Conversion of dormitory to hostel and new design of hotel, Tomioka Silk Mill, Japan

Diplomová práce s názvem „KONVERZE OBJEKTU DORMITORY NA HOSTEL A JEHO NOVÉ ŘEŠENÍ V TOMIOKA SILK MILL, JAPONSKO“ je zpracována dle platných předpisů ve formě architektonické studie. Předmětem této práce jsou dvě varianty konverze objektu pro ubytování dělnic (dormitory). Dílčím úkolem je řešení úpravy zeleně v atriu dormitory a návrh revitalizace náhorní roviny. Objekt se nachází v areálu bývalé přádelny hedvábí ve městě Tomioka v prefektuře Gunma, na ostrově Honšú v Japonsku. Konverze objektu na nový účel vyžaduje doplnění potřebné vybavenosti a některé nutné stavební zásahy pro zajištění provozu hostelu. V obou variantách je zapotřebí částečně upravit také původní objekt při zachování jeho proporcí a objemu, aby nebyla narušena původní koncepce celého areálu a silueta města. Úpravy původního objektu dormitory zahrnují dostavbu vstupního portálu včetně foyer a recepce se zázemím provozu. Použité materiály jsou velké prosklené plochy v kombinaci se světlým pohledovým betonem. Materiály byly vybrány tak, aby byly vždy jasně odlišitelné nové konstrukce (monolitický železobeton) od konstrukcí původních (dřevo). Vnitřní atrium bylo navrženo ve stylu moderní japonské zahrady s různými typy povrchů (vegetační – mech; minerální – štěrk a kamení). Varianta 1 – novostavba dvou objektů vybavenosti. Objekt A jsou umývárny a objekt B je pro stravování a toalety. Hmotu nových objektů tvoří jednoduché hranoly pootočené o 30° a 60° oproti ose dormitory. Jejich hmoty respektují rozměry původního objektu. Objekt A je vysunutý nad hranu svahu a je obložený skleněnými deskami. Objekt B je z jižní strany prosklený, zatímco ze severní strany je kompaktní z pohledového betonu. Objekt A je stavebně i provozně rozdělen středovou stěnou na dvě symetrické části. V závěru objektu je umístěno ofuro (bazének) s výhledem na okolní pohoří. Typologické řešení objektu B zahrnuje oddělené toalety se smíšenou umývárnou v severní části. V jižní části je prostor pro stravování rozdělený výdejním pultem na provozní část a část pro návštěvníky. Objekt A je ze železobetonu a je založen na základové desce. Středová stěna je hlavní nosný konstrukční prvek, která brání příčnému zlomení. Středová stěna je ukotvena do země pomocí pilotů. Objekt B je ze železobetonu a je založen na základových pasech. Varianta 2 – přístavba je tvořena jako jednoduchý hranol, který respektuje pravoúhlou soustavu areálu a míry původního objektu dormitory. Materiály nových konstrukcí jsou beton a sklo stejně jako u ostatních nových přístavků. Pro zajištění intimity prostředí je prosklená část fasády obehnána bambusovým plotem. Tento prostor je využit jako pohledová zelená zahrada. Objekt přístavby je typologicky rozdělen na část pro muže a část pro ženy. Obě části jsou vybaveny bazénkem ofuro. Objekt je monolitický železobetonový skelet založený na patkách.Diploma thesis called “CONVERSION OF DORMITORY TO HOSTEL AND NEW DESIGN OF HOTEL, TOMIOKA SILK MILL JAPAN“ was elaborated according to the regulations in the form of architectural study. The topics of this thesis were two variants of possible conversion of accommodation for workwomen (dormitory). The partial assignment comprised solution to the arrangement of greenery in the atrium of the dormitory, and revitalization of plateau. The building is located in the premise of a former silk mill in the city Tomioka in the Gunma prefecture on the Honshu island in Japan. The conversion of the building for the novel purpose required replenishment of necessary facilities, and some building interventions to assure operation of the hostel. In both variants, partial adjustment of the original building was needed. However, all changes had to maintain proportions and volume of the building not to compromise the original concept of whole premise as well as the skyline of the city. The adjustments of the original building of dormitory consisted of a completion of the entrance portal including a foyer, and a reception with the base of operation. Large glass areas in combination with exposed concrete were used as construction materials. These materials were selected so that the new structures (monolithic ferroconcrete) are clearly distinguishable from original ones (wood). The Internal atrium was designed in the style of modern japan garden with various types of surfaces (vegetation – moss; mineral – gravel and stones). Variant 1 – the new constructions of the two facility buildings. Building A is washroom building, and building B is catering building with toilets. The volumes of individual objects were formed by simple prisms rotated by 30° a 60° against axis of dormitory. These volumes complied with dimensions of the original building. The building A protruded on the edge of the slope, and it was paneled with glass plates. The building B was glassed-in from the south, while the northern side was constructed from exposed concrete in a compact way. The building A was divided to two symmetric parts by a central wall for both structural and functional purposes. At the end of the building, there was an ofuro (swimming pool) providing views of the surrounding mountains. Typological solution of the building B included separate toilets with a mixed washroom, which were located in the northern part of the building. In the southern part, the space for catering was divided to an operational space, and a space for visitors by a dispensing counter. The building A was from reinforced concrete and was founded on the base plate. The central wall represented the main load-bearing structural element that prevents transverse breakage. The central wall was anchored into the ground with piles. The building B was also from reinforced concrete and was based on the strip foundations. Variant 2 – the extension was formed as a simple prism that complied with the rectangular system of the premise and dimensions of the original dormitory building. Employed materials of the new constructions were concrete and glass similarly to the other new extensions. To ensure intimate environment, the glass part of a façade was enclosed by a bamboo fence. This space was also used as a viewable green garden. The building was typologically divided to the parts for women and men. Both parts were equipped with ofuro. The building was monolithic ferroconcrete skeleton based on the footings.

FireProt: web server for automated design of thermostable proteins

There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core. FireProt utilizes sixteen tools and three protein engineering strategies for making reliable protein designs. The server is complemented with interactive, easy-to-use interface that allows users to directly analyze and optionally modify designed thermostable mutants. FireProt is freely available at http://loschmidt.chemi.muni.cz/fireprot.Web of Science45W1W399W39

Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport

Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels, and study of the ligands’ transport through these transport pathways. Caver Web is the first interactive tool allowing both the analyses within a single graphical user interface. The server is built on top of the abundantly used tunnel detection tool Caver 3.02 and CaverDock 1.0 enabling the study of the ligand transport. The program is easy-to-use as the only required inputs are a protein structure for a tunnel identification and a list of ligands for the transport analysis. The automated guidance procedures assist the users to set up the calculation in a way to obtain biologically relevant results. The identified tunnels, their properties, energy profiles and trajectories for ligands’ passages can be calculated and visualized. The tool is very fast (2–20 min per job) and is applicable even for virtual screening purposes. Its simple setup and comprehensive graphical user interface make the tool accessible for a broad scientific community. The server is freely available at https://loschmidt.chemi.muni.cz/caverweb.Caver Web 1.0 je webový server pro komplexní analýzu tunelů a kanálů v proteinech a pro studium transportu ligandu přes tyto transportní cesty. Caver Web je první interaktivní nástroj umožňující obě analýzy v jednom grafickém uživatelském rozhraní. Server je vybudován nad hojně užívaným nástrojem pro detekci tunelů Caver 3.02 a nad CaverDock 1.0 umožňujícím studium transportu ligandů. Program se snadno ovládá, jelikož vyžaduje pouze strukturu proteinu pro identifikaci tunelů a seznam ligandů pro analýzu transportu. Procedury pro automatické nastavení výpočtů asistují uživatelům tak, aby získali biologicky relevantní výsledky. Identifikované tunely, jejich vlastnosti, energetické profily a trajektorie průchodů ligandů mohou být spočítány a vizualizovány. Nástroj je velmi rychlý (2-20 minut na úlohu) a je použitelný dokonce pro virtuální screening. Jeho snadné nastavení a ucelené grafické rozhraní dělá nástroj přístupným pro širokou vědeckou komunitu. Server je volně k dispozici na https://loschmidt.chemi.muni.cz/caverweb

Toxic effects of nine polycyclic aromatic compounds on Enchytraeus crypticus in artificial soil in relation to their properties

a b s t r a c t The aim of this study was to compare the toxic effects of selected two-and three-ringed PAHs (naphthalene, phenanthrene, and anthracene) and their N-heterocyclic analogs with one (quinoline, acridine, and phenanthridine) or two (quinoxaline, phenazine, and 1,10-phenanthroline) nitrogen atoms on the survival and reproduction of Enchytraeus crypticus in artificial soil. Toxicity of compounds was recalculated to soil pore-water concentrations using the data of chemical analyses of 0.01 M CaCl 2 extracts of spiked soils. When toxicity was based on molar concentrations in pore water (mmol/L), it significantly increased with increasing K ow value. This relationship indicates nonpolar narcosis as the general toxicity mechanism of the tested compounds. In addition, significant correlation between the toxicity of PACs and their ionization potential has been identified by multidimensional QSAR models

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions

<div><p>An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been reported recently. However, their ability to pinpoint potentially deleterious variants is limited by the fact that their mechanisms of prediction do not account for the existence of different categories of variants. Consequently, their output is biased towards the variant categories that are most strongly represented in the variant databases. Moreover, most such methods provide numeric scores but not binary predictions of the deleteriousness of variants or confidence scores that would be more easily understood by users. We have constructed three datasets covering different types of disease-related variants, which were divided across five categories: (i) regulatory, (ii) splicing, (iii) missense, (iv) synonymous, and (v) nonsense variants. These datasets were used to develop category-optimal decision thresholds and to evaluate six tools for variant prioritization: CADD, DANN, FATHMM, FitCons, FunSeq2 and GWAVA. This evaluation revealed some important advantages of the category-based approach. The results obtained with the five best-performing tools were then combined into a consensus score. Additional comparative analyses showed that in the case of missense variations, protein-based predictors perform better than DNA sequence-based predictors. A user-friendly web interface was developed that provides easy access to the five tools’ predictions, and their consensus scores, in a user-understandable format tailored to the specific features of different categories of variations. To enable comprehensive evaluation of variants, the predictions are complemented with annotations from eight databases. The web server is freely available to the community at <a href="http://loschmidt.chemi.muni.cz/predictsnp2" target="_blank">http://loschmidt.chemi.muni.cz/predictsnp2</a>.</p></div

Performance of nucleotide-based and protein-based prediction tools and their consensuses, evaluated using the dataset of variants associated with Mendelian diseases.

<p>(A) Observed normalized accuracy and (B) area under the receiver operating characteristic curve (AUC) values are shown as blue and red bars for nucleotide- and protein-based tools and their consensuses, respectively. The horizontal dashed lines represent average performance values for each tool type.</p

Workflow diagram describing the construction of the dataset of variants related to Mendelian diseases.

<p>The dataset was prepared by combining deleterious variants from the ClinVar database with neutral variants from the VariSNP database. The resulting dataset was then divided into independent training and testing subsets for each individual category of variants.</p