Chromatin: a tunable spring at work inside chromosomes

This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the ``extensible worm-like rope'', allowing a straightforward prediction of the force-extension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure

CHALLENGES IN FLYING QUADROTOR UNMANNED AERIAL VEHICLE FOR 3D INDOOR RECONSTRUCTION

Three-dimensional modelling plays a vital role in indoor 3D tracking, navigation, guidance and emergency evacuation. Reconstruction of indoor 3D models is still problematic, in part, because indoor spaces provide challenges less-documented than their outdoor counterparts. Challenges include obstacles curtailing image and point cloud capture, restricted accessibility and a wide array of indoor objects, each with unique semantics. Reconstruction of indoor environments can be achieved through a photogrammetric approach, e.g. by using image frames, aligned using recurring corresponding image points (CIP) to build coloured point clouds. Our experiments were conducted by flying a QUAV in three indoor environments and later reconstructing 3D models which were analysed under different conditions. Point clouds and meshes were created using Agisoft PhotoScan Professional. We concentrated on flight paths from two vantage points: 1) safety and security while flying indoors and 2) data collection needed for reconstruction of 3D models. We surmised that the main challenges in providing safe flight paths are related to the physical configuration of indoor environments, privacy issues, the presence of people and light conditions. We observed that the quality of recorded video used for 3D reconstruction has a high dependency on surface materials, wall textures and object types being reconstructed. Our results show that 3D indoor reconstruction predicated on video capture using a QUAV is indeed feasible, but close attention should be paid to flight paths and conditions ultimately influencing the quality of 3D models. Moreover, it should be decided in advance which objects need to be reconstructed, e.g. bare rooms or detailed furniture

RECONSTRUCTION OF ARCHITECTURAL HERITAGE WITH SYMMETRICAL COMPONENTS

Data capturing through either Lidar or photogrammetry, often results in incomplete and partial information related to a surface due to occlusion or inaccessibility of the clear object vision. In case of asymmetrical objects yet the reconstruction is unattainable by any means, meanwhile the approach for the development of the missing information could be done in cases of symmetrical objects. In this paper we have advised a semi-automatic approach for recreating missing or incomplete information from the partially captured data using space sub-division and 3D transformation. The study has been done on a 175 year-old building whose scanned information is available for only one side and captures a façade with four columns. The idea is to first extract the symmetrical parts through segmentation of different building parts. Then the columns with partial information have been oriented as per a reference plane based on the pose and centre computed from the horizontal parts. The instance is then used to fill in the lost information through duplication and transformation. This approach can be used to recreate structures with symmetrical elements, which are partially destroyed from withering, disaster, or any human intervention

Dendrimers in Nanoscale Confinement: The Interplay between Conformational Change and Nanopore Entrance

Hyperbranched dendrimers are nanocarriers for drugs, imaging agents, and catalysts. Their nanoscale confinement is of fundamental interest and occurs when dendrimers with bioactive payload block or pass biological nanochannels or when catalysts are entrapped in inorganic nanoporous support scaffolds. The molecular process of confinement and its effect on dendrimer conformations are, however, poorly understood. Here, we use single-molecule nanopore measurements and molecular dynamics simulations to establish an atomically detailed model of pore dendrimer interactions. We discover and explain that electrophoretic migration of polycationic PAMAM dendrimers into confined space is not dictated by the diameter of the branched molecules but by their size and generation-dependent compressibility. Differences in structural flexibility also rationalize the apparent anomaly that the experimental nanopore current read-out depends in nonlinear fashion on dendrimer size. Nanoscale confinement is inferred to reduce the protonation of the polycationic structures. Our model can likely be expanded to other dendrimers and be applied to improve the analysis of biophysical experiments, rationally design functional materials such as nanoporous filtration devices or nanoscale drug carriers that effectively pass biological pores

Prognosis in patients with myocardial infarction with ST-elevation depending on the timing of interventional revascularization

Проверена е прогнозата (болничния и следболничния леталитет до края на 6-ия месец) при 300 болни (212 мъже и 88 жени) с първи миокарден инфаркт със ST- елевация (STEMI) на средна възраст 62.9 год. в зависимост от срока на извършената първична коронарна интервенция (PCI) след началото на симптомите. В зависимост от срока на извършената РСІ болните са разделени на 4 групи: до 3-ия, до 6-ия, до 12-ия и до 24-ия час след началото на инфаркта. Болничният леталитет за всички болни е 6.3%, a до края на 6-ия месец - 13.3%, еднакъв при І-ва и ІІ-ра група и достоверно по-малък, отколкото при ІІІ-та и ІV-та група, по-голям при жените, при болните над 65 г., с ФИ <35.0% и с тромботична оклузия на LM и LAD.The prognosis (in-hospital and post-hospitalization lethality by the end of the 6th moth) of 300 patients (212 men and 88 women) with a first myocardial infarction with ST-elevation (STEMI) at an average age of 62.9 years was studied depending on the timing of the conducted primary coronary intervention (PCI) after the onset of symptoms. Depending on the timing of the conducted PCI, the patients were divided into 4 groups: by the 3rd, 6th, 12th, and 24th hour after the onset of the infarction. The patients` in-hospital lethality was 6.3%, and that by the end of the 6th month - 13.3%. It was the same for groups I and II and significantly lower than in groups III and IV; higher in women, in patients over 65 years of age, with ejection fraction (EF) <35.0% and with thrombotic occlusion of LM and LAD

Distributed GIS for automated natural hazard zonation mapping internet-SMS warning towards sustainable society

Today, open systems are needed for real time analysis and warnings on geo-hazards and over time can be achieved using Open Source Geographical Information System (GIS)-based platform such as GeoNode which is being contributed to by developers around the world. To develop on an open source platform is a very vital component for better disaster information management as far as spatial data infrastructures are concerned and this would be extremely vital when huge databases are to be created and consulted regularly for city planning at different scales, particularly satellite images and maps of locations. There is a big need for spatially referenced data creation, analysis, and management. Some of the salient points that this research would be able to definitely contribute with GeoNode, being an open source platform, are facilitating the creation, sharing, and collaborative use of geospatial data. The objective is development of an automated natural hazard zonation system with Internet-short message service (SMS) warning utilizing geomatics for sustainable societies. A concept of developing an internet-resident geospatial geohazard warning system has been put forward in this research, which can communicate alerts via SMS. There has been a need to develop an automated integrated system to categorize hazard and issue warning that reaches users directly. At present, no web-enabled warning system exists which can disseminate warning after hazard evaluation at one go and in real time. The objective of this research work has been to formalize a notion of an integrated, independent, generalized, and automated geo-hazard warning system making use of geo-spatial data under popular usage platform. In this paper, a model of an automated geo-spatial hazard warning system has been elaborated. The functionality is to be modular in architecture having GIS-graphical user interface (GUI), input, understanding, rainfall prediction, expert, output, and warning modules. A simplified but working prototype of the system without the GIS-GUI module has been already tested, validated, and reported. Through this paper, a significantly enhanced system integrated with web-enabled-geospatial information has been proposed, and it can be concluded that an automated hazard warning system has been conceptualized and researched. However, now the scope is to develop it further

Capacity Building for GIS-based SDG Indicator Analysis with Global High-resolution Land Cover Datasets

The support of geospatial data and technologies for the United Nations Sustainable Development Goals (SDG) framework is critical for assessing and monitoring key indicators, revealing the planet’s trajectory towards sustainability. The availability of global open geospatial datasets, especially high-resolution land cover datasets, provides significant opportunities for computing and comparing indicators across different regions and scales. However, barriers to their proficient use remain due to a lack of data awareness, management and processing capacities using geographic information systems software. To address this, the”Capacity Building for GIS-based SDG Indicator Analysis with Global High-resolution Land Cover Datasets” project created open training material on discovering, accessing, and manipulating global geospatial datasets for computing SDG indicators. The material focuses on water and terrestrial ecosystems, urban environments, and climate, by leveraging world-class global geospatial datasets and using the Free and Open Source Software QGIS. The training material is released under a Creative Commons Attribution 4.0 License, ensuring broad accessibility and facilitating continuous improvement

CAPACITY BUILDING FOR GIS-BASED SDG INDICATORS ANALYSIS WITH GLOBAL HIGH-RESOLUTION LAND COVER DATASETS

The support of geospatial data and technologies for the United Nations Sustainable Development Goals (SDG) framework is critical for assessing and monitoring key indicators, revealing the planet’s trajectory towards sustainability. The availability of global open geospatial datasets, especially high-resolution land cover datasets, provides significant opportunities for computing and comparing indicators across different regions and scales. However, barriers to their proficient use remain due to a lack of data awareness, management and processing capacities using geographic information systems software. To address this, the ”Capacity Building for GIS-based SDG Indicator Analysis with Global High-resolution Land Cover Datasets” project created open training material on discovering, accessing, and manipulating global geospatial datasets for computing SDG indicators. The material focuses on water and terrestrial ecosystems, urban environments, and climate, by leveraging world-class global geospatial datasets and using the Free and Open Source Software QGIS. The training material is released under a Creative Commons Attribution 4.0 License, ensuring broad accessibility and facilitating continuous improvement

Extraction of Accurate Biomolecular Parameters from Single-Molecule Force Spectroscopy Experiments

The atomic force microscope (AFM) is able to manipulate biomolecules and their complexes with exquisite force sensitivity and distance resolution. This capability, complemented by theoretical models, has greatly improved our understanding of the determinants of mechanical strength in proteins and revealed the diverse effects of directional forces on the energy landscape of biomolecules. In unbinding experiments, the interacting partners are usually immobilized on their respective substrates via extensible linkers. These linkers affect both the force and contour length (Lc) of the complex at rupture. Surprisingly, while the former effect is well understood, the latter is largely neglected, leading to incorrect estimations of Lc, a parameter that is often used as evidence for the detection of specific interactions and remodeling events and for the inference of interaction regions. To address this problem, a model that predicts contour length measurements from single-molecule forced-dissociation experiments is presented that considers attachment position on the AFM tip, geometric effects, and polymer dynamics of the linkers. Modeled data are compared with measured contour length distributions from several different experimental systems, revealing that current methods underestimate contour lengths. The model enables nonspecific interactions to be identified unequivocally, allows accurate determination of Lc, and, by comparing experimental and modeled distributions, enables partial unfolding events before rupture to be identified unequivocally