gebhart/patrepeval huggingface dataset:
Mycotoxins in Conversation With Bacteria and Fungi (2019)

An important goal of the mycotoxin research community is to develop comprehensive strategies for mycotoxin control and detoxification. Although significant progress has been made in devising such strategies, yet, there are barriers to overcome and gaps to fill in order to design effective mycotoxin management techniques. This is in part due to a lack of understanding of why fungi produce these toxic metabolites. Here we present cumulative evidence from the literature that indicates an important ecological role for mycotoxins, with particular focus on <i>Fusarium</i> mycotoxins. Further, we suggest that understanding how mycotoxin levels are regulated by microbial encounters can offer novel insights for mycotoxin control in food and feed. Microbial degradation of mycotoxins provides a wealth of chemical information that can be harnessed for large-scale mycotoxin detoxification efforts.
Part I: High-Voltage MOS Device Design for Improved Static and RF Performance (2015)

In this paper, for the first time, the key design parameters of a shallow trench isolation-based drain-extended MOS transistor are discussed for RF power applications in advanced CMOS technologies. The tradeoff between various dc and RF figures of merit (FoMs) is carefully studied using well-calibrated TCAD simulations. This detailed physical insight is used to optimize the dc and RF behavior, and our work also provides a design window for the improvement of dc as well as RF FoMs, without affecting the breakdown voltage. An improvement of 50% in RON and 45% in RF gain is achieved at 1 GHz. Large-signal time-domain analysis is done to explore the output power capability of the device.
Adjusting the Distance of Electrochemical Microsensors from Secreting Cell Monolayers on the Micrometer Scale Using Impedance (1999)

There are emerging applications of electrochemical microsensors where the distance of the sensor from an insulating plane needs to be adjusted and/or accurately known. The plane may be merely an obstruction or the source of a species whose release rate needs to be measured. An example is in cell secretion studies where a monolayer of cells is stimulated to secrete ions and/or other biochemical species which then diffuse away from the cells while being measured by a microsensor. Sensor response will thus depend on both the rate of release and the distance of the sensor from the cells. To obtain accurate release rates, the precision of the scheme to control electrode distance from the monolayer needs to be on the micrometer scale for species with ionic diffusivities. Optical (stereomicroscope and microruler) and mechanical (precalibrated micrometer screw) methods to precisely position the electrode are difficult to use under realistic circumstances (due to opaqueness of the chamber, and/or the medium, or irreproducible chamber depth). In this work we propose to correlate electrochemical cell impedance with sensor distance. This scheme has been used to adjust the distance of a chloride (tip diameter ∼250 μm) and a potassium (tip diameter ∼1000 μm) ion-selective microelectrode in the 0−250− and 0−2500-μm range, respectively, from a planar obstruction as well as from a monolayer of cells with a best precision of ±5 μm (n = 6) for the chloride and about ±20 μm for the potassium sensor. Larger electrodes have a broader range of distances over which they are sensitive, albeit with a poorer spatial resolution. This was verified by using Ag disk electrodes of 250 and 500 μm in diameters in AgNO3 solution.
Novel hepatotoxicity biomarkers of extracellular vesicle (EV)-associated miRNAs induced by CCl4 (2020)

Recent findings have revealed that extracellular vesicles (EVs) are secreted from cells and circulate in the blood. EVs are classified as exosomes (40-100 nm), microvesicles (50-1,000 nm) or apoptotic bodies (500-2,000 nm). EVs contain mRNAs, microRNAs, and DNAs and have the ability to transfer them from cell to cell. Recently, especially in humans, the diagnostic accuracy of tumor cell type-specific EV-associated miRNAs as biomarkers has been found to be more than 90 %. In addition, microRNAs contained in EVs in blood are being identified as specific biomarkers of chemical-induced inflammation and organ damage. Therefore, microRNAs contained in the EVs released into the blood from tissues and organs in response to adverse events such as exposure to chemical substances and drugs are expected to be useful as novel biomarkers for toxicity assessment. In this study, C57BL/6 J male mice orally dosed with carbon tetrachloride (CCl4) were used as a hepatotoxicity animal model. Here, we report that not only the known hepatotoxicity biomarkers miR-122 and miR-192 but also 42 novel EV-associated biomarkers were upregulated in mice dosed with CCl4. Some of these novel biomarkers may be expected to be able to use for better understanding the mechanism of toxicity. These results suggest that our newly developed protocol using EV-associated miRNAs as a biomarker would accelerate the rapid evaluation of toxicity caused by chemical substances and/or drugs.
Separating Skills and Concepts for Novel Visual Question Answering (2021)

Generalization to out-of-distribution data has been a problem for Visual Question Answering (VQA) models. To measure generalization to novel questions, we propose to separate them into "skills" and "concepts". "Skills" are visual tasks, such as counting or attribute recognition, and are applied to "concepts" mentioned in the question, such as objects and people. VQA methods should be able to compose skills and concepts in novel ways, regardless of whether the specific composition has been seen in training, yet we demonstrate that existing models have much to improve upon towards handling new compositions. We present a novel method for learning to compose skills and concepts that separates these two factors implicitly within a model by learning grounded concept representations and disentangling the encoding of skills from that of concepts. We enforce these properties with a novel contrastive learning procedure that does not rely on external annotations and can be learned from unlabeled image-question pairs. Experiments demonstrate the effectiveness of our approach for improving compositional and grounding performance.
Molecular and supramolecular chirality in gemini‐tartrate amphiphiles studied by electronic and vibrational circular dichroisms (2009)

This contribution presents an application of electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) to study the molecular and supramolecular chirality in assemblies of gemini-tartrate amphiphiles. Nonchiral dicationic n-2-n amphiphiles (n = 14-20) can self-organize into right- or left-handed structures upon interacting with chiral tartrate counterions. Micellar solutions can also be obtained for shorter alkyl chains (n = 12). First, the conformation of tartrate counterions has been investigated in various environments (micellar solutions and chiral ribbons). ECD and VCD spectra recorded in micellar solutions are independent from the solvent and from the nature of the cations (sodium, cetyl-trimethylammonium, or dimeric surfactant 12-2-12) used and are representative of the anticonformation of the tartrate dianions. On the other hand, drastic changes in the ECD and VCD spectra have been observed in multilayered chiral assemblies of 16-2-16 tartrate. These strong spectral modifications are associated with the chiral arrangement of the tartrate molecules at the surface of the bilayers. Moreover, chirality transfer from counterions to achiral amphiphiles has been clearly evidenced by VCD since circular dichroism has been observed on vibrations related to alkyl chains and gemini headgroups. Finally, ECD and VCD experiments were performed varying the enantiomeric excess of the tartrate. The ECD and VCD intensities do not vary linearly with the enantiomeric excess of the anion and different behaviors have been observed from the two spectroscopic methods: ECD intensities are correlated to the pitch of the ribbons, whereas the VCD intensities are correlated to the dimension of the chiral ribbons.
Interaction of Center Pivot Irrigation and Electrical Transmission (1980)

ABSTRACT CROSSING of irrigated or potentially irrigable land by electrical transmission right-of-way (R-O-W) presents a situation where conflict in land use may arise. This paper quantifies some of the factors involved in this interaction. Theoretical R-O-Ws crossing a quarter-section of irrigated land at various orientations are studied. The interaction is measured in terms of area lost from production, changes in cost of irrigating and changes in expected income. Safety considerations con-cerning irrigation/transmission interaction are discuss-ed.
Adaptive laboratory evolution of Escherichia coli under acid stress (2019)

The ability of <i>Escherichia coli</i> to tolerate acid stress is important for its survival and colonization in the human digestive tract. Here, we performed adaptive laboratory evolution of the laboratory strain <i>E. coli</i> K-12 MG1655 at pH 5.5 in glucose minimal medium. After 800 generations, six independent populations under evolution had reached 18.0 % higher growth rates than their starting strain at pH 5.5, while maintaining comparable growth rates to the starting strain at pH 7. We characterized the evolved strains and found that: (1) whole genome sequencing of isolated clones from each evolved population revealed mutations in <i>rpoC</i> appearing in five of six sequenced clones; and (2) gene expression profiles revealed different strategies to mitigate acid stress, which are related to amino acid metabolism and energy production and conversion. Thus, a combination of adaptive laboratory evolution, genome resequencing and expression profiling revealed, on a genome scale, the strategies that <i>E. coli</i> uses to mitigate acid stress.
New Synthesis of 1,3‐Dihydro‐1,4‐benzodiazepin‐2(2H)‐ones and 3‐Amino‐1,3‐dihydro‐1,4‐benzodiazepin‐2(2H)‐ones: Pd‐Catalyzed Cross‐Coupling of Imidoyl Chlorides with Organoboronic Acids. (2003)

A new approach to the synthesis of 1,4-benzodiazepines and 3-amino-1,4-benzodiazepines, which\nemploys the Pd-catalyzed cross-coupling reaction of an imidoyl chloride with an organometallic\nreagent as the key step, is described. A five-step synthesis of a key intermediate is described and\nit is shown that in only four further steps (three couplings and a TFA-mediated BOC-deprotection)\na wide variety of N1-, C3-amino-, C5-carbon-, or nitrogen-substituted 1,4-benzodiazepines can be\nsynthesized.
Strong Functional Representation Lemma and Applications to Coding Theorems (2017)

This paper shows that for any random variables X and Y, it is possible to represent Y as a function of (X, Z) such that Z is independent of X and I(X; Z| Y) ≤ log(I(X; Y)+1)+4. We use this strong functional representation lemma (SFRL) to establish a tighter bound on the rate needed for one-shot exact channel simulation than was previously established by Harsha et. al., and to establish achievability results for one-shot variable-length lossy source coding and multiple description coding. We also show that the SFRL can be used to reduce the channel with state noncausally known at the encoder to a point-to-point channel, which provides a simple achievability proof of the Gelfand-Pinsker theorem. Finally we present an example in which the SFRL inequality is tight to within 5 bits.
A simple permutation-based test of intermodal correspondence (2020)

Abstract Many key findings in neuroimaging studies involve similarities between brain maps, but statistical methods used to measure these findings have varied. Current state-of-the-art methods involve comparing observed group-level brain maps (after averaging intensities at each image location across multiple subjects) against spatial null models of these group-level maps. However, these methods typically make strong and potentially unrealistic statistical assumptions, such as covariance stationarity. To address these issues, in this paper we propose using subject-level data and a classical permutation testing framework to test and assess similarities between brain maps. Our method is comparable to traditional permutation tests in that it involves randomly permuting subjects to generate a null distribution of intermodal correspondence statistics, which we compare to an observed statistic to estimate a p -value. We apply and compare our method in simulated and real neuroimaging data from the Philadelphia Neurodevelopmental Cohort. We show that our method performs well for detecting relationships between modalities known to be strongly related (cortical thickness and sulcal depth), and it is conservative when an association would not be expected (cortical thickness and activation on the n -back working memory task). Notably, our method is the most flexible and reliable for localizing intermodal relationships within subregions of the brain and allows for generalizable statistical inference.
Determining elastic behavior of composites by the boundary element method (1993)

The boundary element method is applied to determine the effective elastic moduli of continuum models of composite materials. In this paper, we specialize to the idealized model of hexagonal arrays of infinitely long, aligned cylinders in a matrix (a model of a fiber-reinforced material) or a thin-plate composite consisting of hexagonal arrays of disks in a matrix. Thus, one need only consider two-dimensional elasticity, i.e., either plane-strain or plane-stress elasticity. This paper examines a variety of cases in which the inclusions are either stiffer or weaker than the matrix for a wide range of inclusion volume fractions φ2. Our comprehensive set of simulation data for the elastic moduli are tabulated. Using the boundary element method, a key microstructural parameter η2 that arises in rigorous three-point bounds on the effective shear modulus is also computed. Our numerical simulations of the elastic moduli for the hexagonal array are compared to rigorous two-point and three-point bounds on the respective effective properties. In the extreme instances of either superrigid particles or voids, we compare analytical relations for the elastic moduli near dilute and close packing limits to our simulation results.
Simultaneous proton magnetic resonance fingerprinting and sodium MRI (2019)

With the proposed approach, we were able to simultaneously acquire sodium density images in addition to proton T<sub>1</sub> , T<sub>2</sub> , and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>B</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup></mml:math> maps as well as proton density images.
Closed-Loop Diesel Combustion Control Leveraging Ignition Assist (2021)

Diesel engines equipped with ignition assisting actuators may improve combustion in aerial powertrains operating at low temperatures and with fuels of varying ignition behavior. Fuel injection timing can be aided by the additional energy from ignition assist (IA) devices such as glow plugs. This work presents a closed-loop control scheme that coordinates start of injection (SOI) and IA power to regulate both mean and cycle-to-cycle variability (CV) in diesel combustion phasing. Engine experiments at a chilled condition demonstrated the IA’s slow dynamics, high sensitivity to engine thermal state, and large nonlinearities in control authority that justify its limited use as a secondary actuator. A low-order model informed by experiments facilitated closed-loop system simulation. Control of mean combustion phasing was achieved using a PI controller for SOI. Reduction and control of CV within acceptable bounds was achieved with mean Kalman filtering of feedback, adaptation of mean phasing using windowed variance estimation from feedback, and conditional IA activation driven by saturation of the mean phasing or SOI values. Simulation results show the controller can track a desired mean setpoint of the start of combustion within 4-6 engine cycles without amplifying closed-loop CV, and can conditionally actuate IA while coordinating with SOI to manage unplanned disturbances in system CV behavior.
Heritable L1 retrotransposition in the mouse primordial germline and early embryo (2017)

LINE-1 (L1) retrotransposons are a noted source of genetic diversity and disease in mammals. To expand its genomic footprint, L1 must mobilize in cells that will contribute their genetic material to subsequent generations. Heritable L1 insertions may therefore arise in germ cells and in pluripotent embryonic cells, prior to germline specification, yet the frequency and predominant developmental timing of such events remain unclear. Here, we applied mouse retrotransposon capture sequencing (mRC-seq) and whole-genome sequencing (WGS) to pedigrees of C57BL/6J animals, and uncovered an L1 insertion rate of ≥1 event per eight births. We traced heritable L1 insertions to pluripotent embryonic cells and, strikingly, to early primordial germ cells (PGCs). New L1 insertions bore structural hallmarks of target-site primed reverse transcription (TPRT) and mobilized efficiently in a cultured cell retrotransposition assay. Together, our results highlight the rate and evolutionary impact of heritable L1 retrotransposition and reveal retrotransposition-mediated genomic diversification as a fundamental property of pluripotent embryonic cells in vivo.
Zinc-Adeninate Metal–Organic Framework: A Versatile Photoluminescent Sensor for Rare Earth Elements in Aqueous Systems (2019)

Rare earth elements (REEs) are strategically important for national security and advanced technologies. Consequently, significant effort has been devoted towards increasing REE domestic production, including the extraction of REEs from coal, coal combustion byproducts, and their associated waste streams such as acid mine drainage. Analytical techniques for rapid quantification of REE content in aqueous phases can facilitate REE recovery through rapid identification of high-value waste streams. In this work, we show that BioMOF-100 can be used as a fluorescent-based sensitizer for emissive REE ion detection in water, providing rapid (<10 min) analysis times and sensitive detection (parts-per-billion detection limits) for terbium, dysprosium, samarium, europium, ytterbium, and neodymium, even in the presence of acids or secondary metals.
Nickel oxide supported on porous clay heterostructures as selective catalysts for the oxidative dehydrogenation of ethane (2015)

Porous clay heterostructures (PCH) have shown to be highly efficient supports for nickel oxide in the oxidative dehydrogenation of ethane.
Effective Approach for Solving Battle of Water Calibration Network Problem (2011)

This paper presents an effective approach for calibrating an extended period simulation (EPS) model of water distribution system. By using the benchmark model calibration problem, set up for Battle of Water Calibration Networks (BWCN), the EPS model calibration is solved in a progressive manner, optimizing model parameters and engineering judgments. The model calibration approach consists of multiple steps, including: (1) constructing the initial EPS model with the given system and supervisory control and data acquisition (SCADA) data, (2) calibrating pipe properties and pump curves for static and fire flow test data, and (3) calibrating EPS model demands and controls for given SCADA data over 167 h. The calibration was iteratively conducted per district meter area (DMA) and then fine-tuned for the whole system. Although the field data contained some noise, good model calibration was achieved for BWCN. By using the practically measurable hydraulic attributes of pump flows, pressures, and tank levels provided for BWCN, the performance of the calibrated model is compared with those calibrated by 14 teams around the world participating in the BWCN.
Suppressive activity of RGX-365 on HMGB1-mediated septic responses (2022)

RGX-365 is the main fraction of black ginseng conmprising protopanaxatriol (PPT)-type rare ginsenosides (ginsenosides Rg4, Rg6, Rh4, Rh1, and Rg2). No studies on the antiseptic activity of RGX-365 have been reported. High mobility group box 1 (HMGB1) is recognized as a late mediator of sepsis, and the inhibition of HMGB1 release and recovery of vascular barrier integrity have emerged as attractive therapeutic strategies for the management of sepsis. In this study, we examined the effects of RGX-365 on HMGB1-mediated septic responses and survival rate in a mouse sepsis model. RGX-365 was administered to the mice after HMGB1 challenge. The antiseptic activity of RGX-365 was assessed based on the production of HMGB1, measurement of permeability, and septic mouse mortality using a cecal ligation and puncture (CLP)-induced sepsis mouse model and HMGB1-activated human umbilical vein endothelial cells (HUVECs). We found that RGX-365 significantly reduced HMGB1 release from LPS- activated HUVECs and CLP-induced release of HMGB1 in mice. RGX-365 also restored HMGB1-mediated vascular disruption and inhibited hyperpermeability in the mice. In addition, treatment with RGX-365 reduced sepsis-related mortality in vivo. Our results suggest that RGX- 365 reduces HMGB1 release and septic mortality in vivo, indicating that it is useful in the treatment of sepsis.
Synthesis and biological properties of hemin conjugates with unprotected peptides. (2010)

Arginine-containing peptides consisted of 3- and 13- amino acids residues, namely RGD and [5Ala]-indolicidine were synthetized. Monosubstituted hemin derivatives modificated by RGD, [5Ala]-indolicidine and gramicidine S were obtained. Biocide activity and low toxicity of obtained conjugates was shown.
Supplementary Figure 2 from Tumorigenic and Metastatic Activity of Human Thyroid Cancer Stem Cells (2023)

Supplementary Figure 2 from Tumorigenic and Metastatic Activity of Human Thyroid Cancer Stem Cells
Improving Heat Resistance of Silicon Nitride Ceramics with Rare-Earth Silicon Oxynitride (2006)

Heat resistant silicon nitride ceramics sintered with RE2O3 (RE: Sc, Y, and lanthanide) and those with RE2Si2O7 as grain boundary phase were briefly reviewed. High-temperature strength and internal friction of silicon nitride ceramics with sintering additive of RE4Si2O7N2 composition (RE: La, Lu, Sc, and Yb) were measured to select candidates for evaluation of creep resistance. Following the results of high-temperature strength test and internal friction measurement, Yb and Lu were selected for sintering additive systems. Si3N4 powder with 2.4 mol% Yb4Si2O7N2 were gas-pressure hot-pressed at 1800°C for 1 h under 20 MPa in 1 MPa N2 (YB). Si3N4 powder with 1.2 mol% (LU12) and 4.8 mol% (LU48) of Lu2O3 were gas-pressure hot-pressed at 1950°C for 1 h under 20 MPa in 1 MPa N2. High temperature strength of LU12 was at its maximum among the three ceramics. Stress-strain curve of YB was linear at 1200°C, but at 1400°C it was non-linear. The Stress-strain curve of LU48 was non-linear at 1500°C. For LU12 the stress-strain curve was linear, and it was linear even at 1600°C, indicating that LU12 broke as a brittle fracture at 1600°C. LU12 had excellent oxidation resistance, and weight gain during the oxidation at 1500°C for 1000 h was 4 g/m2. Creep resistance of LU48 was higher than that of YB. Creep life time of LU12 at 1500°C under tensile stress of 137 MPa exceeded 1678.5 h. Time-to-failure of LU12 was strongly stress sensitive.
ChemInform Abstract: SYNTHESIS OF 5′‐O‐(R,S)‐(1‐AMINOETHANE‐1‐PHOSPHONYL)URIDINE AND ‐ADENOSINE (1979)

Abstract Das Derivat der phosphorigen Säure (I) reagiert nach Schutz der Aminogruppe (Bildung von (II)) mit den Nucleosiden (III) in Gegenwart von Mesitylensulfonyltriazol (MST) zu den Ethanphosphonylnucleosiden (IV).