit sequences can be selected in order to achieve low peak-to-average-power-ratio (PAPR) of the waveform.
Synchronous Electric Charge Extraction for multiple piezoelectric energy harvesters (2015)

This paper presents a power management circuit implementing a Synchronous Electric Charge Extraction on piezoelectric energy harvesters based on a flyback architecture. The novelty of this circuit lies in its ability to handle multiple energy harvesters operating at different frequencies and different output voltages with a single and standard flyback coupled inductor. The power harvested by the various scavengers is stored in a single and mutual storage capacitor. By construction, the power management circuit is capable of dealing with high input voltages (>100V). Its power consumption is about 1.15μA@3V per energy harvester and its conversion efficiency reaches 83%; its good operation has been validated by simulations and experiments on two vibration energy harvesters.
Towards Device Agnostic Detection of Stress and Craving in Patients with Substance Use Disorder (2023)

Novel technologies have great potential to improve the treatment of individuals with substance use disorder (SUD) and to reduce the current high rate of relapse (i.e. return to drug use). Wearable sensor-based systems that continuously measure physiology can provide information about behavior and opportunities for real-time interventions. We have previously developed an mHealth system which includes a wearable sensor, a mobile phone app, and a cloud-based server with embedded machine learning algorithms which detect stress and craving. The system functions as a just-in-time intervention tool to help patients de-escalate and as a tool for clinicians to tailor treatment based on stress and craving patterns observed. However, in our pilot work we found that to deploy the system to diverse socioeconomic populations and to increase usability, the system must be able to work efficiently with cost-effective and popular commercial wearable devices. To make the system device agnostic, methods to transform the data from a commercially available wearable for use in algorithms developed from research grade wearable sensor are proposed. The accuracy of these transformations in detecting stress and craving in individuals with SUD is further explored.
Intense phosphorescence triggered by alcohols upon formation of a cyclodextrin ternary complex (1993)

Intense phosphorescence is observed when alcohols (ROH) are introduced to aqueous solutions containing 1-bromonaphthalene (1-BrNp) and a glucosyl-modified cyclodextrin (Gβ-CD). Steady-state and time-resolved luminescence measurements and equilibrium constant data are consistent with phosphorescence arising from 1-BrNp as part of a 1-BrNp·Gβ-CD·ROH ternary complex. The association of the 1-BrNp to Gβ-CD is increased in the presence of the alcohols (K = 800 M-1 in the absence of ROH and K = 1900-3400 M-1 in the presence of ROH with the exception of cyclohexanol where K = 760 M-1). However the phosphorescence quantum yields show no obvious correlation with the apparent formation constants of the ternary complex. For instance, the ternary complex of cyclohexanol exhibits the highest phosphorescence quantum yield (φe = 0.035) despite possessing the smallest formation constant. Stern-Volmer analysis shows that the phosphorescence enhancement induced by alcohol is related to its effectiveness in shielding photoexcited 1-BrNp from oxygen. The rate constants for oxygen quenching decrease generally as the bulkiness of the alcohol increases. Accordingly, tert-butyl alcohol and cyclohexanol give rise to the smallest oxygen quenching rate constants and the highest emission quantum yields. The ability of alcohols to trigger an intense luminescence response is a first step in the development of an optical scheme to detect alcohols. The advantage of strategies using a 1-BrNp·Gβ-CD·ROH ternary complex is that alcohol detection occurs by the appearance of bright green phosphorescence relative to a photonically silent background. © 1993 American Chemical Society.
Vesicular Traffic and Golgi Apparatus Dynamics During Mammalian Spermatogenesis: Implications for Acrosome Architecture1 (2000)

Vesicular membrane trafficking during acrosome biogenesis in bull and rhesus monkey spermatogenesis differs from the somatic cell paradigm as imaged dynamically using the Golgi apparatus probes beta-COP, giantin, Golgin-97, and Golgin-95/GM130. In particular, sorting and delivery of proteins seemed less precise during spermatogenesis. In early stages of spermiogenesis, many Golgi resident proteins and specific acrosomal markers were present in the acrosome. Trafficking in both round and elongating spermatids was similar to what has been described for somatic cells, as judged by the kinetics of Golgi protein incorporation into endoplasmic reticulum-like structures after brefeldin A treatment. These Golgi components were retrieved from the acrosome at later stages of differentiation and were completely devoid of immature spermatozoa. Our data suggest that active anterograde and retrograde vesicular transport trafficking pathways, involving both beta-COP- and clathrin-coated vesicles, are involved in retrieving Golgi proteins missorted to the acrosome and in controlling the growth and shape of this organelle.
Functional interference between estrogen-related receptor alpha and peroxisome proliferator-activated receptor alpha/9-cis-retinoic acid receptor alpha heterodimer complex in the nuclear receptor response element-1 of the medium chain acyl-coenzyme A dehydrogenase gene (2003)

We undertook a study of molecular interference of nuclear orphan receptors. Nuclear receptor response element-1 (NRRE-1) from the human medium-chain acyl coenzyme A dehydrogenase (MCAD) gene promoter was shown to contain three hexamer elements (site 1 through 3) that are known to interact with a number of nuclear receptors including chicken ovalbumin upstream promoter transcription factor (COUP-TF) and estrogen-related receptor alpha (ERRalpha). We demonstrated that the peroxisome proliferator-activated receptor alpha/9-cis-retinoic acid receptor alpha (PPARalpha/RXRalpha) heterodimer complex can also bind to the two hexamer repeat sequences (between site 1 and site 3) arranged as an everted imperfect repeat separated by 14 bp (ER14). Mutations of the putative core elements have shown that these three sites are differentially involved in ERRalpha and PPARalpha/RXRalpha binding. Homodimer of ERRalpha was shown to interact between site 1 and site 3 (ER14). To date, no nuclear receptor is known to bind to response elements over such long intervals. Interestingly, site 1 was shown to be essential for ERRalpha binding while site 3 supports its binding only in the presence of site 1. Furthermore, it was shown that the binding profile of ERRalpha and PPARalpha/RXRalpha are competitive rather than making a high order complex within NRRE-1. At the cellular level, transcriptional activation driven by the PPARalpha/RXRalpha complex was counteracted by the expression of ERRalpha in HeLa cells. These results suggest that ERRalpha and PPARalpha/RXRalpha could interfere with each other's function through binding to similar DNA elements, thereby finetuning the transcriptional outcome of the target gene. Our findings suggest a mechanism whereby multiple nuclear receptors can activate or repress DNA binding or transcription via a single pleiotropic regulatory element.