jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Jingwei Zhao | Xing Zhang | Hua HAN | Chang-Lu Tao | Guo‐Qiang Bi | Wenxi Liang
Source: Scientia Sinica Vitae (article, 2020-04-20)
Field: Materials Science — Surfaces, Coatings and Films

Frontiers of electron microscopy for biomedical research <p indent="0mm">Electron microscopy (EM) has been an important tool widely used in biomedical research. Recent progress in physics, informatics, biology and other disciplines has enabled major breakthroughs for EM to achieve higher resolution and throughput. For example, cryogenic sample preparation and direct electron detection helped cryoEM to solve atomic structures of biological macromolecules. In the meantime, biological systems and life processes often span multiple spatial and temporal scales, and demand not only resolution, specificity and throughput, but also in their applicability <italic>in situ</italic>. To this end, the techniques and applications of biomedical EM is advancing in several fronts: (i) For high resolution cryoEM, new electron-optical imaging techniques will achieve higher signal-to-noise ratio, whereas new computational techniques will allow for more precise three-dimensional reconstruction. (ii) For cryo electron tomography (cryoET), optimized cryo-sectioning/milling techniques for tissue/cell samples and new computational methods such as sub-tomogram averaging will enable study of molecular organization <italic>in situ</italic>. Its multimodal integration with light microscopy will enable structure-function studies of subcellular machinery. (iii) For large-scale volume electron microscopy, faster imaging and data processing will allow for high throughput mapping of brain connectomes and other biological structures. (iv) Ultrafast electron microscopy with femtosecond temporal resolution will provide new tools to resolve the dynamic process of protein isomerization as well as the physical and chemical interactions in live cells and tissues. (v) New techniques of data handling and AI-based analysis methods will further facilitate the processing and analysis of the rapidly growing volume of EM data. In this paper, we reviewed the trends, challenges, and possible breakthroughs in EM and related technologies, and discussed perspectives of their applications in biomedical research. Electron microscope ; Nanotechnology ; Materials science ; Physics ; Optics Electron and X-Ray Spectroscopy Techniques
Authors: Thomas Bouvarel
Source: SPIRE - Sciences Po Institutional REpository (preprint, 2020-11-27)
Field: Chemistry — Analytical Chemistry

Polymères à empreintes moléculaires pour l’analyse miniaturisée de traces de stupéfiants et de neurotransmetteurs dans des échantillons biologiques An important part in analytical chemistry is related to the miniaturization and integration of different analytical steps in a single device in order to meet portability and automation issues. However, solutions for the analysis of complex samples with limited volumes containing various analytes of interest that may be found at trace levels are still required. One approach consists in the in situ synthesis of imprinted monoliths within capillaries and their on-line coupling with a separation and/or detection step. After the study of the state-of-the-art concerning the integration of molecularly imprinted polymers in miniaturized extraction and separation devices, the development of miniaturized imprinted monolithic supports and their on-line coupling with a nano-liquid chromatography separation or directly with UV detection were performed for biological applications. Different synthesis pathways were screened. The characterization of the obtained supports was carried out in terms of morphology, permeability and synthesis repeatability. The selectivity of MIP monoliths was evaluated with nano-liquid chromatography by confronting their extraction potential with the one of non-imprinted monoliths synthesized in the same conditions but without the introduction of the template. The extraction protocols and coupling conditions were successfully optimized for the analysis of cocaine in saliva and plasma or the detection of benzoylecgonine in urine with detection thresholds in agreement with the legislation around tens of ng/mL. By exploiting the know-how acquired, other miniaturized imprinted supports were also produced to target neurotransmitters and structural analogues. Molecularly imprinted polymer ; Molecular imprinting ; Chromatography ; Monolith ; Analyte ; Miniaturization ; Nanotechnology ; Materials science ; Extraction (chemistry) ; Porosimetry ; Repeatability ; Sample preparation ; Solid phase extraction ; Chemistry ; Selectivity ; Porosity ; Porous medium ; Organic chemistry Analytical chemistry methods development ; Mass Spectrometry Techniques and Applications ; Microfluidic and Capillary Electrophoresis Applications
Authors: S I Koryagin | О.В. Шарков | Н Л Великанов
Source: МОРСКИЕ ИНТЕЛЛЕКТУАЛЬНЫЕ ТЕХНОЛОГИИ (article, 2020-03-11)
Field: Materials Science — General Materials Science

Изгиб и растяжение судовых композитных элементов Полимерные покрытия давно и прочно завоевали свое место при изготовлении и ремонте судовых конструкций. Одной из причин, сдерживающих их более широкое применение, является отсутствие расчетных зависимостей, позволяющих рассчитать прочностные свойства композитных элементов. Для построения этих зависимостей необходимы дальнейшие экспериментальные исследования, их анализ и обобщение. В работе представлены результаты исследований прочностных свойств металлических конструкций судов с армированным полимерным покрытием при растяжении и изгибе. Экспериментально было установлено, что разрушение покрытия происходило при линейных деформациях основы на границе адгезионного слоя. При загрузке образца сосредоточенной силой определены усилия, при которых произойдет механическое разрушение композиционного образца по адгезионному слою. Построены зависимости разрушающей нагрузки от соотношения толщин основы и покрытия при растяжении и изгибе, проведено сравнение с экспериментальными результатами. Polymer coatings have long and firmly won their place in the manufacture and repair of ship structures. One of the reasons restraining their wider application is the lack of computational dependencies that allow to calculate the strength properties of composite elements. Further experimental studies, analysis and generalization are needed to construct these dependencies. The paper presents the results of studies of strength properties of metal structures of ships with reinforced polymer coating under tension and bending. It was found experimentally that the destruction of the coating occurred during linear deformations of the substrate at the boundary of the adhesive layer. When loading a sample with a concentrated force, the forces at which the mechanical destruction of the composite sample along the adhesive layer will occur are determined. The dependences of the breaking load on the ratio of the thickness of the substrate and the coating under tension and bending are constructed, a comparison with the experimental results is carried out. Materials science ; Coating ; Composite material ; Bending ; Adhesive ; Tension (geology) ; Composite number ; Layer (electronics) ; Substrate (aquarium) ; Polymer ; Structural engineering ; Ultimate tensile strength ; Engineering ; Geology Material Properties and Applications ; Engineering Diagnostics and Reliability ; Material Properties and Failure Mechanisms
Authors: Xia Huang
Source: Repository KITopen (Karlsruhe Institute of Technology) (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

Fabrication of Polymeric Materials via Anodic Aluminum Oxide Templating Fabrication ; Materials science ; Anodic Aluminum Oxide ; Aluminium ; Aluminum oxide ; Anode ; Oxide ; Nanotechnology ; Metallurgy ; Chemistry ; Electrode Anodic Oxide Films and Nanostructures ; Nanofabrication and Lithography Techniques ; Advanced Machining and Optimization Techniques
Authors: Sri Ranga Jai Likith
Source: Digital Collections of Colorado (Colorado State University) (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

Chalcogenide-based van der Waals-layered materials for enhanced electronic and electromechanical properties Since the successful isolation of graphene via mechanical exfoliation at room temperature, other van der Waals (vdW)-layered or quasi-2D materials have gained significant interest in the scientific and technological communities.Quasi-2D (q2D) materials have been shown to unlock a wide variety of unusual and useful thermoelectric, electronic, optoelectronic, electromechanical, and sensing properties (among others) offering several advantages over conventional bulk 3D materials.From an application standpoint however, between the large band gap of hexagonal boron nitride and the zero band gap of graphene, the semiconductor space is mostly limited to Transition Metal Dichalcogenides (TMDCs) -which are semiconductors.There are several ways to improve the diversity of semiconducting 2D or q2D materials, which can lead not only to new materials, but to new phenomena and applications as well; these include alloying, doping, layering (heterostructuring), or discovering and manufacturing new 2D or q2D materials altogether.In the quest for new, versatile, and multifunctional q2D materials, this thesis presents computational studies based on vdW-corrected density functional theory addressing several directions of increasing the range of electronic and electromechanical properties of chalcogenide-based 2D or q2D materials.These studies pertain to group IV monochalcogenides, bilayer and bulk TMDC heterostructures, and surface-doped TMDCs, and have led, respectively, to (i) the discovery of 39 new and potentially synthesizable monochalcogenides, (ii) understanding the range of band gaps and piezoelectric coefficients achievable in bilayer TMDCs and the effects of interlayer registry, and (iii) elucidating the physical origins of the p-type doping measured in molybdenum ditelluride in ambient air. van der Waals force ; Materials science ; Chalcogenide ; Semiconductor ; Graphene ; Band gap ; Doping ; Nanotechnology ; Phosphorene ; Heterojunction ; Thermoelectric effect ; Condensed matter physics ; Optoelectronics ; Chemistry ; Physics 2D Materials and Applications ; Boron and Carbon Nanomaterials Research ; Chalcogenide Semiconductor Thin Films
Authors: Shana De Bruyn
Source: University of the Western Cape Electronic Theses and Dissertations Repository (University of the Western Cape) (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

A baseline evaluation of the cytotoxicity of gold nanoparticles in different types of mammalian cells for future radiosensitization studies Recently nanoparticles (NPs) have been introduced and used in combination with therapeutic approaches to develop nanotechnology-enabled medicine. These nanostructures allow for the exploitation of the physiochemical properties which may be beneficial in cancer treatment. The use of NPs in nanomedicine has proven successful in modern chemotherapeutics and has demonstrated promising potential in in vivo and in vitro radiosensitization studies. This is a baseline study aimed to determine the cytotoxic effects of AuNPs for potential radiosensitization analysis. The study analysed the effects of different AuNP sizes (30, 50 and 80nm), concentrations (5, 10 and 15 μg/ml) over various time periods in CHOK1 and A549 cells. AuNPs were characterised by DLS and ZP analysis and showed that particles were moderately polydispersed and moderately to highly stable in charge. The effects on viability and metabolic activity of cells were determined using crystal violet and the WST-1 assay. Nanomedicine ; Cytotoxicity ; In vivo ; Nanotechnology ; Nanoparticle ; Colloidal gold ; In vitro ; Materials science ; Chemistry ; Pharmacology ; Medicine ; Biology ; Biochemistry ; Biotechnology Nanoparticles: synthesis and applications ; Nanoparticle-Based Drug Delivery ; Field-Flow Fractionation Techniques
Authors: Rachael Knoblauch | Hilla Ben Hamo | Robert S. Marks | Chris D. Geddes
Source: Maryland Shared Open Access Repository (USMAI Consortium) (article, 2020-02-05)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Spectral Distortions in Metal-Enhanced Fluorescence: Experimental Evidence for Ultra-Fast and Slow Transitions Metal-enhanced fluorescence (MEF) has become an increasingly important technology in recent years, with thorough research addressing the fundamentals of MEF. In many studies, spectral distortion is observed in the enhanced spectra as compared to free-space fluorescence emission profiles. Despite this observation, very little experimentation has hitherto been undertaken to investigate the mechanistic underpinnings of spectral distortion in MEF. Herein, we investigate MEF spectral distortion using Rose Bengal and fluorescein on silver nanoparticle substrates, subsequently isolating the coupled fluorescence spectrum for a deeper understanding of the spectral modifications. Clear experimental evidence for bathochromic distortion is reported. Remarkably, we also report hypsochromic distortion in one of the first experimental observations of plasmonic coupling to high-energy excited states. Additionally, the coupled fluorescence spectra from other published literature have also been both extracted and examined, and the subsequent spectral distortions are reported here. The previously asserted theory of radiative decay rate modification for spectral distortion is discussed in the context of both plasmonic properties as well as fluorophore photophysical characteristics including lifetime and quantum yield. The dual enhancement mechanism of MEF is also explored in the context of spectral distortion. The results and discussion reported herein subsequently provide one of the first comprehensive examinations of spectral distortion in MEF to date. Chemistry ; Fluorophore ; Context (archaeology) ; Bathochromic shift ; Fluorescence ; Distortion (music) ; Hypsochromic shift ; Plasmon ; Spectral line ; Excited state ; Nanotechnology ; Photochemistry ; Optoelectronics ; Optics ; Physics ; Atomic physics ; Materials science ; Quantum mechanics Gold and Silver Nanoparticles Synthesis and Applications ; Photochemistry and Electron Transfer Studies ; Nanocluster Synthesis and Applications
Authors: Van Kelly | Aymen al-Rawi | David Lewis | Georg Kustatscher | Tony Ly
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-07-03)
Field: Chemistry — Spectroscopy

Low cell number proteomic analysis using in-cell protease digests reveals a robust signature for cell cycle state classification Abstract Comprehensive proteome analysis of rare cell phenotypes remains a significant challenge. We report a method for low cell number mass spectrometry (MS)-based proteomics using protease digestion of mildly formaldehyde-fixed cells in cellulo , which we call the ‘in-cell digest’. We combined this with AMPL (Averaged MS1 Precursor Library Matching) to quantitatively characterise proteomes from low cell numbers of human lymphoblasts. 4,500 proteins were detected from 2,000 cells and 2,500 proteins were quantitated from 200 lymphoblasts. The ease of sample processing and high sensitivity makes this method exceptionally suited for the proteomic analysis of rare cell states, including immune cell subsets and cell cycle subphases. To demonstrate the method, we characterised the proteome changes across 16 cell cycle states isolated from an asynchronous TK6 human lymphoblast culture, avoiding synchronization. States included late mitotic cells present at extremely low frequency. We identified 119 pseudoperiodic proteins (PsPs) that vary across the cell cycle. Clustering of the PsPs showed abundance patterns consistent with ‘waves’ of protein degradation in late S, at the G2&amp;M border, mid-mitosis and at mitotic exit. These clusters were distinguished by significant differences in predicted nuclear localization and interaction with the APC/C. The dataset also identifies putative APC/C substrates in mitosis and the temporal order in which they are targeted for degradation. We demonstrate that a protein signature made of these 119 high confidence cell cycle regulated proteins can be used to perform unbiased classification of proteomes into cell cycle states. We applied this signature to 296 proteomes that encompass a range of quantitation methods, cell types, and experimental conditions. The analysis confidently assigns a cell cycle state for 49 proteomes, including correct classification for proteomes from synchronized cells. We anticipate this robust cell cycle protein signature will be crucial for classifying cell states in single cell proteomes. Mitosis ; Proteome ; Cell cycle ; Proteomics ; Biology ; Cell ; Cell Cycle Protein ; Cell growth ; Cell division ; Cell biology ; Cell synchronization ; Computational biology ; Protein degradation ; Molecular biology ; Genetics ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Genomics and Phylogenetic Studies
Authors: Mark V. Ivanov | Julia A. Bubis | Vladimir Gorshkov | Daniil A. Abdrakhimov | Frank Kjeldsen | Mikhail V. Gorshkov
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-10-29)
Field: Chemistry — Spectroscopy

Boosting the MS1-only proteomics with machine learning allows 2000 protein identifications in 5-minute proteome analysis ABSTRACT Proteome-wide analyses most often rely on tandem mass spectrometry imposing considerable instrumental time consumption that is one of the main obstacles in a broader acceptance of proteomics in biomedical and clinical research. Recently, we presented a fast proteomic method termed DirectMS1 based on MS1-only mass spectra acquisition and data processing. The method allowed significant squeezing of the proteome-wide analysis to a few minute time frame at the depth of quantitative proteome coverage of 1000 proteins at 1% FDR. In this work, to further increase the capabilities of the DirectMS1 method, we explored the opportunities presented by the recent progress in the machine learning area and applied the LightGBM tree-based learning algorithm into the scoring of peptide-feature matches when processing MS1 spectra. Further, we integrated the peptide feature identification algorithm of DirectMS1 with the recently introduced peptide retention time prediction utility, DeepLC. Additional approaches to improve performance of the DirectMS1 method are discussed and demonstrated, such as FAIMS coupled to the Orbitrap mass analyzer. As a result of all improvements to DirectMS1, we succeeded in identifying more than 2000 proteins at 1% FDR from the HeLa cell line in a 5 minute LC-MS1 analysis. Proteome ; Proteomics ; Computer science ; Orbitrap ; Mass spectrometry ; Boosting (machine learning) ; Mascot ; Turnaround time ; Tandem mass tag ; Artificial intelligence ; Tandem mass spectrometry ; Computational biology ; Quantitative proteomics ; Machine learning ; Chemistry ; Bioinformatics ; Chromatography ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Noah J. Kopcho
Source: eScholarship (California Digital Library) (article, 2020-01-01)
Field: Chemistry — Spectroscopy

Conformational Dynamics of Membrane Proteins Membrane proteins reside along the barrier between intracellular and extracellular milieu. They regulate transport and transduce signal necessary to maintain life. Critical to these functions are dynamic motions capable of transmitting molecules or information. The method of HDX-MS is uniquely suited to studying such conformational dynamics, as the timescales of measurement refer to the broad motions associated with domain movement and catalysis. This work employs HDX-MS to study the dynamics of three unique membrane associated proteins. Kinetic analysis and the method of HDX-MS are extended to characterize in vitro generated monoclonal camelid antibody fragments. Biophysics ; Dynamics (music) ; Chemistry ; Extracellular ; Membrane ; Domain (mathematical analysis) ; Membrane protein ; Biological system ; Physics ; Biology ; Biochemistry ; Mathematics Mass Spectrometry Techniques and Applications ; Monoclonal and Polyclonal Antibodies Research ; Protein purification and stability
Authors: James Sanford | Yang Wang | Joshua Hansen | Marina Gritsenko | Karl Weitz | Cristina E. Tognon | Vladislav Petyuk | Weijun Qian | Tao Liu | Brian Druker | Karin Rodland | Paul Piehowski
Source: Research Square (preprint, 2020-08-04)
Field: Chemistry — Spectroscopy

Evaluation of Differential Peptide Loading on Tandem Mass Tag-Based Proteomic and Phosphoproteomic Data Quality Peptide ; Tandem ; Tandem mass spectrometry ; Computational biology ; Differential (mechanical device) ; Tandem mass tag ; Computer science ; Chemistry ; Proteomics ; Biology ; Chromatography ; Biochemistry ; Mass spectrometry ; Engineering ; Quantitative proteomics Advanced Proteomics Techniques and Applications ; Molecular Biology Techniques and Applications ; Genomics and Phylogenetic Studies
Authors: James Sanford | Yang Wang | Joshua Hansen | Marina Gritsenko | Karl Weitz | Cristina E. Tognon | Vladislav Petyuk | Weijun Qian | Tao Liu | Brian Druker | Karin Rodland | Paul Piehowski
Source: Research Square (preprint, 2020-12-29)
Field: Chemistry — Spectroscopy

Evaluation of differential peptide loading on tandem mass tag-based proteomic and phosphoproteomic data quality Abstract Background: Global and phosphoproteome profiling has demonstrated great utility for the analysis of clinical specimens. One major barrier to the broad clinical application of proteomic profiling is the large amount of biological material required, particularly for phosphoproteomics—currently on the order of 25 mg wet tissue weight, depending on tissue type. For hematopoietic cancers such as acute myeloid leukemia (AML), the sample requirement is in excess of 10 million (1E7) peripheral blood mononuclear cells (PBMCs). Throughout the course of a prospective study, this requirement will certainly exceed what is obtainable from many of the individual patients/timepoints. For this reason, we were interested in examining the impact of differential peptide loading across multiplex channels on proteomic data quality. Methods: To achieve this, we tested a range of channel loading amounts (20, 40, 100, 200, and 400 μg of tryptic peptides, or approximately the material obtainable from 5E5, 1E6, 2.5E6, 5E6, and 1E7 AML patient cells) to assess proteome coverage, quantification precision, and peptide/phosphopeptide detection in experiments utilizing isobaric tandem mass tag (TMT) labeling. Results: As expected, we found that fewer missing values are observed in TMT channels with higher peptide loading amounts compared to those with lower loading. Moreover, channels with lower loading amounts have greater quantitative variability than channels with higher loading amounts. Statistical analysis of the differences in means among the five loading groups showed that the 20 μg loading group was significantly different from the 400 μg loading group. However, no significant differences were detected among the 40, 100, 200 and 400 μg loading groups. Conclusions: These assessment data demonstrate the practical limits of loading differential quantities of peptides across channels in TMT multiplexes, and provide a basis for designing the optimal clinical proteomics study when specimen quantities are limited. Peptide ; Computational biology ; Tandem mass spectrometry ; Tandem ; Tandem mass tag ; Proteomics ; Differential (mechanical device) ; Chemistry ; Computer science ; Biology ; Chromatography ; Mass spectrometry ; Biochemistry ; Engineering ; Quantitative proteomics Advanced Proteomics Techniques and Applications ; Advanced Biosensing Techniques and Applications ; Molecular Biology Techniques and Applications