gebhart/patrepeval huggingface dataset:
Case History: IDHIFA® (Enasidenib), a First-in-Class Selective IDH2 Inhibitor for the Treatment of Acute Myeloid Leukemia (2018)

Medicinal Chemistry Reviews is an outstanding 680 page volume providing timely and critical reviews of important topics in medicinal chemistry. It is provided free of charge to MEDI members in electronic format. Members can also order a print copy, for the cost of printing, shipping and handling
A dynamic content summarization system for opportunistic driver infotainment (2011)

The in-vehicle experience offers a unique challenge for delivering the right amount of information to the driver at the right time. The level of attention required to successfully manage the driving task is often in variable. An ideal in vehicle information delivery system would deliver content to the driver only during low task demand times, such as waiting at a stop light, when the driver's safety would be minimally compromised. The system would also have to respond to sudden changes in the situation such as driver interruption or distraction and terminate gracefully, allowing the driver to refocus on the driving task. In this paper, we present an embedded natural language processing (NLP) system that delivers speech synthesized summarized text content into tailored time slices. The system is also designed to respond dynamically to interruptions. We anticipate that this system could safely deliver speech synthesized content to drivers and allow them to make the most of their time on the road. We have implemented this system on an Atom Z530 processor with 1GB of RAM, a processor comparable to those found in factory installed In-Vehicle Infotainment (IVI) systems and have evaluated it in a laboratory test using a standard NLP corpus to demonstrate this potential.
Abnormal protein kinase C down regulation and reduced substrate levels in non-phorbol ester-responsive 3T3-TNR9 cells. (1990)

The cell line TNR9 (E. Butler-Gralla and H. R. Herschman, J. Cell. Physiol. 107:59-67, 1981) in a Swiss 3T3 cell variant that expresses protein kinase C (PKC) but is mitogenically nonresponsive to the phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA). We have found that PKCs purified from variant and parental cells are identical as judged by kinase activity, protease mapping, and column chromatography. We analyzed cellular levels and subcellular location of PKC in TPA-treated 3T3 and TNR9 cells via immunoprecipitation of [35S]methionine-labeled protein and assay of immune-complex PKC kinase activity. TNR9 cells grew to higher densities than parental 3T3 cells. TNR9 cells at maximal density did not down regulate PKC in response to long-term TPA treatment. We compared the 80-kilodalton (kDa) PKC substrate phosphorylation in 3T3 and TNR9 cells by using two-dimensional gels and found that TNR9 cells treated with TPA for 30 min contained only 10 to 15% as much 32Pi associated with the 80-kDa as did parental cells. The TNR9 80-kDa substrate was present at reduced levels compared with the parental-cell 80-kDa substrate as judged by immunoblot and silver staining. Thus, the loss of mitogenic responsiveness to TPA in TNR9 cells is accompanied by resistance to TPA-mediated down regulation of PKC and reduced phosphosubstrate levels.
Intracranial Administration of Adenovirus Expressing HSV-TK in Combination with Ganciclovir Produces a Dose-Dependent, Self-Limiting Inflammatory Response (1997)

Replication-defective adenovirus expressing the herpes simplex thymidine kinase gene (H5.010RSVtk) may be useful in treating human gliomas. To determine the toxicity of this therapeutic strategy, we injected H5.010RSVtk stereotactically into the normal brain of Wistar rats, cotton rats, and rhesus monkeys in conjunction with systemic ganciclovir (GCV) at 10 mg/kg per day. In the Wistar rat, 5.7 x 10(9) pfu resulted in histopathologic injury consisting of localized necrosis, mild gliosis, marked malacia, and focal astrocytosis; however, 1.0 x 10(8) pfu resulted in only mild gliosis and trace meningitis and approximates a "no toxic effect" dose. A dose of 1.0 x 10(9) pfu in both adenoviral immune and adenoviral naive cotton rats resulted in similar findings. In the rhesus monkey, doses ranging from 1.4 x 10(8) pfu to 1.5 x 10(11) pfu resulted in localized gliosis, necrosis, perivascular cuffing, meningitis, and roughly correlated in severity with increasing dose. No histologic evidence of toxicity was found in non-central nervous system (CNS) tissues, and no virus could be cultured from cerebrospinal fluid (CSF), blood, urine, and stool samples. All animals survived to prescribed end points without signs of general toxicity or neurologic symptoms, except for 2 of the rhesus monkeys, one of which became febrile and the other of which developed a grand mal seizure (both subsequently resolved). These toxicology studies define the parameters for developing a phase I clinical trial.
Characterizing Downhole Fluid Analysis Sensors As Digital Twins: Lessons of the Machine Learning Approach, The Physics Approach and the Integrated Hybrid Approach (2021)

Abstract Digital fluid sampling is a technique utilizing downhole sensors to measure formation fluid properties without collecting a physical sample. Unfortunately, sensors are prone to drift over time due to the harsh downhole environmental conditions. Therefore, constant sensor evaluation and calibration is required to ensure the quality of analysis. A new technique utilizes a virtual sensor as a digital twin which provides a calibration that can be utilized by the physical twin. Digital twin technology enables the end-user to operate and collaborate remotely, rapidly simulate different scenarios, and provide improved accuracy via enhanced up-to-date calibrations. With respect to downhole fluid identification, the contribution of harsh environmental conditions and sensor drift can also be mitigated by realizing a virtual implementation of the fluid behavior and the individual sensor components. Historically, the virtual behavior of a digital twin has been constructed by a combination of complex multi-physics and empirical modeling. More recently, access to large datasets and historical results has enabled the use of machine learning neural networks to successfully create digital twin sensors. In this paper, we explore the efficacy of constructing a digital twin on a single downhole optical fluid identification sensor using both the machine learning nonlinear neural network and the complex, multi-physics' based modeling approaches. Advantages and lessons to be learned from each individual method will be discussed in detail. In doing so, we have found a hybrid approach to be most effective in constraining the problem and preventing over-fitting while also yielding a more accurate calibration. In addition, the new hybrid digital twin evaluation and calibration method is extended to encompass an entire fleet of similar downhole sensors simultaneously. The introduction of digital twin technology is not new to the petroleum industry. Yet there is significant room for improvement in order to identify how the technology can be implemented best in order to decrease costs and improve reliability. This paper looks at two separate methods that scientists and engineers employ to enable digital twin technology and ultimately identify that a hybrid approach between machine learning and empirical physics'-based modeling prevails.
Phased-array sources based on nonlinear metamaterial nanocavities (2015)

Coherent superposition of light from subwavelength sources is an attractive prospect for the manipulation of the direction, shape and polarization of optical beams. This phenomenon constitutes the basis of phased arrays, commonly used at microwave and radio frequencies. Here we propose a new concept for phased-array sources at infrared frequencies based on metamaterial nanocavities coupled to a highly nonlinear semiconductor heterostructure. Optical pumping of the nanocavity induces a localized, phase-locked, nonlinear resonant polarization that acts as a source feed for a higher-order resonance of the nanocavity. Varying the nanocavity design enables the production of beams with arbitrary shape and polarization. As an example, we demonstrate two second harmonic phased-array sources that perform two optical functions at the second harmonic wavelength (∼5 μm): a beam splitter and a polarizing beam splitter. Proper design of the nanocavity and nonlinear heterostructure will enable such phased arrays to span most of the infrared spectrum.
ChemInform Abstract: The Structure of a Stable New Organotellurium Azide: Bis‐ Azidodiphenyltellurium(IV) Oxide. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Machine learning assisted plasmonics and quantum optics (2020)

Within this work, we will discuss our recent and promising advances in the development of machine learning assisted optimization schemes for plasmonic/photonic meta-structures design development. We will showcase that by coupling adversarial autoencoding network with topology optimization, it is possible to expand conventional meta-device design methodology to a global optimization space. In the second part of the talk, we will cover our recent effort on coupling machine learning classification/regression algorithms with quantum measurements. Particularly, we will show that the synergy between advanced machine learning assisted data analysis with quantum optical measurements dramatically reduces data collection time as well as increases the accuracy of the measurements.
The Coronavirus Nucleocapsid Protein Is Dynamically Associated with the Replication-Transcription Complexes (2010)

The coronavirus nucleocapsid (N) protein is a virion structural protein. It also functions, however, in an unknown way in viral replication and localizes to the viral replication-transcription complexes (RTCs). Here we investigated, using recombinant murine coronaviruses expressing green fluorescent protein (GFP)-tagged versions of the N protein, the dynamics of its interactions with the RTCs and the domain(s) involved. Using fluorescent recovery after photobleaching, we showed that the N protein, unlike the nonstructural protein 2, is dynamically associated with the RTCs. Recruitment of the N protein to the RTCs requires the C-terminal N2b domain, which interacts with other N proteins in an RNA-independent manner.
Multi-Plane Image Video Compression (2020)

Multiplane Images (MPI) is a new approach for storing volumetric content. MPI represents a 3D scene within a view frustum with typically 32 planes of texture and transparency information per camera. MPI literature to date has been focused on still images but applying MPI to video will require substantial compression in order to be viable for real world productions. In this paper, we describe several techniques for compressing MPI video sequences by reducing pixel rate while maintaining acceptable visual quality. We focus on using traditional video compression codecs such as HEVC. While certainly a new codec algorithm specifically tailored to MPI would likely achieve very good results, no such devices exist today that support this hypothetical MPI codec. By comparison, hundreds of millions of real-time HEVC decoders are present in laptops and TVs today.
An antagonist of retinoic acid receptors more effectively inhibits growth of human prostate cancer cells than normal prostate epithelium (2004)

Screening of synthetic retinoids for activity against prostate carcinoma cell lines has identified antagonists of retinoic acid receptors (RARs) as potent growth inhibitors (Hammond et al, 2001, Br J Cancer 85, 453–462). Here we report that 5 days of exposure to a high-affinity pan-RAR antagonist (AGN194310) abolished growth of prostate carcinoma cells from 14 out of 14 patients, with half-maximal inhibition between 200 and 800 nM. It had similar effects (at ∼250 nM) on the prostate carcinoma lines LNCaP, DU-145 and PC-3. AGN194310 inhibited the growth of normal prostate epithelium cells less potently, by 50% at ∼1 μ M. The growth of tumour cells was also inhibited more than that of normal cells when RARβ together with RARγ, but not RARα alone, were antagonised. Treatment of LNCaP cells with AGN194310 arrested them in G1 of cell cycle within 12 h, with an accompanying rise in the level of p21waf1. The cells underwent apoptosis within 3 days, as indicated by mitochondrial depolarisation, Annexin V binding and DNA fragmentation. Apoptosis was caspase-independent: caspases were neither cleaved nor activated, and DNA fragmentation was unaffected by the pan-caspase inhibitor Z-VAD-FMK. The ability of AGN 194310 to induce apoptosis of prostate cancer cells and its differential effect on malignant and normal prostate epithelial cells suggests that this compound may be useful in the treatment of prostate cancer.
Channel Capacity Under Sub-Nyquist Nonuniform Sampling (2014)

This paper investigates the effect of sub-Nyquist sampling upon the capacity of an analog channel. The channel is assumed to be a linear time-invariant Gaussian channel, where perfect channel knowledge is available at both the transmitter and the receiver. We consider a general class of right-invertible time-preserving sampling methods which includes irregular nonuniform sampling, and characterize in closed form the channel capacity achievable by this class of sampling methods, under a sampling rate and power constraint. Our results indicate that the optimal sampling structures extract out the set of frequencies that exhibits the highest signal-to-noise ratio among all spectral sets of measure equal to the sampling rate. This can be attained through filterbank sampling with uniform sampling grid employed at each branch with possibly different rates, or through a single branch of modulation and filtering followed by uniform sampling. These results reveal that for a large class of channels, employing irregular nonuniform sampling sets, while are typically complicated to realize in practice, does not provide capacity gain over uniform sampling sets with appropriate preprocessing. Our findings demonstrate that aliasing or scrambling of spectral components does not provide capacity gain in this scenario, which is in contrast to the benefits obtained from random mixing in spectrum-blind compressive sampling schemes.
Machine Learning-based Prediction Models for Diagnosis and Prognosis in Inflammatory Bowel Diseases: A Systematic Review (2021)

Machine learning-based prediction models based on routinely collected data generally perform better than traditional statistical models in risk prediction in IBD, though frequently have high risk of bias. Future studies examining these approaches are warranted, with special focus on external validation and clinical applicability.
Isolation of an active-site peptide of lipoprotein lipase from bovine milk and determination of its amino acid sequence. (1986)

Lipoprotein lipase from bovine milk reacted stoichiometrically with diisopropylphosphorofluoridate (DFP), an inactivator of serine esterases, resulting in the loss of enzymatic activity against triacylglycerols.The reaction obeyed first-order kinetics with a rate constant of 0.69 h-'.In order to isolate the peptide containing the diisopropylphosphoryl moiety (DIP), partially purified lipoprotein lipase was covalently labeled with [3H]DFP, and the labeled protein was reduced, carboxymethylated, and further purified to about 90% homogeneity.Cyanogen bromide cleavage followed by gel filtration yielded a radioactive peptide of 6-8 kDa.This peptide was succinylated and then digested with Staphylococcus aureus Vs proteinase.From this digest, a peptide containing 0.95 mol of rSH] DIP/mol of peptide was isolated by gel-permeation chromatography followed by reverse-phase high performance liquid chromatography.Automated Edman degradation provided the following sequence: Ala-Ile-Gly-Ile-His-Trp-Gly-Gly-(DIP)Ser-Pro-Asn-Gln-Lys-Asn-Gly-Ala-Val-Phe-Ile-Asn-(Ser,Leu)-Glu.Analysis of the sequence for secondary structure suggests that the reactive serine of lipoprotein lipase is in a &turn, a structure similar to those of the active sites of most other serine proteinases.Lipoprotein lipase appears to share this secondary structure with other serine hydrolases despite significant differences in the primary structure of this domain.Lipoprotein lipase (EC 3.1.1.34)plays a central role in the regulation of lipid metabolism (1,2).Although the physiological functions of lipoprotein lipase are well established, its amino acid sequence, molecular properties, and catalytic mechanism are still not well defined.Earlier work using lipoprotein lipase from bovine milk (3) and rat heart (4) indicated that this enzyme can be inactivated by phenylmethanesulfonyl fluoride, diisopropylphosphorofluoridate (DFP'), and diethyl p-nitrophenyl phosphate (paraoxon).
U nderstanding the fluid dynamics associated with macro scale ultrasonic separators (2015)

Acoustic standing wave fields are widely used in MEMS applications to separate micron sized particles from fluids. However, the use and understanding of macro scale ultrasonic separators are still limited and challenging. These systems rely on acoustic radiation forces for trapping and clumping of dispersed phase particles. The clumps of particles then continuously separate out due to enhanced gravity or buoyancy in a flowing system. Typical flow Reynolds numbers are less than 50, particle concentrations up to 20%, ultrasonic standing wave fields at frequencies of 2 MHz, and acoustic pressure amplitudes of about 1 MPa. At such small Reynolds numbers, the flow is dominated by shear forces and the drag on clumps of particles is significantly lower than Stokes drag on a single particle. The fluid dynamics associated with these systems is extremely complex due to the coupling between the fluid flow field, suspended particles, and acoustic radiation forces. This work discusses the key physics involved and explains our current understanding of operation of macro scale acoustic separators. The status of CFD efforts to predict the flow fields and particle clumping in such systems is presented and compared to experimental results.
p-Coumaroylnoradrenaline, a Novel Plant Metabolite Implicated in Tomato Defense against Pathogens (2003)

The Avr9 peptide elicitor from the fungus Cladosporium fulvum, the bacterial pathogen Pseudomonas syringae pathovar tomato carrying the avirulence gene avrPto (Pst (avrPto)), and the organophosphorous insecticide fenitrothion induce resistance-related responses in tomato lines carrying the Cf-9, Pto, and Fen genes, respectively. These responses were associated with synthesis of p-coumaroyloctopamine and p-coumaroylnoradrenaline, a novel compound for plants. In susceptible near isogenic tomato lines (Cf-0, pto, fen) and wounded tomato leaves, the levels of these compounds were reduced or undetectable. The elevated levels of p-coumaroyloctopamine and p-coumaroylnoradrenaline were accompanied by elevated mRNA levels of genes encoding phenylalanine ammonia lyase, p-coumarate CoA ligase, and hydroxycinnamoyl-CoA:tyramine N-(hydroxycinnamoyl)transferase (THT), enzymes that are involved in the hydroxycinnamic acid amide biosynthesis. Southern hybridization indicated that THT is encoded by a multigene family in tomato. Four different THT full-length cDNAs were derived by reverse transcriptase-PCR using degenerate primers based on potato and tobacco THT sequences. Transcripts for all four homologs were present in unchallenged tomato leaves, but only tomTHT1-3 was highly expressed following challenge with Pst (avrPto). Furthermore, tomTHT1-3 showed a more substantial and rapid induction in the incompatible interaction than in the compatible interaction. The cDNAs tomTHT1-3, tomTHT7-1, and tomTHT7-8 encoded proteins with a high degree of amino acid sequence homology, although the recombinant proteins had different preferences for octopamine and noradrenaline. The fourth cDNA, tomTHT1-4, directed synthesis of a truncated enzymatically inactive protein due to the presence of a premature stop codon.
High Intracellular Seed Train BiP Levels Correlate With Poor Production Culture Performance in CHO Cells (2018)

Consistent cell culture performance is a prerequisite to ensure product quality consistency and achieve productivity goals for the manufacture of recombinant protein therapeutics, including monoclonal antibodies. Here a peculiar observation is reported where high levels of intracellular BiP in seed train cultures are consistently predictive of poor cell culture performance in the subsequent inoculum and production cultures for a monoclonal antibody produced in CHO cells. This investigation suggests that in this cell line the high intracellular BiP levels in the seed train are triggered by a slightly lower culture pH, which interferes with proper antibody folding and secretion. While the seed train culture does not display any obvious signs of the problem at slightly lower culture pH, inoculum trains, and production cultures sourced from these low pH seed trains display significantly lower cell growth and cell size. High intracellular BiP levels may interfere with UPR signaling, thereby hampering a proper and timely UPR response in the production media. Studies of other problematic cell lines have shown a similar correlation between intracellular BiP accumulation and poor production performance. The authors believe intracellular BiP levels in seed train should hence be low in order to increase the success rate in production.
Fabrication of non-biofouling polyethylene glycol micro- and nanochannels by ultraviolet-assisted irreversible sealing (2006)

We present a simple and widely applicable method to fabricate micro- and nanochannels comprised entirely of crosslinked polyethylene glycol (PEG) by using UV-assisted irreversible sealing to bond partially crosslinked PEG surfaces. The method developed here can be used to form channels as small as approximately 50 nm in diameter without using a sophisticated experimental setup. The manufactured channel is a homogeneous conduit made completely from non-biofouling PEG, exhibits robust sealing with minimal swelling and can be used without additional surface modification chemistries, thus significantly enhancing reliability and durability of microfluidic devices. Furthermore, we demonstrate simple analytical assays using PEG microchannels combined with patterned arrays of supported lipid bilayers (SLBs) to detect ligand (biotin)-receptor (streptavidin) interactions.
Coin-based Secure Computations (2022)

Abstract In the history of cryptography, many cryptographic protocols have relied on random coin tosses to prove their security. Although flipping coins is indispensable in this manner, the coins themselves have never been in the spotlight. Therefore, we would like to make physical coins rise to the level of cryptography, just as a deck of physical playing cards has been used to perform a secure multi-party computation. Such a card-based protocol is known to be helpful both to perform a secure computation without any black-box computers and to understand the principles of secure protocols. In this paper, we propose a new framework of secure multi-party computation using physical coins, named a coin-based protocol . One advantage of the use of coins is that they are more ubiquitous than cards. Whereas a face-down card can conceal the information about its face side, one side of a coin reveals the information of its other side. Hence, more careful design is required for a secure coin-based protocol than for a card-based one. We formalize a computational model of the coin-based protocol and explicitly give protocols for NOT, AND, COPY, OR, and XOR computations. We also discuss the composability of the extended protocols and how to implement them in practice.