gebhart/patrepeval huggingface dataset:
Adding a positive charge at residue 46 of Drosophila alcohol dehydrogenase increases cofactor specificity for NADP+ (1994)

We previously reported that the D39N mutant of Drosophila alcohol dehydrogenase (ADH), in which Asp-39 is replaced with asparagine, has a 60-fold increase in affinity for NADP+ and a 1.5-fold increase in kcat compared to wild-type ADH [Chen et al. (1991) Eur. J. Biochem. 202, 263-267] and proposed that this part of ADH is close to the 2'-phosphate on the ribose moiety of NADP+. Here we report the effect of replacing Ala-46 with an argine residue, and A46R mutant, on binding of NADP+ to ADH and its catalytic efficiency with the NADP+ cofactor, and a modeling of the three-dimensional structure of the NAD(+)-binding region of ADH. The A46R mutant has a 2.5-fold lower Km(app)NADP+ and a 3-fold higher kcat with NADP+ compared to wild-type ADH; binding of NAD+ to the mutant was unchanged and kcat with NAD+ was lowered by about 30%. For the A46R mutant, the ratio of kcat/Km of NAD+ to NADP+ is 85, over ten-fold lower than that for wild-type ADH. Our model of the 3D structure of the NAD(+)-binding region of ADH shows that Ala-46 is over 10 A from the ribose moiety of NAD+, which would suggest that there is little interaction between this residue and NAD+ and explain why its mutation to arginine has little effect on NAD+ binding. However, the positive charge at residue 46 can neutralize some of the coulombic repulsion between Asp-39 and the 2'-phosphate on the ribose moiety of NADP+, which would increase its affinity for the A46R mutant. We also constructed a double mutant, D39N/A46R mutant, which we find has a 30-fold lower Km(app)NADP+ and 8-fold higher kcat with NADP+ as a cofactor compared to wild-type ADH; binding of NAD+ to this double mutant was lowered by 5-fold and kcat was increased by 1.5-fold. As a result, kcat/Km for the double mutant was the same for NAD+ and NADP+. The principle effect of the two mutations in ADH is to alter its affinity for the nucleotide cofactor; kcat decreases slightly in A46R with NAD+ and remains unchanged or increases in the other mutants.
Diffusive Transport in Quasi-2D and Quasi-1D Electron Systems (2009)

Quantum-confined semiconductor structures are the cornerstone of modern-day electronics. Spatial confinement in these structures leads to formation of discrete low-dimensional subbands. At room temperature, carriers transfer among different states due to efficient scattering with phonons, charged impurities, surface roughness and other electrons, so transport is scattering-limited (diffusive) and well described by the Boltzmann transport equation. In this review, we present the theoretical framework used for the description and simulation of diffusive electron transport in quasi-two-dimensional and quasi-one-dimensional semiconductor structures. Transport in silicon MOSFETs and nanowires is presented in detail.
Recognition by pregnancy serums of non-HL-A alloantigens selectively expressed on B lymphocytes. (1975)

A group of alloantibodies are found in pregnancy sera which react with antigens present on B lymphocytes and monocytes but are not detectable on the vast majority of unstimulated T cells. This specificity distinguishes them from HL-A antibodies which react with both cell types. They were readily recognized through indirect fluorescent antibody analysis by employing the combination of B-cell lymphoid lines and normal peripheral blood T cells. Different sera gave a variety of patterns of reactivity with a panel of 11 lymphoid lines. Similar differential patterns were also observed with normal B cells from different individuals particularly after concentrating the B cells. The antibodies were also cytotoxic to B cells and this procedure gave parallel results to the fluorescence method. The pattern of reactions obtained indicated a very heterogeneous system similar to that for HL-A. Special study of certain of the sera provided evidence that the lymphocyte-defined determinants of the mixed lymphocyte reaction system were involved. For convenience the term HL-B has been employed for these antigens.
ChemInform Abstract: Gold‐ and Silver‐Mediated Cycloisomerizations of N‐Propargylamides. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Is the optic nerve compartment syndrome implicated in the pathogenesis of the high‐tension form of primary open‐angle glaucoma? (2019)

None declared.
Mechanisms underlying plant resilience to water deficits: prospects for water-saving agriculture (2004)

Drought is one of the greatest limitations to crop expansion outside the present-day agricultural areas. It will become increasingly important in regions of the globe where, in the past, the problem was negligible, due to the recognized changes in global climate. Today the concern is with improving cultural practices and crop genotypes for drought-prone areas; therefore, understanding the mechanisms behind drought resistance and the efficient use of water by the plants is fundamental for the achievement of those goals. In this paper, the major constraints to carbon assimilation and the metabolic regulations that play a role in plant responses to water deficits, acting in isolation or in conjunction with other stresses, is reviewed. The effects on carbon assimilation include increased resistance to diffusion by stomata and the mesophyll, as well as biochemical and photochemical adjustments. Oxidative stress is critical for crops that experience drought episodes. The role of detoxifying systems in preventing irreversible damage to photosynthetic machinery and of redox molecules as local or systemic signals is revised. Plant capacity to avoid or repair membrane damage during dehydration and rehydration processes is pivotal for the maintenance of membrane integrity, especially for those that embed functional proteins. Among such proteins are water transporters, whose role in the regulation of plant water status and transport of other metabolites is the subject of intense investigation. Long-distance chemical signalling, as an early response to drought, started to be unravelled more than a decade ago. The effects of those signals on carbon assimilation and partitioning of assimilates between reproductive and non-reproductive structures are revised and discussed in the context of novel management techniques. These applications are designed to combine increased crop water-use efficiency with sustained yield and improved quality of the products. Through an understanding of the mechanisms leading to successful adaptation to dehydration and rehydration, it has already been possible to identify key genes able to alter metabolism and increase plant tolerance to drought. An overview of the most important data on this topic, including engineering for osmotic adjustment or protection, water transporters, and C4 traits is presented in this paper. Emphasis is given to the most successful or promising cases of genetic engineering in crops, using functional or regulatory genes. as well as to promising technologies, such as the transfer of transcription factors.
Discrete Fourier transforms when the number of data samples is prime (1968)

The discrete Fourier transform of a sequence of N points, where N is a prime number, is shown to be essentially a circular correlation. This can be recognized by rearranging the members of the sequence and the transform according to a rule involving a primitive root of N. This observation permits the discrete Fourier transform to be computed by means of a fast Fourier transform algorithm, with the associated increase in speed, even though N is prime.
Countries' survival in networked international environments (2017)

This paper applies a recently developed power allocation game in [1] to study the countries' survival problem in networked international environments. In the game, countries strategically allocate their power to support the survival of themselves and their friends and to oppose that of their foes, where by a country's survival is meant when the country's total support equals or exceeds its total threats. This paper establishes conditions that characterize different types of networked international environments in which a country may survive, such as when all the antagonism among countries makes up a complete or bipartite graph.
Comments on the Use of Olfactory Displays for Virtual Environments (1996)

Currently, the hardware to produce virtual environments does not include olfactory displays, in spite of the fact that a wealth of sensory information is available from the olfactory sense. This paper reviews the physiological and psychological aspects of olfaction and discusses the use of olfactory displays for virtual environments. Further, it outlines the information that will be needed by the virtual environment research community to integrate olfactory stimuli into virtual environments.
Friendly object tracking and foreign object detection and localization with an SDAC wireless sensor network (2004)

This paper presents a proof-of-concept wireless sensor network for detecting and tracking friendly objects and detecting and localizing foreign objects. The network incorporates a novel sensor network methodology to sense its surroundings, decide in-network what the situation in its surroundings is, act on this decision, and communicate its results to a user (SDAC). The system also performs in-network data fusion and data reduction and demonstrates the use of an adaptable hardware and software platform. The end user is presented with a geographical information systems (GIS) viewer showing when and where objects are detected. The viewer is able to display tracking information about friendly objects by searching a database for events involving specific friendly objects.
Dynamic nuclear polarization weighted spectroscopy of multispin electronic-nuclear clusters (2023)

Nuclear spins and paramagnetic centers in a solid randomly group to form clusters featuring nearly degenerate, hybrid states whose dynamics are central to processes involving nuclear spin-lattice relaxation and diffusion. Their characterization, however, has proven notoriously difficult mostly due to their relative isolation and comparatively low concentration. Here, we combine magnetic field cycling experiments, optical spin pumping, and variable radiofrequency (RF) excitation to probe transitions between hybrid multispin states formed by strongly coupled electronic and nuclear spins in diamond. Leveraging bulk nuclei as a collective time-integrating sensor, we probe the response of these spin clusters as we simultaneously vary the applied magnetic field and RF excitation to reconstruct multidimensional spectra. We uncover complex nuclear polarization patterns of alternating sign that we qualitatively capture through analytical and numerical modeling. Our results unambiguously expose the impact that strongly hyperfine-coupled nuclei can have on the spin dynamics of the crystal, and inform future routes to spin cluster control and detection.
Supplementary Table S2 from TG2 and NF-κB Signaling Coordinates the Survival of Mantle Cell Lymphoma Cells via IL6-Mediated Autophagy (2023)

&lt;p&gt;Clinical features of the MCL patients.&lt;/p&gt;
Surface-Facet-Dependent Phonon Deformation Potential in Individual Strained Topological Insulator Bi2Se3 Nanoribbons (2015)

Strain is an important method to tune the properties of topological insulators. For example, compressive strain can induce superconductivity in Bi2Se3 bulk material. Topological insulator nanostructures are the superior candidates to utilize the unique surface states due to the large surface to volume ratio. Therefore, it is highly desirable to monitor the local strain effects in individual topological insulator nanostructures. Here, we report the systematical micro-Raman spectra of single strained Bi2Se3 nanoribbons with different thicknesses and different surface facets, where four optical modes are resolved in both Stokes and anti-Stokes Raman spectral lines. A striking anisotropy of the strain dependence is observed in the phonon frequency of strained Bi2Se3 nanoribbons grown along the ⟨112̅0⟩ direction. The frequencies of the in-plane Eg(2) and out-of-plane A1g(1) modes exhibit a nearly linear blue-shift against bending strain when the nanoribbon is bent along the ⟨112̅0⟩ direction with the curved {0001} surface. In this case, the phonon deformation potential of the Eg(2) phonon for 100 nm-thick Bi2Se3 nanoribbon is up to 0.94 cm(–1)/%, which is twice of that in Bi2Se3 bulk material (0.52 cm(–1)/%). Our results may be valuable for the strain modulation of individual topological insulator nanostructures.
Ethane 1,2-di-amineborane as a new derivative of ammonia borane for hydrogen storage: desorption and relaxational properties (2013)

Trabajo presentado en el Workshop Smart and Green Interfaces - COST Meeting, celebrado en Praga (República Checa) del 21 al 22 de marzo de 2013.
Transcriptional network analysis of human astrocytic endfoot genes reveals region-specific associations with dementia status and tau pathology (2018)

The deposition of misfolded proteins, including amyloid beta plaques and neurofibrillary tangles is the histopathological hallmark of Alzheimer's disease (AD). The glymphatic system, a brain-wide network of perivascular pathways that supports interstitial solute clearance, is dependent upon expression of the perivascular astroglial water channel aquaporin-4 (AQP4). Impairment of glymphatic function in the aging rodent brain is associated with reduced perivascular AQP4 localization, and in human subjects, reduced perivascular AQP4 localization is associated with AD diagnosis and pathology. Using human transcriptomic data, we demonstrate that expression of perivascular astroglial gene products dystroglycan (DAG1), dystrobrevin (DTNA) and alpha-syntrophin (SNTA1), are associated with dementia status and phosphorylated tau (P-tau) levels in temporal cortex. Gene correlation analysis reveals altered expression of a cluster of potential astrocytic endfoot components in human subjects with dementia, with increased expression associated with temporal cortical P-tau levels. The association between perivascular astroglial gene products, including DTNA and megalencephalic leukoencephalopathy with subcortical cysts 1 (MLC1) with AD status was confirmed in a second human transcriptomic dataset and in human autopsy tissue by Western blot. This suggests changes in the astroglial endfoot domain may underlie vulnerability to protein aggregation in AD.
Melting points of rare earth (RE) substituted 123 superconductors (1991)

The substantial variation in the melting behavior of the 123 (RE) high‐Tc superconductor (HTSC) phase Re1Ba2Cu3O6.5+δ with substitution of different RE’s has been noted and partially studied before. Because of the enormous practical importance of the melting points in the processing of this major HTSC compound (e.g., in melt growth or regrowth, use as crucibles or melt substrates, non‐melting dispersoids, etc.), we have undertaken an operational study of the softening and melting behavior for all accessible RE elements forming a superconducting 123 phase; we report this study here.
A Supramolecular Approach to Enzyme Immobilization in Micro‐Channels (2012)

Abstract A supramolecular assembly scheme is developed to enable the facile in‐situ immobilization of enzymes in a microfluidic channel system. A combination of orthogonal supramolecular interactions of host (β‐cyclodextrin)–guest (adamantane) and biotin–Streptavidin (SAv) interactions are employed to generate reusable homogeneous enzyme layers in microchannels. The structural integrity and catalytic activity of the immobilized enzyme calf‐intestine alkaline phosphatase (AlkPh) is demonstrated. From the kinetic analysis of a dephosphorylation reaction, the specificity constant k cat /K M for immobilized alkaline phosphatase in the channels is on the order of 10 5 M −1 s −1 and comparable to known literature values in other environments. These observations are ascribed to the good access of the substrate to favorably oriented enzymes across the microchannel. Therefore, this study demonstrates the great potential for adopting a supramolecular assembly scheme to immobilize enzymes in microfluidic devices.
Abstract 4132: Predictive classifiers for response to c-Met targeted therapies in lung and colon cancer (2011)

Abstract A fundamental challenge in the development of cancer therapies is the co-development of companion biomarkers to select patients most likely to respond to treatment prior to the availability of clinical outcomes data. We developed a methodology that leverages large scale public ‘omics data to identify candidate predictive biomarker panels to identify patients with a greater likelihood of responding to targeted therapies. We applied this approach to generate mechanism-based predictive biomarkers using our causal Knowledgebase as a substrate, as well as standard gene expression-based biomarkers for c-Met targeted therapy use in lung and colon cancers, and validated the methodology using clinical data. Gene signatures for c-Met activation in lung and colon were applied to individual lung and colon cancer training set patients to stratify them by c-Met activation levels. Data from patients identified as having high and low levels of c-Met activation were used to develop mechanism-based and gene expression-based classifiers to predict response to c-Met targeted therapies in lung and colon cancer. Validation of these classifiers requires transcriptomic data with associated clinical outcomes from c-Met inhibitor trials. In the absence of such, we verified this general approach using data from Inflammatory Bowel Disease (IBD) patients treated with the TNF inhibitor Infliximab, for which published colon transcriptomic data and associated clinical outcomes data are available {GSE16879} We developed a gene signature to assess TNF pathway activation and stratify a training set of IBD patients, then generated gene expression and mechanism-based classifiers from patients with high and low TNF signaling. These classifiers were tested on an independent test set of IBD patients treated with Infliximab {GSE12251}; the mechanism and gene expression-based classifiers predicted responders with positive and negative predictive values of 85%/88% and 70%/100% respectively. This method can be applied to other targets, pathways and diseases and may facilitate companion diagnostic development by enabling the selection of appropriate patient populations prior to treatment and clinical trial participation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4132. doi:10.1158/1538-7445.AM2011-4132
Cytotoxicity and metabolism of 4-hydroxy-2-nonenal and 2-nonenal in H2O2-resistant cell lines. Do aldehydic by-products of lipid peroxidation contribute to oxidative stress? (1990)

Toxic aldehydes, such as 4-hydroxy-2-nonenal (4HNE) and 2-nonenal (2NE), formed during lipid peroxidation have been isolated and implicated in the cytotoxic effects of oxidative stress. We have investigated the cytotoxicity and metabolism of 4HNE and 2NE in control (HA-1) cells and in two H2O2-resistant Chinese hamster fibroblast cell lines. The H2O2-resistant cells were found to be significantly more resistant than HA-1 cells to the cytotoxicity of 4HNE, as determined by clonogenic cell survival (dose-modifying factors at 10% isosurvival of 2.0-3.0). The H2O2-resistant cells demonstrated a significant 2-3-fold increase in the amount of 4HNE removed (mol/cell) from culture media containing 72 microM-4HNE when compared with HA-1 cells. The enhanced ability of H2O2-resistant cells to metabolize 4HNE was abolished by heating the cells at 100 degrees C for 45 min. Similar results were obtained with 2NE. Total glutathione and glutathione transferase activity, believed to be involved in cellular detoxification of 4HNE, were found to be significantly increased (2-3-fold) in the resistant cells when compared with the HA-1 cells. These results show that cell lines adapted and/or selected in a highly peroxidative environment are also resistant to the cytotoxicity of aldehydes formed during lipid peroxidation. This resistance appears to be related to increased cellular metabolism of these aldehydes, possibly through the glutathione transferase system. These findings suggest that the formation of aldehydes due to lipid peroxidation may contribute significantly to the mechanisms of oxidant-induced injury and the selective pressure exerted by H2O2-mediated cytotoxicity in culture.
Robust Planning with Emergent Human-like Behavior for Agents Traveling in Groups (2021)

To enable robots to smoothly interact with humans during their travels together as a group, robots need the ability to adapt their motions under environmental changes and ensure all group members’ routes are feasible. To achieve this ability, robots require knowledge of the final destination and the subgoals in between. In practice, such information is seldom shared explicitly among group members, and may be frequently updated. Under this uncertain setting, maintaining travel efficiency and behavior appropriateness becomes a challenge. Previous literature approached the problem by generating compliant coordinating motions inspired by human groups, with subgoal uncertainty remaining isolated from the plan evaluation process. We show that such coordination can lead the robot to "bad" transient states where inefficient planning and lost tracking may incur. We propose to resolve the problem by formulating the coordinating motion as a Bayesian stochastic game, to plan for the robot as a group member, in the meanwhile considering the long-term effect of uncertainty during path coordination. We show that the approach improves travel efficiency and partner tracking robustness, by preventing assertive decisions during the inference update process. Moreover, the approach presents "agency", in the sense that it can generate human-like motions, which can be applied and contribute to the pedestrian simulation literature; the approach also affords variants from the human-like motions to generate robot behaviors based on sensing capabilities, contributing to the methodology of robot behavior design.
Synthesis and characterisation of free standing, onedimensional, Al–SiC based functionally gradient material (2001)

In the present study, an aluminium–silicon carbide based functionally gradient material was successfully synthesised using a new technique termed here as gradient slurry disintegration and deposition process. The gradient of SiC was successfully established using this technique for 21 wt-%SiC. The results were confirmed using microstructural characterisation techniques, microhardness measurements, and wear rate determination. The results further revealed that an increase in the weight percentage of silicon carbide particulates along the deposition direction lead to a concurrent increase in porosity, degree of clustering, and microhardness while the nature of silicon carbide/aluminium interfacial integrity remained the same. The results of wear rate determination indicated that a difference of ∼9.53 vol.-%SiC on the opposite faces of the functionally gradient material led to the wear resistance increasing to ∼31.5× that of the high aluminium end. An attempt is made to interrelate the processing methodology, microstructure, microhardness, and wear rate results obtained in the present study.