gebhart/patrepeval huggingface dataset:
Molecular dynamics analysis of Superoxide Dismutase 1 mutations suggests decoupling between mechanisms underlying ALS onset and progression (2022)

ABSTRACT Mutations in the superoxide dismutase 1 ( SOD1 ) gene are the second most common known cause of ALS. SOD1 variants express high phenotypic variability and over 200 have been reported in people with ALS. Investigating how different SOD1 variants affect the protein dynamics might help in understanding their pathogenic mechanism and explaining their heterogeneous clinical presentation. It was previously proposed that variants can be broadly classified in two groups, ‘wild-type like’ (WTL) and ‘metal binding region’ (MBR) variants, based on their structural location and biophysical properties. MBR variants are associated with a loss of SOD1 enzymatic activity. In this study we used molecular dynamics and large clinical datasets to characterise the differences in the structural and dynamic behaviour of WTL and MBR variants with respect to the wild-type SOD1, and how such differences influence the ALS clinical phenotype. Our study identified marked structural differences, some of which are observed in both variant groups, while others are group specific. Moreover, applying graph theory to a network representation of the proteins, we identified differences in the intramolecular contacts of the two classes of variants. Finally, collecting clinical data of approximately 500 SOD1 ALS patients carrying variants from both classes, we showed that the survival time of patients carrying an MBR variant is generally longer (~6 years median difference, p &lt; 0.001) with respect to patients with a WTL variant. In conclusion, our study highlights key differences in the dynamic behaviour of the WTL and MBR SOD1 variants, and wild-type SOD1 at an atomic and molecular level. We identified interesting structural features that could be further investigated to explain the associated phenotypic variability. Our results support the hypothesis of a decoupling between mechanisms of onset and progression of SOD1 ALS, and an involvement of loss-of-function of SOD1 with the disease progression.
Performance comparison between electrical copper-based and optical fiber-based backplanes (2013)

A performance comparison between the electrical Cu-based backplane and a full-optical fiber-based backplane is presented in terms of capacity and power consumption. By means of systematic simulations we find the electrical configuration, which allows to optimize the Cu-based backplane by exploiting the best technologies available today. On the other hand, a fiber-based optical backplane is proposed by exploiting the most performing VCSEL sources. Limitations of the electrical and optical approaches are discussed, considering their capabilities to support up to about 25-Gb/s transmission and the possibility to evolve towards higher bit-rates.
Hierarchical Visualization System for High Performance Computing (2010)

The article proposes a scientific data visualization system for high performance computing. Suggested system has hierarchical architecture where software modules of the system are implemented on the different hardware modules. Supercomputer IBM Blue Gene /P is used as the main test system. Visualization system includes parallel modules for video rendering, video enhancement, video compression and video up-sampling. System proposes visualization for 2D displays, 3D displays, multidisplay complexes. The results of using proposed visualization system for 3D torus network simulation are presented.
A novel stereoselective synthesis of the macrocycle of haem d1 that establishes its absolute configuration as 2R,7R (1993)

A novel route to isobacteriochlorins is developed that allows the stereoselective synthesis of the macrocycle of haem d1 and so establishes its absolute configuration 2R,7R.
Directional wave spectra from daylight scattering (1975)

A first-order analysis of the skylight scattered from the sea surface for understanding the mechanism of transfer of wave profile to photographic image has been given by Kasevich et al. (1971). The analysis is now extended to second order and numerically evaluated for clear blue and uniform overcast skies. The theoretical results indicate experimental conditions required to obtain a photographic transparency with optical transmittance linearly proportional to sea wave profile. Experimental parameters include sun angle, camera orientation, and maximum wave slope. Fourier analysis of the transparency by coherent optical processing methods will give the directional power density spectrum of the wave field (Stilwell, 1969).
Detection of buried defect using actinic darfkfield microscopy (2003)

International audience
Unique epigenetic influence of H2AX phosphorylation and H3K56 acetylation on normal stem cell radioresponses (2016)

Normal tissue injury resulting from cancer radiotherapy is often associated with diminished regenerative capacity. We examined the relative radiosensitivity of normal stem cell populations compared with non-stem cells within several radiosensitive tissue niches and culture models. We found that these stem cells are highly radiosensitive, in contrast to their isogenic differentiated progeny. Of interest, they also exhibited a uniquely attenuated DNA damage response (DDR) and muted DNA repair. Whereas stem cells exhibit reduced ATM activation and ionizing radiation-induced foci, they display apoptotic pannuclear H2AX-S139 phosphorylation (γH2AX), indicating unique radioresponses. We also observed persistent phosphorylation of H2AX-Y142 along the DNA breaks in stem cells, which promotes apoptosis while inhibiting DDR signaling. In addition, down-regulation of constitutively elevated histone-3 lysine-56 acetylation (H3K56ac) in stem cells significantly decreased their radiosensitivity, restored DDR function, and increased survival, signifying its role as a key contributor to stem cell radiosensitivity. These results establish that unique epigenetic landscapes affect cellular heterogeneity in radiosensitivity and demonstrate the nonubiquitous nature of radiation responses. We thus elucidate novel epigenetic rheostats that promote ionizing radiation hypersensitivity in various normal stem cell populations, identifying potential molecular targets for pharmacological radioprotection of stem cells and hopefully improving the efficacy of future cancer treatment.
Effects of Gas Adsorption on the Electrical Conductivity of Single-Wall Carbon Nanohorns (2006)

We present significant electrical conductivity responses of the pelletized as-prepared and oxidized (ox-) single-wall carbon nanohorns (SWNHs) on adsorption of CO(2) and O(2). The morphological and pore structures of both pelletized SWNHs were examined by transmission electron microscopy (TEM) and nitrogen adsorption isotherm, leading to explicit evidences of the formation of nanoscale windows on the wall by oxidation. The SWNH and ox-SWNH induced a semiconducting behavior, strongly responded to CO(2) and O(2) adsorptions, and each exhibited n-type- and p-type-like conductivities. The electrical conductivity increase and decrease for CO(2) and O(2) adsorption, respectively, were observed for SWNH, whereas ox-SWNH showed a marked electrical conductivity drop on CO(2) adsorption and almost no change on O(2) adsorption. The dramatically different electrical conductivity response of ox-SWNH is presumed to be ascribed to the annihilation of pentagons in the single graphene wall by oxidation.
Presenilin 2 deficiency causes a mild pulmonary phenotype and no changes in amyloid precursor protein processing but enhances the embryonic lethal phenotype of presenilin 1 deficiency (1999)

Mutations in the homologous presenilin 1 (PS1) and presenilin 2 (PS2) genes cause the most common and aggressive form of familial Alzheimer's disease. Although PS1 function and dysfunction have been extensively studied, little is known about the function of PS2 in vivo. To delineate the relationships of PS2 and PS1 activities and whether PS2 mutations involve gain or loss of function, we generated PS2 homozygous deficient (-/-) and PS1/PS2 double homozygous deficient mice. In contrast to PS1(-/-) mice, PS2(-/-) mice are viable and fertile and develop only mild pulmonary fibrosis and hemorrhage with age. Absence of PS2 does not detectably alter processing of amyloid precursor protein and has little or no effect on physiologically important apoptotic processes, indicating that Alzheimer's disease-causing mutations in PS2, as in PS1, result in gain of function. Although PS1(+/-) PS2( -/-) mice survive in relatively good health, complete deletion of both PS2 and PS1 genes causes a phenotype closely resembling full Notch-1 deficiency. These results demonstrate in vivo that PS1 and PS2 have partially overlapping functions and that PS1 is essential and PS2 is redundant for normal Notch signaling during mammalian embryological development.
Automatic Generation of Technical Documentation (1994)

Natural-language generation (NLG) techniques can be used to automatically produce technical documentation from a domain knowledge base and linguistic and contextual models. We discuss this application of NLG technology from both a technical and a usefulness (costs and benefits) perspective. This discussion is based largely on our experiences with the IDAS documentation-generation project, and the reactions various interested people from industry have had to IDAS. We hope that this summary of our experiences with IDAS and the lessons we have learned from it will be beneficial for other researchers who wish to build technical-documentation generation systems.
Surface Segregation of Al of the Bilayers of Pure Cu and Cu-Al Alloy Films (2001)

The segregation of Al at the surface of pure Cu and Cu-5 atom % Al alloy thin film bilayers was investigated as a function of the Al content, anneal temperature and time, and annealing ambient. Rutherford backscattering spectrometry was used to follow Al movement through the thickness of the film. Al appears to segregate on the surface as an oxide. The amount of Al segregating on the surface of the samples annealed at temperatures ⩽400°C increases to about At the same time, a small amount of Al is retained in the overlying Cu through which Al is diffusing to the surface. The Al at surface is equivalent to The formation of this oxide was self-limiting at temperatures less than the crystalline transformation temperature of and has structure similar to the surface oxide on pure Al, grown at similar temperatures. At higher temperatures (500 and 600°C) the oxide apparently crystallizes, allowing migration of Al and thus leading to continued growth of the oxide. It is hypothesized that the residual oxygen (or other oxidizing species like water) reacts with Al arriving on the surface, providing the thermodynamically favored driving force to migrate Al from the alloy film through the overlying pure Cu film to the surface leading to both the homogenization of the Al content in the bilayer and oxide formation on the surface. © 2001 The Electrochemical Society. All rights reserved.
Rational physical agent reasoning beyond logic (2009)

The title compound, C(22)H(28)N(2)O(4), contains two independent centrosymmetric mol-ecules (A and B). In the previous structure determination [Xia et al. (2007 ▶). Acta Cryst. E63, o259] both A and B were modelled as neutral mol-ecules with the H atoms of the the O-H groups included in calculated positions. In this redetermination, the transferrable H atoms were located in difference maps and freely refined, indicating that one mol-ecule (A) crystallizes in the neutral (nonzwitterionic) form and the other in the zwitterionic form, namely 6,6'-dimeth-oxy-2,2'-[hexane-1,6-diylbis(nitrilo-dimethyl-idyne)]-di-phenol-6,6'-dimeth-oxy-2,2'-[hexane-1,6-diylbis(nitrilio-di-methyl-idyne)]diphenolate (1/1). This finding is supported by significant differences in the C-O(H) (A) and C-O(-) (B) bond lengths. In the crystal, the zwitterionic mol-ecules (B) are involved in inter-molecular N-H⋯O hydrogen bonds forming one-dimensional chains along [001]. Each independent mol-ecule forms an intra-molecular O-H⋯N (A) or N-H⋯O (B) hydrogen bond. In mol-ecule B, one of the -CH(2)- groups is disordered over two sets of sites with refined occupancies of 0.659 (8) and 0.341 (8).
Le gammare, outil biologique pour caractériser la contamination chimique et la toxicité des eaux douces (2012)

/ Irstea développe un outil biologique pour diagnostiquer la contamination chimique et la toxicité des milieux aquatiques d'eau douce. Cet outil repose sur l'utilisation du crustacé Gammarus fossarum. Les organismes sont directement exposés dans le milieu naturel (encagement). Le dispositif permet d'étudier aussi bien les petits et les grands cours d'eau (canaux). Les teneurs en contaminants dans les organismes et les effets biologiques déterminés sont confrontés à des valeurs seuils pré-définis permettant de classer les milieux étudiés en fonction de leur niveau de contamination et de leur toxicité. Cet outil de diagnostic répond aux attentes des réseaux de surveillance et des études opérationnelles (identification de rejets, qualification de la qualité de rejets, suivi d'amélioration des milieux suite à une restauration, etc..).
ChemInform Abstract: Novel Photochemical Addition of Aromatic Aldehydes to Ketene Dithioacetal S,S‐Dioxides and Its Application to Organic Synthesis. (1999)

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.
Miniaturized fiber-coupled confocal fluorescence microscope with an electrowetting variable focus lens using no moving parts (2015)

We report a miniature, lightweight fiber-coupled confocal fluorescence microscope that incorporates an electrowetting variable focus lens to provide axial scanning for full three-dimensional (3D) imaging. Lateral scanning is accomplished by coupling our device to a laser-scanning confocal microscope through a coherent imaging fiber-bundle. The optical components of the device are combined in a custom 3D-printed adapter with an assembled weight of &lt;2&#x2009;&#x2009;g that can be mounted onto the head of a mouse. Confocal sectioning provides an axial resolution of &#x223C;12&#x2009;&#x2009;&#x3BC;m and an axial scan range of &#x223C;80&#x2009;&#x2009;&#x3BC;m. The lateral field-of-view is 300&#xA0;&#x3BC;m, and the lateral resolution is 1.8&#xA0;&#x3BC;m. We determined these parameters by imaging fixed sections of mouse neuronal tissue labeled with green fluorescent protein (GFP) and fluorescent bead samples in agarose gel. To demonstrate viability for imaging intact tissue, we resolved multiple optical sections of ex vivo mouse olfactory nerve fibers expressing yellow fluorescent protein (YFP).
Spatial Component-wise Convolutional Network (SCCNet) for Motor-Imagery EEG Classification (2019)

We study brain-computer interfaces (BCI) based on the decoding of motor imagery (MI) from electroencephalography (EEG) neuromonitoring. The robustness of MI-BCI is a major concern in practical applications, and hence various efforts in the literature have been made to enhance the MI classification accuracy from EEG signals. Recently, classifiers based on convolutional neural networks (CNN) have achieved state-of-the-art performance. In further exploration of applying CNNs to EEG data, we propose a spatial component-wise convolutional network (SCCNet), featuring an initial convolutional layer for spatial filtering, a common processing in EEG analysis for signal enhancement and noise reduction. Through a series of optimization and validation, we show the superiority of SCCNet in MI EEG classification, outperforming other existing CNNs.
Microvessel Network Formation and Interactions with Pancreatic Islets in Three-Dimensional Chip Cultures (2019)

The pancreatic islet is a highly vascularized micro-organ, and rapid revascularization postislet transplantation is important for islet survival and function. However, the various mechanisms involved in islet revascularization are not fully understood, and we currently lack good <i>in vitro</i> platforms to explore this. Our aim for this study was to generate perfusable microvascular networks in a microfluidic chip device, in which islets could be easily integrated, to establish an <i>in vitro</i> platform for investigations on islet-microvasculature interactions. We compared the ability of mesenchymal stem cells (MSCs) and fibroblasts to support microvascular network formation by human umbilical vein endothelial cells (HUVECs) and human induced pluripotent stem cell-derived endothelial colony-forming cell in two-dimensional and three-dimensional models of angiogenesis, and tested the effect of different culture media on microvessel formation. HUVECs that were supported by MSCs formed patent and perfusable networks in a fibrin gel, whereas networks supported by fibroblasts rapidly regressed. Network morphology could be controlled by adjusting relative cell numbers and densities. Incorporation of isolated rat islets demonstrated that islets recruit local microvasculature <i>in vitro</i>, but that the microvessels did not invade islets, at least during the course of these studies. This <i>in vitro</i> microvascularization platform can provide a useful tool to study how various parameters affect islet integration with microvascular networks and could also be utilized for studies of vascularization of other organ systems. Impact statement To improve pancreatic islet graft survival and function posttransplantation, rapid and adequate revascularization is critical. Efforts to improve islet revascularization are demanding due to an insufficient understanding of the mechanisms involved in the process. We have applied a microfluidics platform to generate microvascular networks, and by incorporating pancreatic islets, we were able to study microvasculature-islet interactions in real time. This platform can provide a useful tool to study islet integration with microvascular networks, and could be utilized for studies of vascularization of other organ systems. Moreover, this work may be adapted toward developing a prevascularized islet construct for transplantation.
Quantitative X-ray phase contrast computed tomography with grating interferometry (2021)

The ability of biomedical imaging data to be of quantitative nature is getting increasingly important with the ongoing developments in data science. In contrast to conventional attenuation-based X-ray imaging, grating-based phase contrast computed tomography (GBPC-CT) is a phase contrast micro-CT imaging technique that can provide high soft tissue contrast at high spatial resolution. While there is a variety of different phase contrast imaging techniques, GBPC-CT can be applied with laboratory X-ray sources and enables quantitative determination of electron density and effective atomic number. In this review article, we present quantitative GBPC-CT with the focus on biomedical applications.
In-silico driven design and development of spirobenzimidazo-quinazolines as potential DNA gyrase inhibitors (2020)

DNA gyrase and Topoisomerase IV are promising antibacterial drug targets as they regulate bacterial DNA replication and topology. In a quest for novel DNA topoisomerase inhibitors, a multidisciplinary approach was adopted that involves computational prediction of binding sites and molecular modelling followed by green synthesis and biological evaluation of antibacterial activity of spirobenzimidazo quinazolines derivatives. Using basic quantum chemistry principles, we evaluated spirobenzimidazo quinazolines derivatives with their pharmacokinetic profiles. Based on the results of the aforesaid in-silico studies, we synthesized a series of titled compounds using green synthetic methodology that were validated as potential antimicrobial agents. Quantum chemoinformatics based predicted activity for the synthesized compounds 9b, 9c, and 9j was concomitant with biological evaluation of broadspectrum antibacterial activity. Biological evaluation revealed that inhibition of biofilm formation was due to their potential antibacterial activity. We believe that the novel spirobenzimidazo quinazolines have the potential to be alternatives to aminocoumarins and classical quinazolines upon detailed target specific biological studies.
User controlled object sharing between Java VM instances (2017)

String objects, the most commonly used objects in Java programs, are immutable (read-only) and easily identified. Previous analysis of sharing string objects in the Java Virtual Machine showed promising results, however it is clear that sharing a wider set of objects would result in better performance. Automatic object selection for sharing is non-trivial, because in the current state, only read-only objects can be shared. This attribute cannot easily be determined during runtime by an algorithm; the developer on the other hand can. This paper presents the development of an Application Programmer Interface (API) to allow programmers to use the Java Virtual Machine (JVM) internal sharing functionality. Furthermore, we present the usage of the sharing API using open-source software as real-world test cases. The evaluation shows that the balance between memory savings and start-up time overhead is reasonable.
Improvements to generator differential protection based on the criterion of signs of the DC-component (2013)

Generator differential protection is one of the most important electrical protections of synchronous generator. Its operation principle is based on the comparison of the input current and output current at each phase winding and it allows the trip when the currents are not similar. In many cases, a false differential current causes unwanted trip commands as a result of the saturation of current transformers (CTs). In this paper, the proposed criterion can identify whether it is an external fault or an internal fault in the protection zone and it allows preventing trip commands which have been caused by the saturation of the CTs.
Comparative Effects of Bone Marrow-derived Versus Umbilical Cord Tissue Mesenchymal Stem Cells in an Experimental Model of Bronchopulmonary Dysplasia (2022)

Bronchopulmonary dysplasia (BPD) is a life-threatening condition in preterm infants with few effective therapies. Mesenchymal stem or stromal cells (MSCs) are a promising therapeutic strategy for BPD. The ideal MSC source for BPD prevention is however unknown. The objective of this study was to compare the regenerative effects of MSC obtained from bone marrow (BM) and umbilical cord tissue (UCT) in an experimental BPD model. In vitro, UCT-MSC demonstrated greater proliferation and expression of anti-inflammatory cytokines as compared to BM-MSC. Lung epithelial cells incubated with UCT-MSC conditioned media (CM) had better-wound healing following scratch injury. UCT-MSC CM and BM-MSC CM had similar pro-angiogenic effects on hyperoxia-exposed pulmonary microvascular endothelial cells. In vivo, newborn rats exposed to normoxia or hyperoxia (85% O2) from postnatal day (P) 1 to 21 were given intra-tracheal (IT) BM or UCT-MSC (1 × 106 cells/50 μL), or placebo (PL) on P3. Hyperoxia PL-treated rats had marked alveolar simplification, reduced lung vascular density, pulmonary vascular remodeling, and lung inflammation. In contrast, administration of both BM-MSC and UCT-MSC significantly improved alveolar structure, lung angiogenesis, pulmonary vascular remodeling, and lung inflammation. UCT-MSC hyperoxia-exposed rats however had greater improvement in some morphometric measures of alveolarization and less lung macrophage infiltration as compared to the BM-MSC-treated group. Together, these findings suggest that BM-MSC and UCT-MSC have significant lung regenerative effects in experimental BPD but UCT-MSC suppresses lung macrophage infiltration and promotes lung epithelial cell healing to a greater degree.