gebhart/patrepeval huggingface dataset:
Conformational Changes in the Spike Glycoprotein of Murine Coronavirus Are Induced at 37°C either by Soluble Murine CEACAM1 Receptors or by pH 8 (2002)

The spike glycoprotein (S) of the murine coronavirus mouse hepatitis virus (MHV) binds to viral murine CEACAM receptor glycoproteins and causes membrane fusion. On virions, the 180-kDa S glycoprotein of the MHV-A59 strain can be cleaved by trypsin to form the 90-kDa N-terminal receptor-binding subunit (S1) and the 90-kDa membrane-anchored fusion subunit (S2). Incubation of virions with purified, soluble CEACAM1a receptor proteins at 37 degrees C and pH 6.5 neutralizes virus infectivity (B. D. Zelus, D. R. Wessner, R. K. Williams, M. N. Pensiero, F. T. Phibbs, M. deSouza, G. S. Dveksler, and K. V. Holmes, J. Virol. 72:7237-7244, 1998). We used liposome flotation and protease sensitivity assays to investigate the mechanism of receptor-induced, temperature-dependent virus neutralization. After incubation with soluble receptor at 37 degrees C and pH 6.5, virions became hydrophobic and bound to liposomes. Receptor binding induced a profound, apparently irreversible conformational change in S on the viral envelope that allowed S2, but not S1, to be degraded by trypsin at 4 degrees C. Various murine CEACAM proteins triggered conformational changes in S on recombinant MHV strains expressing S glycoproteins of MHV-A59 or MHV-4 (MHV-JHM) with the same specificities as seen for virus neutralization and virus-receptor activities. Increased hydrophobicity of virions and conformational change in S2 of MHV-A59 could also be induced by incubating virions at pH 8 and 37 degrees C, without soluble receptor. Surprisingly, the S protein of recombinant MHV-A59 virions with a mutation, H716D, that precluded cleavage between S1 and S2 could also be triggered to undergo a conformational change at 37 degrees C by soluble receptor at neutral pH or by pH 8 alone. A novel 120-kDa subunit was formed following incubation of the receptor-triggered S(A59)H716D virions with trypsin at 4 degrees C. The data show that unlike class 1 fusion glycoproteins of other enveloped viruses, the murine coronavirus S protein can be triggered to a membrane-binding conformation at 37 degrees C either by soluble receptor at neutral pH or by alkaline pH alone, without requiring previous activation by cleavage between S1 and S2.
Fabrication of a lattice structure with periodic open pores through three-dimensional printing for bone ingrowth (2022)

Lattice structures for implants can be printed using metal three-dimensional (3D)-printing and used as a porous microstructures to enhance bone ingrowth as orthopedic implants. However, designs and 3D-printed products can vary. Thus, we aimed to investigate whether targeted pores can be consistently obtained despite printing errors. The cube-shaped specimen was printed with one side 15 mm long and a full lattice with a dode-thin structure of 1.15, 1.5, and 2.0 mm made using selective laser melting. Beam compensation was applied, increasing it until the vector was lost. For each specimen, the actual unit size and strut thickness were measured 50 times. Pore size was calculated from unit size and strut thickness, and porosity was determined from the specimen's weight. The actual average pore sizes for 1.15, 1.5, and 2.0 mm outputs were 257.9, 406.2, and 633.6 μm, and volume porosity was 62, 70, and 80%, respectively. No strut breakage or gross deformation was observed in any 3D-printed specimens, and the pores were uniformly fabricated with < 10% standard deviation. The actual micrometer-scaled printed structures were significantly different to the design, but this error was not random. Although the accuracy was low, precision was high for pore cells, so reproducibility was confirmed.
Innentitelbild: Effizienter Zugang zu Titanaaziridinen durch C‐H‐Aktivierung von N‐Methylanilinen bei Raumtemperatur (Angew. Chem. 14/2015) (2015)

Zwei auf einen StreichN-Methylaniline werden in Gegenwart eines Bis(η5,η1-pentafulventitan)komplexes durch zweifache Bindungsaktivierung direkt in Titanaaziridine überführt. Basierend auf dieser Umsetzung berichten S. Doye, R. Beckhaus et al. in ihrer Zuschrift auf S. 4458 ff. über die Isolierung und Untersuchung sämtlicher Schlüsselintermediate der titankatalysierten Hydroaminoalkylierung von Alkenen. Damit wird erstmals ein experimenteller Beleg für den bisher nur vorgeschlagenen Reaktionsmechanismus dieser auch industriell relevanten Reaktion erbracht.
AUTOMATIC DIFFERENTIATION FOR MORE EFFICIENT SYSTEM ANALYSIS AND OPTIMIZATION (1998)

Abstract This paper reports on the benefits of using automatic differentiation (AD) to improve the efficiency of multidisciplinary analysis and optimization processes. Automatic differentiation technology provides researchers with new opportunities to use sensitivities for analysis and optimization. This research confirms that analysis and optimization applications in which the use of sensitivity information had previously been avoided or ruled out, as computationally prohibitive, need to be revisited. In this research, two applications are investigated in which the use of AD is observed to improve efficiency. The efficiency of solution strategies for non-hierarchic (i.e., coupled) system analysis is improved using automatic differentiation generated sensitivities. Calculation of sensitivities via AD allows for efficient application of Newton's method and a modified form of Newton's method to converge non-hierarchic system analyses. The line search strategy employed within a generalized reduced gradient (GRG) optimizer is improved through the use of AD generated sensitivities. Using the AD-based line search strategy within the GRG method results in a significant reduction in the number of system analyses and the CPU time required for optimization
Poster Abstract: Automatic Calibration of Device Attitude in Inertial Measurement Unit Based Traffic Probe Vehicles (2016)

Probe vehicles consist in mobile traffic sensor networks that evolve with the flow of vehicles, transmitting velocity and position measurements along their path, generated using GPSs. To address the urban positioning issues of GPSs, we propose to replace them with inertial measurement units onboard vehicles, to estimate vehicle location and attitude using inertial data only. While promising, this technology requires one to carefully calibrate the orientation of the device inside the vehicle to be able to process the acceleration and rate gyro data. In this article, we propose a scheme that can perform this calibration automatically by leveraging the kinematic constraints of ground vehicles, and that can be implemented on low-end computational platforms. Preliminary testing shows that the proposed scheme enables one to accurately estimate the actual accelerations and rotation rates in the vehicle coordinates.
An X-band GaN HEMT power amplifier design using an artificial neural network modeling technique (2001)

In this paper, the first gallium nitride (GaN) based high electron mobility transistor (HEMT) power amplifier design using an artificial neural network (ANN) modeling technique is presented. The ANN technique was used to model the small signal behavior of a device with a gate periphery of 1 mm and a gate length of 1 /spl mu/m over the broad frequency range from 1 GHz to 26 GHz with multiple bias points, based on fitting calculated S-parameters to measured S-parameters. A single stage amplifier constructed using these parameters showed a gain of about 7 dB and an output power of 1.2 W at 8 GHz when biased at V/sub ds/ = 20 V and I/sub ds/ 220 mA in class AB mode. The good agreement between measured and simulated results was shown in both S-parameter modeling and in amplifier design.
Low-Cost Plastic Plasmonic Substrates for Operation in Aqueous Environments (2010)

We report a novel design of a multilayer stack to attain surface-plasmon-coupled emission (SPCE) enhancements in liquid medium. Variation in thickness of the multilayer affects the position and depth of resonance plasmon dips. Numerical investigation resulted in an optimal stack configuration that supports long-range surface plasmons. SPCE substrates were prepared on plain BK7 glass and Teflon-AF coated polycarbonate (PC-T) substrates by modifying their surface functionalities using plasma etching. The changes in refractive indices due to the presence of the fluoropolymer layer help reduce the SPCE exit angle from α = 75° (plain BK7) to α = 60° (PC-T) in water without requiring specialized optics.
Origin of tunnel electroresistance effect inPbTiO3-based multiferroic tunnel junctions (2015)

The mechanism of the tunnel electroresistance effect of a $\mathrm{Co}\text{/}\mathrm{PbTi}{\mathrm{O}}_{3}\text{/}\mathrm{L}{\mathrm{a}}_{0.7}\mathrm{S}{\mathrm{r}}_{0.3}\mathrm{Mn}{\mathrm{O}}_{3}$ multiferroic tunnel junction is studied in detail using experimental and theoretical methods. Based on experimental data, we present a model that explains the correlation between the polarization of the ferroelectric material and the observed resistance state based on the effective change of the tunnel barrier thickness. We show that the observed thickness variation can neither be completely attributed to the asymmetric inverse piezoelectric effect in the classical sense, nor to asymmetric screening of the polarization charge. The analysis of detailed ab initio calculations quantitatively demonstrates that a mixture of electronic and structural phenomena is responsible for the change in effective tunnel barrier thickness upon polarization reversal. On the one hand, the ferroelectric material exhibits a reversible metallization at one of the interfaces, which shifts the boundary between the ferroelectric material and the electrode. On the other hand, a piezoelectric effect that stems from different terminations of the ferroelectric ultrathin film towards the electrodes magnifies this effect. Combined, the electrically switchable effective change in thickness is as large as 0.15 nm, which dominates the resistive switching effect in the presented junction that involves a 3.2 nm thin $\mathrm{PbTi}{\mathrm{O}}_{3}$ film. This work contributes to the deeper understanding of fundamental mechanisms that lead to tunnel electroresistance and imposes new ways for tailoring the characteristics of electroresistive tunnel junctions.
Prognostic value of functional SMAD4 localization in extrahepatic bile duct cancer (2022)

Abstract Background. SMAD4 is a key mediator of TGFβ signaling and one of the mutated genes in extrahepatic bile duct cancer (eBDC). SMAD4 has dual functions, in carcinogenesis via silencing and in tumor invasion/metastasis via signaling, depending on tumor stage. We investigated the localization of functional SMAD4 (e.g., invasion or metastasis) and its association with chemo-radiation therapy. Methods. We performed SMAD4 immunostaining on 98 resected eBDC specimens and evaluated the presence of the functional form of nuclear SMAD4 at the central lesion, invasion front, and metastatic lymph node. We also examined the influence on chemotherapy after recurrence (n=33) and neoadjuvant chemo-radiation therapy (NAC-RT, n=21) and the prognostic value of using retrospective data. Results. In 73 patients without NAC-RT, 8.2% had loss of SMAD4 expression and 23.3% had heterogeneous expression. Patients without SMAD4 expression at any site had significantly poorer overall survival (OS) than other patients ( P= 0.014). Expression of SMAD4 at the invasion front was related to survival (recurrence-free survival [RFS] P= 0.033; OS P= 0.047), and no SMAD4 expression at the metastatic lymph node was related to poorer OS ( P= 0.011). The patients who had high SMAD4 expression had poorer prognosis after recurrence (RFS P= 0.011; OS P= 0.056). At the residual cancer in the resected specimen, SMAD4 was highly expressed after NAC-RT ( P= 0.039). Conclusions. Loss of SMAD4 protein expression was a poor prognostic factor in resectable eBDC. However, the intensity of functional SMAD4 in eBDC is a marker of resistance to chemotherapy and malignant potential at advanced stages.
Solubilization of Pyridone-Based Fluorescent Tag by Complexation in Cucurbit[7]uril (2019)

Aimed at further exploring the hosting properties of cucurbit[7]uril (CB7), we have exploited the spectroscopic and photophysical properties of a known fluorescent label as the guest molecule, namely, 3-cyano-6-(2-thienyl)-4-trifluoromethyl pyridine (TFP), in neat solvents. The formation of an inclusion host-guest complex with CB7 was checked by UV-vis absorption spectroscopy, and the value of binding constant (9.7 × 10<sup>5</sup> M<sup>-1</sup>) was extracted from the spectrophotometric data. The modulation of keto-enol equilibrium in TFP by the local environment is governed by the interplay between dimerization through intermolecular hydrogen bonding between individual solute molecules, favoring the enol form, and intermolecular hydrogen bonding between TFP and the surrounding solvents, favoring the keto form. Time-resolved fluorescence results established that the macromolecular CB7 host stabilizes preferentially the neutral enol form over the keto form of TFP. Unprecedentedly, our results reveal a linear dependence of the amplitudes of the extracted decay-associated spectra from the time-resolved fluorescence spectra of TFP on the sum of polarity/polarizability and hydrogen bonding parameters of the local environment, confirming that TFP at micromolar concentration in the CB7 complexes is experiencing a methanol-like environment. The results rationalized the 42-fold enhancement in the solubility of TFP in water media by complexation in CB7.
ChemInform Abstract: Synthesis of Novel 2‐Oxo‐4‐thia‐1‐azabicyclo(3.3.0)oct‐7‐ene‐8‐carboxylic Acid Derivatives. (1992)

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.
An improved SOM-based approach to dynamic task assignment of multi-robots (2010)

In this paper, an improved self organizing map (SOM)-based approach is proposed for multi-robot systems to tackle the task assignment problem which focuses on the self-organization issue with a large number of robots and a large number of task locations in dynamic environments subject to uncertainties. It is capable of dynamically controlling a group of mobile robots to achieve different task locations from arbitrary initial locations and directions. In the proposed approach, the robot motion planning is integrated with the task assignment, thus the robots start to move once the overall task is given. The group of mobile robots can automatically arrange the total task, and dynamically adjust their motion whenever the environment is changed, such as when some robots break down, some robots and/or some tasks are added, or the situation accruing when some tasks are changed. Different from our early study, the current direction of every robot is considered during the robot motion planning. The effectiveness and efficiency of the proposed approach are demonstrated by simulation studies.
Family Outcomes From a Randomized Control Trial of Relapse Prevention Therapy in First-Episode Psychosis (2009)

anzctr.org.au Identifier: ACTRN12605000514606.
Design and Optimization of Electromagnetic Sensor Based On CRLH Resonator (2018)

An electromagnetic sensor with high sensitivity loaded with CRLH resonator (composite right left hand) for liquid mixture application is designed and optimized in this paper. The sensor is characterized by miniaturized dimension 15mm by 14mm, the substrate is based on FR4 epoxy, very short testing surface 10mm by 8mm, leading to a very high sensitivity. The operating frequency is from 1.0 GHz 1.50 GHz. The sensor is designed and simulated using the commercial software HFSS, the geometrical dimensions are optimized for better performance. Three types of liquid are tested given as; methanol, ethanol and distilled water, the CRLH resonator enable high sensitivity and miniaturized devise, the obtained results are very interesting compared to the literature..
A proteomic analysis of seeds from Bt-transgenic Brassica napus and hybrids with wild B. juncea (2015)

Transgene insertions might have unintended side effects on the transgenic host, both crop and hybrids with wild relatives that harbor transgenes. We employed proteomic approaches to assess protein abundance changes in seeds from Bt-transgenic oilseed rape (Brassica napus) and its hybrids with wild mustard (B. juncea). A total of 24, 15 and 34 protein spots matching to 23, 13 and 31 unique genes were identified that changed at least 1.5 fold (p < 0.05, Student's t-test) in abundance between transgenic (tBN) and non-transgenic (BN) oilseed rape, between hybrids of B. juncea (BJ) × tBN (BJtBN) and BJ × BN (BJBN) and between BJBN and BJ, respectively. Eight proteins had higher abundance in tBN than in BN. None of these proteins was toxic or nutritionally harmful to human health, which is not surprising since the seeds are not known to produce toxic proteins. Protein spots varying in abundance between BJtBN and BJBN seeds were the same or homologous to those in the respective parents. None of the differentially-accumulated proteins between BJtBN and BJBN were identical to those between tBN and BN. Results indicated that unintended effects resulted from transgene flow fell within the range of natural variability of hybridization and those found in the native host proteomes.
The Synthesis of Secamine and Presecamine Skeletons and the Isolation of Tetrahydrosecamine from <I>Amsonia elliptica</I> ROEM et SCHULT (1971)

michelalbine (7) by TLC and spectral [UV(EtOH), IR (KBr), nuclear magnetic resonance (DMSO)] comparisons with natural base (2).Sodium borohydride reduction of 5 seems to have proceeded in a highly stereoselective manner to give only 6 which eventually was converted to dl-michelalbine.Diastereoisomer (6a) was not detected in the reduction product.
Two new species of Oidiodendron from boreal forest soils (1968)

Oidiodendron periconioides Morrall sp. nov. and O. chlamydosporicum Morrall sp. nov. are described from Canadian boreal forest soils. O. gracile Zhdanova is considered to be a nomen dubium.
Hot purge gas regeneration of adsorption beds with solute condensation: Experimental studies (1985)

Abstract Activated carbon beds with adsorbed n ‐octane are regenerated using hot air. Effects of pressure, feed temperature, and initial loading on temperature and concentration breakthrough curves are studied. For moderate and high values of these variables, effluent vapors are found to be saturated with hydrocarbon during part of the heating step, indicating the presence presence of liquid within the bed. Regeneration behavior is predicted with reasonable accuracy using a nonisothermal stage model.
A Modular, Argon-Driven Flow Platform for Natural Product Synthesis and Late-Stage Transformations (2020)

A modular flow platform for the synthesis of natural products and their analogs was designed. To access different reaction setups with a maximum of flexibility, interchangeable 3D-printed components serve as backbone. By switching from conventional liquid- to gas-driven flow, reagent and solvent waste is minimized which translates into an advantageous sustainability and economy profile. To enable inert conditions, practical “Schlenk-in-flow” techniques for the safe handling of oxygen- and moisture sensitive reagents were developed. Adopting these techniques, reproducible transformations in natural product synthesis were achieved.
Characteristic Changes in Cell Surface Glycosylation Accompany Intestinal Epithelial Cell (IEC) Differentiation: High Mannose Structures Dominate the Cell Surface Glycome of Undifferentiated Enterocytes (2015)

Changes in cell surface glycosylation occur during the development and differentiation of cells and have been widely correlated with the progression of several diseases. Because of their structural diversity and sensitivity to intra- and extracellular conditions, glycans are an indispensable tool for analyzing cellular transformations. Glycans present on the surface of intestinal epithelial cells (IEC) mediate interactions with billions of native microorganisms, which continuously populate the mammalian gut. A distinct feature of IECs is that they differentiate as they migrate upwards from the crypt base to the villus tip. In this study, nano-LC/ESI QTOF MS profiling was used to characterize the changes in glycosylation that correspond to Caco-2 cell differentiation. As Caco-2 cells differentiate to form a brush border membrane, a decrease in high mannose type glycans and a concurrent increase in fucosylated and sialylated complex/hybrid type glycans were observed. At day 21, when cells appear to be completely differentiated, remodeling of the cell surface glycome ceases. Differential expression of glycans during IEC maturation appears to play a key functional role in regulating the membrane-associated hydrolases and contributes to the mucosal surface innate defense mechanisms. Developing methodologies to rapidly identify changes in IEC surface glycans may lead to a rapid screening approach for a variety of disease states affecting the GI tract.
Supplementary Data and Methods from Expansion of Tumor-Infiltrating CD8<sup>+</sup> T cells Expressing PD-1 Improves the Efficacy of Adoptive T-cell Therapy (2023)

&lt;p&gt;Supplementary Figures: (Fig. S1) Multi-parametric flow cytometric analysis of tumor-infiltrating T lymphocyte subsets from freshly excised MC38 tumors; (Fig. S2) Expression of co-inhibitory and co-stimulatory molecules over the course of tumor progression; (Fig. S3) Tumor-reactivity of CD137+ and PD-1+ TILs, freshly after isolation from tumors and after in vitro expansion; (Fig. S4) Kinetic of expansion of different CD8 TIL subsets isolated from MC38 tumors; (Fig. S5) CDR3 spectratype analysis. Supplementary Tables: (Table S1) Number of CDR3 fragments which dominance hierarchy changed after TIL expansion; (Table S2) Number of TCR-Vbeta families that lose, preserve or acquire new dominant CDR3 fragments after TIL expansion. Supplemental Material and Methods: Spectratyping.&lt;/p&gt;
A family of intermediate filament-like proteins is sequentially assembled into the cytoskeleton of Toxoplasma gondii (2020)

The intracellular protozoan parasite Toxoplasma gondii divides by a unique process of internal budding that involves the assembly of two daughter cells within the mother. The cytoskeleton of Toxoplasma, which is composed of microtubules associated with an inner membrane complex (IMC), has an important role in this process. The IMC, which is directly under the plasma membrane, contains a set of flattened membranous sacs lined on the cytoplasmic side by a network of filamentous proteins. This network contains a family of intermediate filament-like proteins or IMC proteins. In order to elucidate the division process, we have characterized a 14-member sub-family of Toxoplasma IMC proteins that share a repeat motif found in proteins associated with the cortical alveoli in all alveolates. By creating fluorescent protein fusion reporters for the family members we determined the spatio-temporal patterns of all 14 IMC proteins through tachyzoite development. This revealed several distinct distribution patterns and some provide the basis for novel structural models such as the assembly of certain family members into the basal complex. Furthermore we identified IMC15 as an early marker of budding and, lastly, the dynamic patterns observed throughout cytokinesis provide a timeline for daughter parasite development and division.
Surveillance of Travellers: An Additional Tool for Tracking Antimalarial Drug Resistance in Endemic Countries (2013)

The results have not shown different trends in resistance between parasites derived from travellers or from parasites within-country. This work highlights the value of an international database of drug responses in travellers as an additional tool to assess the emergence of drug resistance in endemic areas where information is limited.