gebhart/patrepeval huggingface dataset:
The use of whole genome copy number variation (CNV) to measure genomic instability in mCRPC CTCs. (2016)

307 Background: AR targeted therapies in combination with PARP inhibitors have recently shown efficacy in mCRPC patients with specific DNA repair gene mutations in metastatic tissue biopsies. Homologous recombination DNA repair deficiencies (HRD), associated with response to PARP inhibitors, can also be assessed by genomic instability/scarring. Accurate genomic scarring measurement in tumors can be confounded by intra-tumor heterogeneity and/or non-tumor genome contamination. To better identify PARPi sensitivity in mCRPC patients, we developed a genomic instability and scarring assay starting from single CTCs. Methods: VCaP, LnCaP or PC3 cell lines were spiked into healthy donor blood. Individual spiked cells were identified and recovered for genomic analysis using the standard Epic CTC assay. Post recovery, cells were lysed, whole genome amplified, constructed into shotgun libraries and sequenced to ~2M 2x150bp PE reads. Following alignment, whole genome copy number and instability analysis was performed to identify large scale transitions (LST, n of chromosomal breaks between adjacent regions of at least 10 Mb), % of genome altered (percentage of 1Mbp bins with copy number alterations), as well as specific tumor suppressor/oncogene copy number alterations. The association of PTEN loss with increases in genomic instability and scaring was performed. Results: Loss of PTEN function was previously shown to be associated with genomic instability. Our assessment of PTEN deletion was confirmed in PC3, while at least one genomic copy was observed in LnCaP and VCaP. The number of LSTs and % of genome altered was higher in PC3 (n = 19 +/- 3; 9.3% +/- 2.6%) than both VCaP and LnCap (n = 8 +/- 2; 6.1% +/- 0.4%). Conclusions: The association of higher genomic instability in a PTEN null cell line (PC3) vs. those with either heterozygous (LnCaP) or wild type (VCaP) PTEN status, matches published reports associating PTEN loss with increased genomic instability. Although, PC3 only demonstrates mild PARPi sensitivity in vitro, the detection of increased genomic scarring vs. cells with at least 1 functional PTEN allele confirms the assays ability to quantify genome instability at the single cell level from CTCs in a liquid biopsy.
IL-8 induces the epithelial-mesenchymal transition of renal cell carcinoma cells through the activation of AKT signaling (2016)

The epithelial-mesenchymal transition (EMT) process has increasingly been examined due to its role in the progression of human tumors. Renal cell carcinoma (RCC) is one of the most common urological tumors that results in patient mortality. Previous studies have demonstrated that the EMT process is closely associated with the metastasis of RCC; however, the underlying molecular mechanism has not been determined yet. The present study revealed that interleukin (IL)-8 was highly expressed in metastatic RCC. IL-8 could induce the EMT of an RCC cell line by enhancing N-cadherin expression and decreasing E-cadherin expression. Furthermore, IL-8 could induce AKT phosphorylation, and the phosphatidylinositol-4,5-bisphosphate 3-kinase inhibitor LY294002 could inhibit the EMT of RCC cells that was induced by IL-8. Therefore, these results suggest that IL-8 is able to promote the EMT of RCC through the activation of the AKT signal transduction pathway, and this may provide a possible molecular mechanism for RCC metastasis.
Multitrophic interactions in terrestrial systems : the 36th Symposium of the British Ecological Society, Royal Holloway College, University of London, 1995 (1997)

Preface Part I. Interactions between Plants and Lower Organisms Introductory Remarks N. J. Fokkema 1. Bacterial antagonist-fungal pathogen interactions on the plant aerial surface B. Seddon, S. G. Edwards, E. Markellou and N. E. Malathrakis 2. Interactions between beneficial soil bacteria and root pathogens: mechanisms and ecological impact C. Keel and G. Defago 3. Interactions between fungi and plant pathogens in soil and the rhizosphere J. M. Whipps 4. Interactions between mycorrhizal fungi and rhizosphere microorganisms within the context of sustainable soil-plant systems J. M. Barea, C. Azcon-Aguilar and R. Azcon 5. Interactions between arbuscular mycorrhizal fungi and foilar pathogens: consequences for host and pathogen H. M. West Concluding Remarks N. J. Fokkema Part II. Plant-Microbe-Animal Interactions Introductory Remarks J. B. Whittaker 6. Interactions between arbuscular mycorrhizas and plant parasitic nematodes in agro-ecosystems R. W. Roncadori 7. Interactions between insects and mycorrhizal fungi A. C. Gange and E. Bower 8. Indirect interactions between insect herbivores and pathogenic fungi on leaves P. E. Hatcher and P. G. Ayres 9. Fungal endophytes, herbivores and the structure of grassland communities K. Clay 10. A Catch 22: the utilisation of endophytic fungi for pest management R. A. Prestidge and O. J - P. Ball Concluding Remarks J. B. Whittaker Part III. Plant-Animal Interactions Introductory Remarks R. Karban 11. Induced responses in trees: mediators of interactions among macro- and micros-herbivores? S. H. Faeth and D. Wilson 12. Host-plant mediated interactions between spatially separated herbivores: effects on community structure G. J. Masters and V. K. Brown 13. Gall-inducing insect herbivores in multitrophic systems P. W. Price, G. W. Fernandes and R. Declerck-Floate 14. Host-multiparasitoid interactions T. H. Jones, M. P. Hassell and H. C. J. Godfray 15. Vertebrate effects on plant-invertebrate food webs T. Tscharntke Concluding Remarks R. Karban Part IV. Complex Animal Interactions Introductory Remarks R. M. May 16. Two's company, three's a crowd: host-pathogen-parasitoid dynamics M. Begon, S. Sait and D. J. Thompson 17. Community modules R. D. Holt 18. Outlines of food webs in a low arctic tundra landscape in relation to three theories on trophic dynamics L. Oksanen, M. Aunapuu, T. Oksanen, M. Scneider, P. Ekerholm, P. A. Lundberg, T. Armulik, V. Aruoja and L. Bondestad 19. Compartmentalisation of resource utilisation within soil ecosystems J. C. Moore and P. C. De Ruiter 20. Food-web patterns: what do we really know? S. J. Hall and D. G. Raffaelli Concluding Remarks R. M. May Indexes.
Epidemic Shigella dysenteriae Type 1 in Burundi: Panresistance and Implications for Prevention (1994)

An epidemic of Shigella dysenteriae type 1 infections has affected Africa since 1979. Reported dysentery cases increase sharply in Burundi during September through December. Of stool samples from 189 patients reporting bloody diarrhea in November 1990, a pathogen was identified in 123 (65%). The pathogen was S. dysenteriae type 1 in 82 (67%). All S. dysenteriae type 1 isolates were resistant to ampicillin, chloramphenicol, nalidixic acid, streptomycin, sulfisoxazole, tetracycline, and trimethoprim-sulfamethoxazole. Thirty-two specimens (26%) yielded other Shigella species. Patients with S. dysenteriae type 1 were more likely than those with other Shigella infections to have abdominal pain, "lots of blood" in the stool, blood in the stool specimen examined by the interviewer, recent contact with a person with dysentery, or recent antimicrobial treatment. Thus, the seasonal increase in dysentery was due largely to multidrug-resistant S. dysenteriae type 1, clinical and epidemiologic features may predict such infection, and efforts to control this epidemic must focus on preventing transmission.
Different Doses of β‐Cryptoxanthin May Secure the Retina from Photooxidative Injury Resulted from Common LED Sources (2021)

Retinal damage associated with loss of photoreceptors is a hallmark of eye diseases such as age-related macular degeneration (AMD) and diabetic retinopathy. Potent nutritional antioxidants were previously shown to abate the degenerative process in AMD. <i>β</i>-Cryptoxanthin (BCX) is an essential dietary carotenoid with antioxidant, anti-inflammatory, and provitamin A activity. It is a potential candidate for developing intervention strategies to delay the development/progression of AMD. In the current study, the effect of a novel, highly purified BCX oral formulation on the rat retinal damage model was evaluated. Rats were fed with BCX for four weeks at the doses of 2 and 4 mg/kg body weight in the form of highly bioavailable oil suspension, followed by retinal damage by exposing to the bright light-emitting diode (LED) light (750 lux) for 48 hrs. Animals were sacrificed after 48 hours, and eyes and blood samples were collected and analyzed. BCX supplementations (2 and 4 mg/kg) showed improvements in the visual condition as demonstrated by histopathology of the retina and measured parameters such as total retinal thickness and outer nuclear layer thickness. BCX supplementation helped reduce the burden of oxidative stress as seen by decreased serum and retinal tissue levels of malondialdehyde (MDA) and restored the antioxidant enzyme activities in BCX groups. Further, BCX supplementation modulated inflammatory markers (IL-1<i>β</i>, IL-6, and NF-<i>κ</i>B), apoptotic proteins (Bax, Bcl-2, caspase 3), growth proteins and factors (GAP43, VEGF), glial and neuronal proteins (GFAP, NCAM), and heme oxygenase-1 (HO-1), along with the mitochondrial stress markers (ATF4, ATF6, Grp78, Grp94) in the rat retinal tissue. This study indicates that oral supplementation of BCX exerts a protective effect on light-induced retinal damage in the rats via reducing oxidative stress and inflammation, also protected against mitochondrial DNA damage and cellular death.
Rational Design of Biomolecular Templates for Synthesizing Multifunctional Noble Metal Nanoclusters toward Personalized Theranostic Applications (2016)

Biomolecule-templated or biotemplated metal nanoclusters (NCs) are ultrasmall (<2 nm) metal (Au, Ag) particles stabilized by a certain type of biomolecular template (e.g., peptides, proteins, and DNA). Due to their unique physiochemical properties, biotemplated metal NCs have been widely used in sensing, imaging, delivery and therapy. The overwhelming applications in these individual areas imply the great promise of harnessing biotemplated metal NCs in more advanced biomedical aspects such as theranostics. Although applications of biotemplated metal NCs as theranostic agents are trending, the rational design of biomolecular templates suitable for the synthesis of multifunctional metal NCs for theranostics is comparatively underexplored. This progress report first identifies the essential attributes of biotemplated metal NCs for theranostics by reviewing the state-of-art applications in each of the four modalities of theranostics, namely sensing, imaging, delivery and therapy. To achieve high efficacy in these modalities, we elucidate the design principles underlying the use of biomolecules (proteins, peptides and nucleic acids) to control the NC size, emission color and surface chemistries for post-functionalization of therapeutic moieties. We then propose a unified strategy to engineer biomolecular templates that combine all these modalities to produce multifunctional biotemplated metal NCs that can serve as the next-generation personalized theranostic agents.
What Changes in Poly(3-Hydroxybutyrate) (PHB) When Processed as Electrospun Nanofibers or Thermo-Compression Molded Film? (2016)

In the present study, PHB film was prepared by thermo-compression molding and PHB nanofibers mat was produced through electrospinning process. The nanofibers morphology was confirmed by SEM. The film and nanofibers crystallinity degree was estimated by different methods. FTIR and WAXD indicated that PHB film is more crystalline than PHB nanofibers. However, DSC analysis suggested that a PHB nanofibers phase change might occur while the temperature rises. SAXS indicated that PHB film and nanofibers have low electron density contrast between the alternating crystalline and amorphous layers. The influence of nanofiber morphology on the mechanical, surface and thermal properties was also shown in TG analysis, tensile tests and contact angle measurements.
Thermal analysis of the influence of nonlinear, unbalanced and asymmetric loads on current conducting capacity of LV-cables (2004)

Asymmetry, unbalance and nonlinearity of loads affect the current distribution in both phase and neutral conductor cores in three phase power supply systems. Consequently, temperature distribution in the cable section which is directly related to the power dissipation is influenced. Applying a maximum insulation temperature as boundary condition, the power conducting capacity of LV-cables will substantially be affected by asymmetry, unbalance and especially nonlinearity of loads. The most relevant combinations of asymmetry, unbalance, and nonlinearity were analyzed. The temperature distribution in the cable section is thermally calculated and is subsequently simulated, using 2D finite element modelling. Finally, measurements of the cable temperature arc performed verifying the simulation results.
Posttranslational Modification of Ataxin-7 at Lysine 257 Prevents Autophagy-Mediated Turnover of an N-Terminal Caspase-7 Cleavage Fragment (2009)

Polyglutamine (polyQ) expansion within the ataxin-7 protein, a member of the STAGA [SPT3-TAF(II)31-GCN5L acetylase] and TFTC (GCN5 and TRRAP) chromatin remodeling complexes, causes the neurodegenerative disease spinocerebellar ataxia type 7 (SCA7). Proteolytic processing of ataxin-7 by caspase-7 generates N-terminal toxic polyQ-containing fragments that accumulate with disease progression and play an important role in SCA7 pathogenesis. To elucidate the basis for the toxicity of these fragments, we evaluated which posttranslational modifications of the N-terminal fragment of ataxin-7 modulate turnover and toxicity. Here, we show that mutating lysine 257 (K257), an amino acid adjacent to the caspase-7 cleavage site of ataxin-7 regulates turnover of the truncation product in a repeat-dependent manner. Modification of ataxin-7 K257 by acetylation promotes accumulation of the fragment, while unmodified ataxin-7 is degraded. The degradation of the caspase-7 cleavage product is mediated by macroautophagy in cell culture and primary neuron models of SCA7. Consistent with this, the fragment colocalizes with autophagic vesicle markers, and enhanced fragment accumulation increases in these lysosomal structures. We suggest that the levels of fragment accumulation within the cell is a key event in SCA7 neurodegeneration, and enhancing clearance of polyQ-containing fragments may be an effective target to reduce neurotoxicity in SCA7.
A zero order minimization algorithm using a neural network (2003)

The algorithm for solving the problem of unconditional minimization of goal function, F(x), through the use of artificial neural network is offered in this paper. It is known about F(x) only that it exists. The algorithm has been tested on model tasks.
Influence of Thermal and Flow Boundary Perturbations on Convection Heat Transfer Characteristics. Numerical Analysis based on Adjoint Formulation. (2000)

A mumerical approach based on adjoint formulation of convection heat transfer is proposed to predict the change of heat transfer characteristics for arbitrary thermal and flow boundary perturbations. In order to obtain the adjoint system of the convection heat transfer problem, we formally linearize the governing equations by the perturbation method and then derive the adjoint system for the perturbation system. As a result, it is shown that the numerical solutions of the base and the adjoint problems enable us to predict the changes of heat transfer characteristics, such as a change of total heat transfer rate or a change of temperature at a specific location, when the thermal and flow boundary conditions are perturbed. An application example is presented to demonstrate the proposed method.
TaClo as a neurotoxic lead: improved synthesis, stereochemical analysis, and inhibition of the mitochondrial respiratory chain. (1995)

"TaClo", a highly halogenated tetrahydro-beta-carboline derived from the biogenic amine tryptamine ("Ta") and the synthetic hypnotic chloral ("Clo"), has to be considered as a dopaminergic neurotoxin potentially occurring in vivo. For the preparation of TaClo on a large scale, an improved synthetic pathway was elaborated. The distinct neurotoxic activity of TaClo warrants its intensive study also under stereochemical aspects. For this reason, an analytic device for the separation and stereochemical attribution of its two enantiomers, (R)-TaClo and (S)-TaClo, was developed, based on chromatography on a chiral HPLC phase. Elucidation of the absolute configuration was achieved by CD spectroscopy and confirmed by X-ray crystallography. TaClo exhibits highly selective in vitro inhibition of complex I of the mitochondrial respiratory chain, the required concentrations being much lower than those needed for related halogen-free beta-carbolines or for MPP+ (1-methyl-4-phenyl-pyridinium ion), the active metabolite of MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine). Furthermore, TaClo as a novel lead structure stimulated chemical and neuropharmacological investigations also on related highly halogenated beta-carbolines. Thus, some of the tested compounds--both potential TaClo metabolites and unnatural derivatives--showed even an enhanced inhibition of the mitochondrial respiration in vitro.
Sur la date du traité entre Pharnace et Chersonèse Taurique (2016)

Le traité entre Pharnace du Pont et Chersonèse de Tauride est daté « du mois de Daisios, de la cent cinquante-septième année, comme le compte le roi Pharnace » . Il y a plus de cent ans, le premier éditeur, R. Kh. Loeper, suivi par l’éditeur des IOSPE (n° 402), avait rapproché l’inscription de Polybe, XXV, 2, 1-15, y avait vu un écho de la paix conclue entre Pharnace et ses ennemis de la guerre pontique de 183/ 2-180/ 79, et avait daté le traité d’avril/ mai 179 selon une ère débutant avec l’avènement du supposé fondateur du royaume du Pont, Mithridate II de Kios (336 ?). Alors que dans les années 1980, prenant en compte l’ère séleucide, on avait pensé pouvoir descendre le traité de Pharnace avec Chersonèse au printemps 155, la présente contribution réévalue la durée de règne de Mithridate IV (ca 170-ca 150), frère et successeur de Pharnace, notamment à la lumière de sa production monétaire et de la date de sa dédicace capitoline, probablement haute (peu après 167). Pharnace ayant régné de ca 196 à ca 170, le traité ne peut dater de 155. L’ère utilisée par Pharnace ne fait pas mention de l’avènement de Mithridate II de Kios, puisque les sources littéraires et l’archéologie montrent que le véritable fondateur de la dynastie est le fils de ce dernier, Mithridate Ier Ktistès. On peut émettre l’hypothèse que Pharnace utilise une ère sinopéenne, commençant à l’équinoxe de l’automne 336 et introduite après sa conquête de la ville dont il fit sa capitale. Datant du printemps 179, le traité peut être interprété comme la volonté des Chersonésitains de chercher la protection du roi du Pont, contre les Scythes, et peu leur importait la clause concernant l’obligation de préserver l’amicitia envers Rome.
Images from Red Cells (2023)

Erythrocytes are fascinating cells. Despite their apparent simplicity, they are able to control tissue oxygenation, ions exchange, and energy supply. Given their peculiar bending elasticity and deformability, they may assume, in normal and pathological conditions, different conformations that sometimes make red blood cell (RBC) morphology a “biological picture”. Not surprisingly, several congenital RBC disorders derive their nomenclature from erythrocyte morphology. The beauty of the images is not certainly limited to clinical and diagnostics aspects, but also to basic research in human and other species, following treatments or drug administration, red cell aging, conservation, or during erythroid differentiation.This new Research Topic is intended to stimulate submission of full research articles, review or short reports, based on an image connected in some way to the red cell. Images may be described in a context of a research work on red cell pathology, such as atypical/complex phenotypes and diagnosis, but also for example from normal cells subjected to treatments, stress or manipulations. They should not be limited to a microscopy image of a red cell but also to the visual output of an analytical procedure. The Research Topic “Images from Red Cell” could be appealing for researchers in the field, and is intended to be open not only to attendees of the 2020 Virtual ERCS meeting, but also to the greater community of red cell researchers around the world.
University Collaboration - Research Collaboration and Teaching Collaboration (2018)

Multidisciplinary, multicultural, and multitasking has taken center stage in the global educational debate. Globalization and improvement in communication have affected the way organisations operate and hence influenced whom they hire. Today, it is common practice to work with people from diverse backgrounds and it requires competencies that go beyond general project management. Intercultural awareness, networking in different global communities, and learning to develop specific communication strategies for different stakeholders is all part of the package of skills and competencies that are required in today’s interconnected world. This has indirect implication on the nature of skills and competencies institutions/universities must equip their students with to enable them to compete successfully in the working world.
Characteristics and human factors of older drivers: improvement opportunities in automotive interior design (2017)

This paper analyses the characteristics and human factors of older drivers and how those can influence the driving experience. This research analyses recent studies in ergonomics, interaction and influence of the technologies applied to design of the physical interfaces and their respective in-vehicle devices, with the aim of identifying improvement opportunities in enabling usability design for on-board tasks. The research methodology is descriptive with a collection of baseline studies within the auto industry, ergonomics, health and the mobility and behaviour of older drivers. It is concluded that even the latest car models do not fully provide the highest levels of safety and comfort that could be achieved, with some manufacturers opting to include extra resources to mitigate the changes that result from ageing and driving. It is suggested to create automotive interior design recommendations in a way that improves the safety, comfort and inclusion of older drivers.
Procedural Function-Based Spatial Microstructures (2010)

We propose a new approach to modelling heterogeneous objects containing internal spatial geometric structures with size of details orders of magnitude smaller than the overall size of the object. The proposed function-based procedural representation provides compact, precise, and arbitrarily parametrized models of coherent microstructures, which can undergo blending, deformations, and other geometric operations, and can be directly rendered and fabricated without generating any auxiliary representations (such as polygonal meshes and voxel arrays). In particular, modelling of regular lattices and cellular microstructures as well as irregular porous media is discussed and illustrated. Examples of rendering and digital fabrication of microstructure models are presented.