gebhart/patrepeval huggingface dataset:
Protein‐Based Encapsulation Strategies: Toward Micro‐ and Nanoscale Carriers with Increased Functionality (2022)

Proteins and peptides are attractive chemical building blocks to encapsulate and protect active substances thanks to their biocompatibility, biodegradability, low immunogenicity, and added functionality compared to synthetic polymers. This review provides a comprehensive overview of micro- and nanocapsules predominantly made of proteins-both natural and artificially produced-and peptides, detailing their different fabrication techniques and possible applications in various fields, including food technology and healthcare. Emphasis is given on the capability of proteins and peptides to assemble into capsular structures in the absence (e.g., protein cages and polypeptide-based coacervates) or presence of a template, as well as on the physical nature of the carriers core, i.e., gaseous, liquid, or solid.
MMIC Vector Topology Enabling Multi RF Functionalities for 5G and Beyond (2021)

This paper presents a vector topology of a monolithic microwave integrated circuit (MMIC) capable of performing several radiofrequency (RF) functionalities essential for future wireless communications and geolocation in the millimeter frequency band. The proposed circuit can address several usage modes such as conventional frequency heterodyning for high-speed IQ modulation and demodulation. In addition, the device can be configured in six-port quadratic detection mode to achieve optimum power added efficiency (PAE). The topology developed in 65 nm FDSOI CMOS technology achieves broadband V-band frequency operation and combines vector precision for both high data rates and phase state determination. The results presented concern QPSK modulation schemes at data rates up to 4 Gbps as well as essential geolocation metrics such as time domain of arrival (TDoA) and angle of arrival (AoA). The combination of vector accuracy/PAE together with wide linear operating range makes this topology a viable candidate for next generation radio frequency systems.
Eat Dirt — The Hygiene Hypothesis and Allergic Diseases (2002)

There has been an epidemic of both autoimmune diseases (in which the immune response is dominated by type 1 helper T [Th1] cells, such as type 1 diabetes, Crohn's disease, and multiple sclerosis) and allergic diseases (in which the immune response is dominated by type 2 helper T [Th2] cells, such as asthma, allergic rhinitis, and atopic dermatitis), as documented in the article by Bach in this issue of the Journal. 1 The occurrence of these diseases is higher in more affluent, Western, industrialized countries. One theory proposed to explain this increase in the prevalence of autoimmune and allergic diseases is . . .
Real-Time Measurements of Cell Proliferation Using a Lab-on-CMOS Capacitance Sensor Array (2018)

We describe a capacitance sensor array that has been incorporated into a lab-on-CMOS system for applications in monitoring cell viability. This paper presents analytical models, calibration results, and measured experimental results of the biosensor. The sensor has been characterized and exhibits a sensitivity of 590 kHz/fF. We report results from benchtop tests and in vitro experiments demonstrating on-chip tracking of cell adhesion as well as monitoring of cell viability. Human ovarian cancer cells were cultured on chip, and measured capacitance responses were validated by comparison with images from photomicrographs of the chip surface. Analysis was performed to quantify cell proliferation and adhesion, and responses to live cells were estimated to be 100 aF/cell.
A combination of plasma phospholipid fatty acids and its association with incidence of type 2 diabetes: The EPIC-InterAct case-cohort study (2017)

A combination of individual fatty acids, characterised by high concentrations of linoleic acid, odd-chain fatty acids, and very long-chain fatty acids, was associated with lower incidence of T2D. The specific fatty acid pattern may be influenced by metabolic, genetic, and dietary factors.
Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing (2021)

Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. Using a combination of RNA sequencing and DNA affinity purification sequencing, we performed a global survey of the N. crassa sulfur starvation response and the role of CYS-3 in regulating sulfur-responsive genes. The CYS-3 transcription factor bound the promoters and regulated genes involved in sulfur metabolism. Additionally, CYS-3 directly activated the expression of a number of uncharacterized transporter genes, suggesting that regulation of sulfur import is an important aspect of regulation by CYS-3. CYS-3 also directly regulated the expression of genes involved in mitochondrial electron transfer. During sulfur starvation, genes involved in nitrogen metabolism, such as amino acid and nucleic acid metabolic pathways, along with genes encoding proteases and nucleases that are necessary for scavenging nitrogen, were activated. Sulfur starvation also caused changes in the expression of genes involved in carbohydrate metabolism, such as those encoding glycosyl hydrolases. Thus, our data suggest a connection between sulfur metabolism and other aspects of cellular metabolism. <b>IMPORTANCE</b> Identification of nutrients present in the environment is a challenge common to all organisms. Sulfur is an important nutrient source found in proteins, lipids, and electron carriers that are required for the survival of filamentous fungi such as Neurospora crassa. Here, we transcriptionally profiled the response of N. crassa to characterize the global response to sulfur starvation. We also used DNA affinity purification sequencing to identify the direct downstream targets of the transcription factor responsible for regulating genes involved in sulfur uptake and assimilation. Along with genes involved in sulfur metabolism, this transcription factor regulated a number of uncharacterized transporter genes and genes involved in mitochondrial electron transfer. Our data also suggest a connection between sulfur, nitrogen, and carbon metabolism, indicating that the regulation of a number of metabolic pathways is intertwined.
Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis (2017)

The crystal structure of the large terminase from the Geobacillus stearothermophilus bacteriophage D6E shows a unique relative orientation of the N-terminal adenosine triphosphatase (ATPase) and C-terminal nuclease domains. This monomeric 'initiation' state with the two domains 'locked' together is stabilized via a conserved C-terminal arm, which may interact with the portal protein during motor assembly, as predicted for several bacteriophages. Further work supports the formation of an active oligomeric state: (i) AUC data demonstrate the presence of oligomers; (ii) mutational analysis reveals a trans-arginine finger, R158, indispensable for ATP hydrolysis; (iii) the location of this arginine is conserved with the HerA/FtsK ATPase superfamily; (iv) a molecular docking model of the pentamer is compatible with the location of the identified arginine finger. However, this pentameric model is structurally incompatible with the monomeric 'initiation' state and is supported by the observed increase in kcat of ATP hydrolysis, from 7.8 ± 0.1 min-1 to 457.7 ± 9.2 min-1 upon removal of the C-terminal nuclease domain. Taken together, these structural, biophysical and biochemical data suggest a model where transition from the 'initiation' state into a catalytically competent pentameric state, is accompanied by substantial domain rearrangements, triggered by the removal of the C-terminal arm from the ATPase active site.
iNetModels 2.0: an interactive visualization and database of multi-omics data (2021)

It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.
Towards a Comprehensive Understanding and Accurate Evaluation of Societal Biases in Pre-Trained Transformers (2021)

Andrew Silva, Pradyumna Tambwekar, Matthew Gombolay. Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2021.
Stability of Thin Resist Walls (1992)

The physical strength of poly (methyl methacrylate) (PMMA) resist is an important factor for making very dense patterns with most types of lithography. For lines placed closely together using the lift‐off technique, a thin wall of PMMA remains to act as the metal line spacer. When placed in contact with a suitable developer, thin polymer walls may swell and buckle, depending on the desired aspect ratio of the thin walls. We use electron beam lithography and a high‐contrast developer solution to study the relationship of the maximum height‐to‐width ratio of the PMMA walls necessary to avoid buckling, and the resulting effects on metal thickness after lift‐off. Maximum achievable aspect‐ratios for our developer system were found to be constant (nearly 5:1) for widths from 20 to 45 nm and lengths of tens of microns. Theoretical predictions based on the hypothesis of a swelling‐induced elastic instability are in excellent agreement with the experiments.
The Business Case for Green Chemistry in Drug Discovery (2015)

The global pharmaceutical industry is widely viewed as inefficient and unable to provide medicines for the entire global population. Greening the pharmaceutical industry is important for attaining sustainability and assuring the wide availability of new medicines essential for human health. Green chemistry techniques that are environmentally friendly and reduce cost are important. Additional approaches that improve the efficiency of drug discovery are also green, by virtue of improving the business efficiency of the industry as a whole. These approaches include in silico techniques for improving the success rate of drugs in development. New synthetic methodologies that reduce the cost of drug synthesis, improve access to drug candidate molecules, and introduce important structural diversity into drug discovery also meet green criteria. Drug targeting of the active site is important for improving success rates for drugs in development and minimizing the effective doses of drugs. Reverse pharmacology, based on traditional knowledge, is a strikingly different approach to drug discovery. Reverse pharmacology can also be very efficient and effective for discovering new medicines.
On the Impact of Energy-Accuracy Tradeoff in a Digital Cellular Neural Network for Image Processing (2015)

This paper studies the opportunities of energy-accuracy tradeoff in cellular neural network (CNN). Algorithmic characteristics of CNN is coupled with hardware-induced error distribution of a digital CNN cell to evaluate energy-accuracy tradeoff for simple image processing tasks as well as a complex application. The analysis shows that errors modulate the cell dynamics and propagate through the network degrading the output quality and increasing the convergence time. The error propagation is determined by the task being performed by the CNN, specifically, the strength of the feedback template. Controlling precision is observed to be a more effective approach for energy-accuracy tradeoff in CNN than voltage over scaling.
Two Stage Estimation for the Echo Paths in Stereophonic Acoustic Echo Cancellation (2006)

A novel algorithm is introduced for estimating the echo path responses for stereophonic acoustic echo cancellation. When the Wiener solution for the echo path responses is non-unique, the echo paths are estimated in two stages. In a first stage, one of the non-unique Wiener solutions is estimated. Then in a second stage, a disturbance is introduced and the left and right misalignment vectors can be formulated as the Wiener solution with respect to the residual signals appearing after adding the disturbance. The aim is to take advantage of the knowledge about the specific disturbance which is introduced. Adaptive algorithms based on this two stage idea are used. It is shown with a series of numerical simulations that the proposed algorithm converges much faster than a corresponding conventional one stage adaptive algorithm.
Flexible Organic Tribotronic Transistor for Pressure and Magnetic Sensing (2017)

Flexible electronics has attracted enormous interest in wearable electronics and human-machine interfacing. Here, a flexible organic tribotronic transistor (FOTT) without a top gate electrode has been demonstrated. The FOTT is fabricated on a flexible polyethylene terephthalate film using the p-type pentacene and poly(methyl methacrylate)/Cytop composites as the conductive channel and dielectric layer, respectively. The charge carriers can be modulated by the contact electrification between the dielectric layer and a mobile triboelectric layer. Based on the fabricated FOTT, pressure and magnetic sensors have been developed, respectively, that exhibit great sensitivity, fast response time, and excellent stability. The FOTT in this simple structure shows bright potentials of tribotronics in human-machine interaction, electronic skins, wearable electronics, intelligent sensing, and so on.
Short communication: Volatiles in microfluidized raw and heat-treated milk (2019)

As innovative processing equipment is introduced to milk processing, it is essential to determine its effect on milk aroma, a critical factor in consumer acceptance of the final dairy product. Microfluidization is known to cause severe high-pressure homogenization of milk fat and, although severe processing is known to release undesired aromas, no information is available on the levels of the volatile compounds in milk immediately after microfluidization. We hypothesized that microfluidization would alter levels of volatile compounds in milk that may affect aroma. The concentration of 11 selected volatile compounds in raw, thermized, pasteurized, and UHT 3.0% fat milk samples were compared before and after microfluidization at 170 MPa and common 2-stage homogenization at 15 MPa. Overall, the different milk samples had similar trends in response to homogenization, although UHT milk started with lower values of nonanoic acid, and acetone and higher levels of hexanal and heptanol. In many cases, microfluidization did not significantly alter volatile levels compared with the starting milk. Heptanal was the only compound observed to increase in thermized and UHT milk, whereas nonanoic acid and acetone decreased in raw, thermized, and pasteurized milks and octanoic acid decreased in thermized and UHT milks. The highest levels of almost all of the volatiles were found in the 2-stage homogenized milk. Overall, microfluidization had minimal effect on the volatile compound profiles of milk, although sensory evaluation is needed to confirm effects on aroma and flavor.
A dendritic β-galactosidase-responsive folate–monomethylauristatin E conjugate (2015)

We report the study of a new drug delivery system programmed for the selective internalisation and the subsequent enzyme-catalysed release of two monomethylauristatin E molecules inside FR-positive cancer cells. This targeting device is the most potent β-galactosidase-responsive folate-drug conjugate developed so far, killing cancer cells expressing a medium level of FR at low nanomolar concentrations.
Dispersion-Engineered Silicon Nitride Supercontinuum for Frequency Comb Metrology at the 10−15 Level (2017)

Supercontinuum generation in dispersion engineered silicon nitride waveguides is used to perform frequency comb metrology by measuring the relative stability of two cavity-referenced optical clock lasers at 3.8×10-15 at τ = 2 seconds.
The Uses of Green Fluorescent Protein in Prokaryotes (2005)

This chapter contains sections titled: Introduction Bacterial Development and Cell Biology Bacteria in Complex Environments Green Fluorescent Protein as a Genetic Tool Perspectives Acknowledgments References
Apoptosis in Parthenogenetic Preimplantation Porcine Embryos1 (2004)

Parthenogenesis (PA) of the oocyte is essential to a number of oocyte- or embryo-related technologies such as intracytoplasmic sperm injection and cloning by nuclear transfer. This study investigated the onset and frequency of apoptosis in PA- porcine embryos and the morphological changes that conform to the general criteria of apoptotic cell death by using a terminal deoxynucleatidyl transferase-mediated deoxyuridine 5-triphosphate nick-end labeling (TUNEL) assay. PA embryos had a higher degree of apoptotic cell death during in vitro culture, a lower cleavage rate (45% vs. 71%), and a lower development rate to the blastocyst stage (16% vs. 29%), relative to in vitro fertilization (IVF). The earliest positive TUNEL signal in the PA embryos was detected on Day 6, 1 day later than that in IVF embryos. Apoptosis in PA embryos increased from 15% of the embryos on Day 6 to 29% on Day 8. The mean level of apoptosis of the PA embryos was statistically higher than that of IVF embryos, except on Day 5. In particular, apoptosis in PA embryos was twice that of IVF embryos on Day 6 (15% vs. 6.7%) and Day 8 (29% vs. 13%). The mean cell number in PA blastocysts was significantly lower than that of IVF blastocysts, whereas the percentage of apoptosis in PA blastocysts was significantly higher than that of IVF blastocysts. There was a high percentage of haploid (62.5%) PA blastocysts. The ploidy may contribute to a high level of apoptosis. These results may help to explain the mechanism of parthenogenetic developmental failure and may lead to methods that will improve parthenogenetic development.
Photochemistry of 2-(N-Acyl-N-alkylamino)cyclohex-2-enones : Formation of Spiro-β-lactams(Organic,Chemical) (1986)

La photoirradiation des composes du titre conduit aux N-alkyl aza-1spiro [3.5] nonanediones-2,5 substituees en 3(A); reaction identique a partir de [N-benzyl N-methylthioacetyl amino]-2 cyclopentene-2one. Etude RX du derive N-benzyl methylthio-3 de A
Supplemental Figure 5 from Mast Cell–Derived Prostaglandin D&lt;sub&gt;2&lt;/sub&gt; Inhibits Colitis and Colitis-Associated Colon Cancer in Mice (2023)

&lt;p&gt;Supplemental Figure&lt;/p&gt;
Data-driven foot-based intonation generator for text-to-speech synthesis (2015)

We propose a method for generating F0 contours for text-tospeech synthesis. Training speech is automatically annotated in terms of feet, with features indicating start and end times of syllables, foot position, and foot length. During training, we fit a foot-based superpositional intonation model comprising accent curves and phrase curves. During synthesis, the method searches for stored, fitted accent curves associated with feet that optimally match to-be-synthesized feet in the feature space, while minimizing differences between successive accent curve heights. We tested the proposed method against the HMMbased Speech Synthesis System (HTS) by imposing contours generated by these two methods onto natural speech, and obtaining quality ratings. Test sets varied in how well they were covered by the training data. Contours generated by the proposed method were preferred over HTS-generated contours, especially for poorly-covered test items. To test the new method’s usefulness for processing marked-up text input, we compared its ability to convey contrastive stress with that of natural speech recordings, and found no difference. We conclude that the new method holds promise for generating comparatively highquality F0 contours, especially when training data are sparse and when mark-up is required.
User Collision for Joint Utilization of Electromagnetic Frequency Band: Frequency Allocation, Interference Reduction and Security Threat Mitigation in Radio Propagation and Remote Sensing (2002)

The user community of electromagnetic frequency bands within the ULF to FUV bands is rapidly increasing; and the electromagnetic spectrum is being overtaxed in providing required band allocations, resulting in direct confrontations between the active and the passive user groups. The active user group includes the entire terrestrial-space & mobile tele/video-communications industry, tele-navigation, the military and active remote sensing communities, whose interests among themselves are colliding increasingly, requiring introduction of RFI reduction. An introduction to these highly important aspects of securing our capabilities in terrestrial space-tele/video-communications & navigation as well as in military surveillance and environmental stress change monitoring at ground, from air and space is given.
Normalisation of Test Results in Air Screw Compressor Measurements as a Basis for Performance Estimation of Refrigeration and Process Gas Compressors (2011)

Common use of screw compressors is in compression of air. However, application of screw compressors in refrigeration and air conditioning, as well as in process gas compression is increasing rapidly in recent years. The existing experimental data basis for air compressors may conveniently serve as a source for performance estimation of these compressors. A procedure was derived in this work to find scale factors which connect compressors operating with different fluids and it was applied for performance estimation of refrigeration and process gas screw compressors on the basis of measurements obtained for air compressors. Refprop 8 by NIST was used for calculation of thermodynamic properties of real fluids and ideal gas relation was used for air.