Search

In 2006, the Stayky team of the Northern Expedition of the Institute of Archaeology discovered the multi-layered settlements on the edge of the plateau north of the village and on the Dnieper islands opposite it and carried out the rescue excavations of the well-known center including the various settlements and a Cossack cemetery. The materials of the settlement structure have already been published, as well as the exploration of the historical and cultural heritage of the settlement. The paper describes the results of research of the cemetery. During the campaign ca. 250 m2 of area with 26 burials made according to the canons of Christian rituals have been unearthed. They have no grave goods, except, probably, of burial 16, just below of which a coin blank or demonetized product and a silver Riga solid from the Baltic possessions of Sweden, minted in 1653 by Queen Christina, were found. The absence of other synchronous materials in the layers of the site allows to connect these finds not with the settlement structures but with the cemetery. And the single artifacts of previous ages, collected in two graves, belong to the surrounding layer. Despite the partial destruction of some burials by the quarry and the damage of shallow pits by further household activities it was observed that the skeletons laid supine with arms crossed on the chest or abdomen, although during skeletonization the arms could move to the pelvis and along the body. Certain deviations are noted in the position of the head and lower jaw in particular. The graves are 0.35—0.90 m deep, the deceased were directed with the head to the west with a slight deviation to the south, usually associated with the seasonal place of the Sun above the horizon. Gender and age differences have not been traced by the depth or direction of burials, although a higher concentration of graves, possibly a family plot, was found in one of the excavation area. Mutual overlaps of burials are few, although the damage of some graves with a moving of bones was observed. Processing of anthropological materials by specialists allowed to trace the peculiarities of ethnic features and physical development of the inhabitants of the site.

For the first time in the history of archeological research in Volodymyr the cross-section of the ramparts of «Valy» hill-fort were made. According to external morphological features the hill-fort belongs to the «Volyn type», and most researchers consider it to be remains of the citadel of annalistic city. There is no direct evidence of the latter but the available written sources directly indicate the location of the brick castle of Casimir the Great in the 14th century and the later wooden-earthen headman’s castle. Just the main task of the work was to ascertain the conformity of the ramparts to these objects. The internal structure of the rampart was explored by laying a stepped trench measuring 2 × 11 m at the end of the rampart at the place of its gap (entrance to the territory of hill-fort). The cross-section made it possible to record the stratigraphic column of layers and backfills for more than 6 m long and to ascertain the general picture of the rampart construction. It was learned that the embankment of the rampart was carried out above the level of the cultural layer which occured on a yellow homogeneous loess-like loam (possibly the virgin soil). The generalization of the layers traced above for 5.96 m allows us to identify three of their main groups which probably reflect the sequence of erecting of the rampart at this area. The first large-scale backfill, which formed the basis of the embankment, was traced in the square 5. It consisted mainly of yellow loess-like loam with inclusions of limestone fragments. The middle part of the embankment was explored in squares 2—4, where the complex stratigraphic sequence of various layers and strata have been traced, which, in addition to loess-like yellow loam with limestone fragments, included the larger backfills of dark gray sand with inclusions of yellow loam and the same soil with inclusions of debris. Finally, the upper part of the embankment, explored in the square 1, consisted of dark gray humused sand with inclusions of clay and charcoal. Since this layer contained a lot of pottery of the Late Middle Ages, it is possible that this is a filling of the late medieval building inserted into the embankment. The research revealed material from different times, dating from the Bronze Age to nowadays. The dating of the embankment of rampart is indicated by the findings of late medieval pottery in its middle part. They confirm the written reports about the construction of a wooden-earthen headman’s castle in the 15th century. Some structural features of the rampart are in good agreement with historical data. In particular, the first backfill at the base of the embankment of yellow loess-like loam had significant inclusions of fragments of limestone, which may be the remains of the masonry of the walls of Casimir the Great castle, dismantled in 1370. Dating the construction of rampart to the 15th century indicates that the explored hill-fort was not the citadel of Old Volodymyr. On the other hand, it allows us to re-date at least the part of hill-forts of «Volyn type», which are traditionally attributed to the 10th—11th centuries.

Minting own coin is one of the attributes of state formation. The first coins of the Old Rus are represented by gold and silver specimens dating from the late tenth — early eleventh century. Gold coins are very rare, the silver ones are presented much more. Most modern researchers believe that the production of silver coins was started by Volodymyr Sviatoslavych and ended under Yaroslav Volodymyrovych after the beginning of his reign in Kyiv. In 2020 the third known hoard of silver coins was discovered near Gorodnytsia village, Novohrad-Volynskyi district, Zhytomyr region. It was found accidently by local resident S. M. Komar who in the next day after discovery handed it over to the authorities which was recorded in the relevant documents. The expedition of the Institute of Archaeology of the National Academy of Sciences of Ukraine conducted archaeological research at the hoard location. The place where the silver coins have been occurred was recorded. Several more coins were found in the pit where the hoard was and nearby. Surrounding area was examined. Near the hoard the presence of land- and waterways, which functioned in the medieval period, was recorded. Near the river Sluch there are convenient places for crossing. During the exploration of the area adjacent to the hoard in order to study the archaeological context the settlement was discovered. The artifacts found on it date it to the 9th—13th and 16th—18th centuries. Powerful fortifications in the form of moats, ramparts and escarpments have been preserved. Probably, the formation of the silver hoard is connected with the ancient roads along the Sluch River and the Old Rus settlement on the site of the modern settlement of Gorodnytsia. In total 38 silver coins were in the hoard. 31 of them belonged to the minting of Volodymyr Sviatoslavych, and 7 to Sviatopolk Yaropolkovych. Vladimir’s coins are presented in three types — II (6 copies), III (16 copies) and IV (9 copies). Sviatopolk’s coins represent all three of his existing numismatic types — I (4 copies), II (2 copies) and III (1 copy). 10 silver coins of Volodymyr and 1 of Svyatopolk are represented by previously unknown stamp pairs. 2 coins of Vladimir, which have an unknown combination of stamps, are of particular scientific interest.

In 2017 the archaeological exploration in the zone of construction of the transmission line in the Makariv district of Kyiv region took place. Three sites — Nalyvaikivka 1 (second half of the 10th — 11th, 12th—13th centuries), Farm 2 (2nd—1st millennium BC) and Farm 3 (11th century) were excavated. The total area of excavation was 165 m2. The settlement Nalyvaykivka 1 is located in the area with high wetlands and had the necessary conditions for the extraction of iron and forestry — extraction of tar, charcoal and harvesting. The site Nalivaykivka 1 was the Medieval industrial rural settlements. The site Nalyvaykivka 1 contains a lot of artifacts related to iron production. They represent the different stages of the metallurgical process. Fragments of furnace for iron production have been found. The specific design of the metallurgical furnace was ascertained. The location near ore deposits (the iron-mining center in the Kolonshchyna region) and near the powerful product market (Kyiv) led to the craft character of the settlement. Probably it was part of the group of settlements pecialized in the production and primary processing of iron. The materials of the Ferma 3 settlement confirm the high economic level of the rural district of Kyiv region in comparison with the material culture of the Old Rus cities. There were no any archaeological objects excavated at the settlement. But in the cultural layer the interesting finds were recorded: the bi-conical shape whorl made of pink shale; the small iron knife with a straight back, the blade separated from the shank ledge; the anvil (?) will slip; the iron arrowhead with broken edge; iron bits; bronze vessel; metallurgical slag; shale fragment of pink; iron awl. The presence of Byzantine amphorae, glass bracelets, bronze vessels, items of military or hunting equipment testifies to the active trade and craft relations of rural and urban population of Kyiv Rus.

Archaeological sites of the chronicle Iskorosten located in the modern city of Korosten, Zhytomyr region, have been attracting the attention of historians and archaeologists for almost 200 years. F. A. Kozubovsky, I. P. Rusanova, M. P. Kuchera, B. A. Zvizdetsky examined the site. The paper contains the results of surveys of the site in 2013 which made significant additions to understanding of the nature of settlement 1 and the ancient chronicle city. Findings of scientific value were discovered, and the topography of the settlement was clarified. During the excavations of a part of the defensive moat of the settlement 1 the numerous fragments of wheel-made pottery were discovered. According to its morphological features it could be dated to the to the first half the tenth century. Finds of household items, parts of clothing and jewelry were also recorded. The details of the decoration of military equipment — belt plates are the finds of great interest. These heart-shaped plates made of gilded silver and decorated with floral ornaments made by stamping on the matrix. The surface is additionaly decorated with embossed small elements of or-nament. The large thick plates with slotted holes and smaller ones without slots can be distinguished. The similarity of the size, details of the shape and ornament indicate that they probably come from one belt set and were made on two matrices by one craftsman. The real discovery in the study of the capital of Drevlians land can be named the finding of the location of citadel (Detynets) cultural layers. Most scholars considered them irretrievably lost for science. The small elevation at the beginning of the entrance onto the hill on the swampy floodplain of the tributary of Uzh river turned out to the place where in the 30s of the twentieth century the cultural layers of the citadel were moved.

10 pags, 3 figs, 2 tabs. -- Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s00249-021-01518-4., Equilibrium binding constants (Kb) between chemical compounds and target proteins or between interacting proteins provide a quantitative understanding of biological interaction mechanisms. Reported uncertainties of measured experimental parameters are critical for decision-making in many scientific areas, e.g., in lead compound discovery processes and in comparing computational predictions with experimental results. Uncertainties in measured Kb values are commonly represented by a symmetric normal distribution, often quoted in terms of the experimental value plus-minus the standard deviation. However, in general, the distributions of measured Kb (and equivalent Kd) values and the corresponding free energy change ΔGb are all asymmetric to varying degree. Here, using a simulation approach, we illustrate the effect of asymmetric Kb distributions within the realm of isothermal titration calorimetry (ITC) experiments. Further we illustrate the known, but perhaps not widely appreciated, fact that when distributions of any of Kb, Kd and ΔGb are transformed into each other, their degree of asymmetry is changed. Consequently, we recommend that a more accurate way of expressing the uncertainties of Kb, Kd, and ΔGb values is to consistently report 95% confidence intervals, in line with other authors' suggestions. The ways to obtain such error ranges are discussed in detail and exemplified for a binding reaction obtained by ITC., This research was funded by grant no. S-LLT-20-2 from the Research Council of Lithuania (DM). MB and MJM aknowledge Fundacao para a Ciencia e Tecnologia (FCT), Portugal, for the financial support to Projects UIDB/00081/2020 and UIDB/00313/2020, respectively. The authors also acknowledge the COST action ARBRE-MOBIEU CA15126 supported by COST (European Cooperation in Science and Technology).

Currently, the complex of the hill-fort by the meandering bend of the Bug River channel is divided into two parts: the western one where the castle is located, and the eastern one where the city is obviously placed. During the exploration the rampart of the eastern part of the fortified complex was cut by the trench. The body of rampart is stand on the ancient original surface which looked like a humus substance. It consisted of three consecutive fillings. The first is gray soil up to 0.2 m thick, the second is white sand up to 0.8 m thick, and the third, most high (up to 1.4 m) is the yellow sand that covered the previous one from inside of the rampart. The yellow sand was cut through by well visible pit at the bottom of which the bones, probably human skulls have been found. These filings contained several fragments of pots of the fourteenth and fifteenth centuries. From inside the rampart was covered by the powerful cultural layer that contained various finds from the fourteenth to the twentieth centuries. The original layer of humus sand was well visible under the body of rampart and worse under the cultural layer. In the original surface the materials of the 12th—13th and 15th—16th centuries were found. Particularly the hinged lock of the 15th—16th centuries found in the original layer of humus is noteworthy. The majority of partially explored objects were located on the inside of the rampart. Latest of them, the object 1 of the 19th century, was occurred in the cultural layer and the rest, objects 2—6, were found while cleaning the virgin soil at the bottom of the trench. Moreover, large objects 3—4 were located outside the rampart, under the powerful cultural layer, and small objects 5—6 — under the body of the rampart. Thus, the explored site in the area of the future rampart was virtually uninhabited in the Old Rus period and was poorly used during the 14th—15th centuries. It is ascertained that the fortifications of Lytovezh hill-fort consisted of the rampart up to 2.1 m high of artificial origin built in the late medieval period, most probably in the 16th—17th centuries.

Interactions between charges play a role in protein stability and contribute to the energetics of binding between various charged ligands. Ionic surfactants are charged molecules, whose interactions with proteins are still rather poorly understood despite their wide applications. Here, we show by isothermal titration calorimetry that cationic alkylammonium surfactants bind to negatively charged polyaspartate and polyglutamate homopolymers stoichiometrically, i.e., one surfactant molecule per charged amino acid. Similarly, negatively charged alkyl sulfates (e.g., sodium dodecyl sulfate) and alkane sulfonates bind stoichiometrically to positively charged polylysine, polyornithine, and polyarginine homopolymers. In these reactions, the interacting counterparts form ion pairs and the resulting electrostatically neutral complex coprecipitates from solution. The enthalpies and heat capacities are determined for various pairs of ionic surfactants and charged amino acid homopolymers. These results show the energetic contributions of ionic headgroups and the CH2 group to surfactant interactions with proteins.

The first archaeological excavations at the Malyn ancient settlement had been initiated in 1878 by V. B. Antonovych. In the 20th century, the site has been explored by such outstanding scientists as P. M. Tretiakov, M. P. Kuchera, B. A. Zvizdetskyi. On the basis of the found artifacts, the site has been attributed as one of the earliest town settlements of the Eastern Slavs, and the discovered materials have been used to generate the concept of the early development of the towns in the East Slavonic area. Starting from 2016, the expedition of the Institute of Archaeology of the National Academy of Science of Ukraine regularly explores the site to investigate the fundamental issues of the early Slavonic towns in Eastern Europe genesis. During the field season of 2017, scientists discovered the remains of the defense constructions dating back to the earliest period of the site formation. The new data which enable to characterize the settlement surroundings has become an important result of the research in 2017. The artifacts discovered at the surrounding areas of the site indicate that culture layers of all the neighboring grounds available for settling (except for the flood lands of the Irsha river) are synchronous to those found at the settlement.

In the summer of 2015, Zhytomyr expedition conducted archaeological research at the burial mounds at the tract of Long Niva near the village Tepenitsa Olevsky district of Zhytomyr region. As a result, the burial with a stone construction under the embankment was explored and studied. The stone cover was discovered right after the turf layer and completely covered the embankment as if it was an armor. The construction consisted of granite fragments and pieces of quartzite and sandstone. At the bottom of the embankment were stone boulders of large size that became smaller at the top of burial. At the level of the mainland around the embankment placed small ditch that had a form of two arcuate sections. Remains of a skeleton or gravel pit in the burial mound was not discovered (cenotaph). Two large fragments of the potter’s pot was found on the sand pit in the central part of the embankment at the level of the ancient horizon. The practical absence of inventory does not allow date the archaeological complex clearly. A fragment of the pot can be attributed to two chronological periods: the end of IX — the first half of the X century or the second half of the XIII — XIV centuries. The stone constructions in the burial mounds are not inherent for Old Russian time in Ukraine. Stone fixt only in slightly more than 1 % of all investigated burial mounds. The discovery of such rare complex forced the authors refer to the history of research of this type of monuments on the territory of Ukraine. In the Middle Dnieper area, burial mounds with stone structures are located in two regions: on the territory of Zhytomyr Polissya (Ubort river basin, Slovechansko-Ovruch ridge) and in Porossya. The burial groups in Zhytomyr region were explored by the excavations of Ya. V. Yarotsky (1902), O. A. Fotinsky (1904), M. B. Shchukin (1976), B. A. Zvizdetsky (1988, 1996—1999), the exploration of V. O. Misiats (1961, 1978), A. P. Tomashevsky and S. V. Pavlenko (1996, 2006, 2013). There are 18 gravediggers with stone burial mounds on this territory currently. 42 burial mounds were excavated (more than 300 known). At the 29 burial complexes were fixed stones fragments. These sights don’t occupy a separate compact area and located next to burial mounds consisting exclusively of mounds with simple earthen embankments. Only at the 7 necropolises majority burial mounds contains stones. On other monuments such burial mounds was few. Different methods of using stones have been recorded in investigated burial mounds. Often different variants of stone designs are fixed in one monument. Different kinds of stone were used for constructions: sandstone, granite, quartzite. In burial mounds with stone structures under the embankment are fixed various types of burial ceremony (cremation on the site, cremation on the side, inhumation on the horizon, inhumation in undermount pits, cenotaph). The ritual is accompanied by typical Slavic equipment. The earliest complexes are dated by the X century, the most recent are the second half of the XIII century. Stone barrows Porossya are known since the middle of the nineteenth century (about 500 individual complexes was fixet). They were discovered by V. B. Antonovych (70s of XIX century), T. M. Movchanivsky (1928), V. Ye. Kozlovskaya (30s of the XX century), R. S. Orlov and P. M. Pokas (1986, 1988). 9 burial mounds with stone constructs under the embankment are known on the territory of Porossya. 78 monuments have been investigated at 5 a monuments, 37 of them — with stone crepes (the structure was mostly fixed in the of circle form of boulders, which engird the embankment). The burial ceremony and accompanying equipment are typical for Slavic monuments. There are two main hypotheses about the origin of this type of monuments. According to the first, the stone structures in the mounds are a purely practical tradition of local people, which arose in the territories characterized by significant presence of the stone (O. A. Fotinsky, V. B. Antonovych, A. V. Petrauskas). According to the second hypotheses, use of a stone is a tradition of the Slavic alien population. Ya. V. Yarotsky considered that this is a memorial of the Dregovichi burial mounds of Zhytomyr Polissya, Western Balts (Yotvingians) — I. P. Rusanova, B. A. Zvizdetsky, A. P. Tomashevsky, mixed Baltic-Dregoviches population — V. V. Sedov and A. P. Motsia. The tradition of using stones in the burial mounds of Porosyya was explained by the borrowing of the elements of the burial ceremony of the nomads S. V. Shamray, I. P. Rusanovа and O. P. Motsia. Influenced by the coming population from the western and northern territories of Old Rus — L. I. Ivanchenko. Some researchers have ruled out both hypotheses.

In the paper the materials of the VIII—IX centuries from the Early Slavic settlement Obukhiv 2 at the territory of the Middle Dnieper are analyzed. At the settlement 9 000 m2 were excavated and more then 100 archaeological objects from the I millenium AD have been explored. The stages of the development of Early Slavs material culture at the Middle Dnieper area are demonstrated. The dwellings, household pits and outdoor fireplaces belong to the Volyntseve phase(VIII—IX c. AD). To this phase the pithouses with log contractions and complicated wattle-and-daub kilns, hand- and weelmade “Volyntseve type” pottery, imported goods from Saltov culture etc. also belong. These materials permit to classify two types of material complexes of this settlement. Both complexes belong to the Volyntseve culture and reflect the stages of its formation and features of development. Complexes of the Obukhiv settlement of the third quarter of the I millenium AD allow us to say that the formation of the main features of the Volyntseve culture could occur on their basis. One can see it in the continuity of the territory settlement, the construction of houses and kilns, the ceramic complex, etc. The Obukhiv settlement, along with a number of Right-Bank Early-Slavic settlements, can be correlated with the annalistic tribe of Polans.

Objectives Pancreatic ductal adenocarcinoma is one of the deadliest cancers for which few curative therapies are available to date. Heat shock protein 90 (Hsp90) inhibitors have shown activity against numerous cancers in vitro; therefore, we tested whether they could be used to target pancreatic ductal adenocarcinoma. Methods Inhibitors of Hsp90 ATPase activity were applied on low-passage pancreatic cell line cultures (Panc10.05, Panc215, A6L) in a dose-response manner, and the inhibitor in vitro effect on cell growth was evaluated. Seven of novel Hsp90 inhibitors based on resorcinol fragment and 5 commercially available Hsp90 inhibitors (17-AAG, AT-13387, AUY-922, ganetespib, and rifabutin) as well as control compound triptolide were tested yielding IC50 values in 2- and 3-dimensional assays. Results The novel Hsp90 inhibitors exhibited strong effects on all 3 tested pancreatic cell line cultures (Panc10.05, Panc215, A6L) reaching the IC50 of 300 to 600 nM in 2- and 3-dimensional assays. Conclusions Novel Hsp90 inhibitors can be developed as antipancreatic cancer agents. Their chemical structures are simpler, and they are likely to exhibit lower side effects than the much more complex inhibitors used as controls.

The use of general-purpose and specialized programs is an indispensable part of modern prosthetics. Individual prosthetic modules computer modeling requires visual data processing and implementation technologies such as 3D scanning, mathematical modeling, computer-aided design (CAD) tools, and 3D printing for all stages from design to manufacturing. This paper proposes the automated system for creating prosthetic socket for lower limbs, based on the 3D model correction by using the Rhinoceros software and the Grasshopper plugin. After creating a three-dimensional model based on 3D printing technology the individual connecting modules of prostheses (prosthetic sockets) can be made.

The requirements for the development of a software for the analysis of an electronic geometric model obtained by 3D scanning are given. An algorithm for analyzing a full-size human body 3D-model has been developed. The requirements for the completeness and form of presentation of the initial information are briefly considered. An algorithm for analyzing 3D scanning data of a patient for designing clothes has been developed. The data obtained will be used in the development of an ordering algorithm based on the measurement data and 3D scanning analysis.

The formation of amyloid fibril plaques in the brain creates inflammation and neuron death. This process is observed in neurodegenerative disorders, such as Alzheimer’s and Parkinson’s diseases. Alpha-synuclein is the main protein found in neuronal inclusions of patients who have suffered from Parkinson’s disease. S100A9 is a calcium-binding, pro-inflammation protein, which is also found in such amyloid plaques. To understand the influence of S100A9 on the aggregation of α-synuclein, we analyzed their co-aggregation kinetics and the resulting amyloid fibril structure by Fourier-transform infrared spectroscopy and atomic force microscopy. We found that the presence of S100A9 alters the aggregation kinetics of α-synuclein and stabilizes the formation of a particular amyloid fibril structure. We also show that the solution’s ionic strength influences the interplay between S100A9 and α-synuclein, stabilizing a different structure of α-synuclein fibrils.

Twelve carbonic anhydrase (CA) isoforms catalyze carbon dioxide hydration to bicarbonate and acid protons and are responsible for many biological functions in human body. Despite their vital functions, they are also responsible for, or implicated in, numerous ailments and diseases such as glaucoma, high altitude sickness, and cancer. Because CA isoforms are highly homologous, clinical drugs designed to inhibit enzymatic activity of a particular isoform, can also bind to others with similar affinity causing toxic side effects. In this study, the affinities of twelve CA isoforms have been determined for nineteen clinically used drugs used to treat hypertension related diseases, i.e. thiazides, indapamide, and metolazone. Their affinities were determined using a fluorescent thermal shift assay. Stopped flow assay and isothermal titration calorimetry were also employed on a subset of compounds and proteins to confirm inhibition of CA enzymatic activity and verify the quantitative agreement between different assays. The findings of this study showed that pharmaceuticals could bind to human CA isoforms with variable affinities and inhibit their catalytic activity, even though the drug was intended to interact with a different (non-CA) protein target. Relatively minor structural changes of the compounds may cause significant changes in affinity and selectivity for a particular CA isoform.

The protein POT1 (Protection of Telomeres 1) is an integral part of the shelterin complex that protects the ends of human chromosomes from degradation or end fusions. It is the only component of shelterin that binds single-stranded DNA. We describe here the application of two separate fluorescent thermal shift assays (FTSA) that provide quantitative biophysical characterization of POT1 stability and its interactions. The first assay uses Sypro Orange™ and monitors the thermal stability of POT1 and its binding under a variety of conditions. This assay is useful for the quality control of POT1 preparations, for biophysical characterization of its DNA binding and, potentially, as an efficient screening tool for binding of small molecule drug candidates. The second assay uses a FRET-labeled human telomeric G-quadruplex structure that reveals the effects of POT1 binding on thermal stability from the DNA frame of reference. These complementary assays provide efficient biophysical approaches for the quantitative characterization of multiple aspects of POT1 structure and function. The results from these assays provide thermodynamics details of POT1 folding, the sequence selectivity of its DNA binding and the thermodynamic profile for its binding to its preferred DNA binding sequence. Most significantly, results from these assays elucidate two mechanisms for the inhibition of POT1 – DNA interactions. The first is by competitive inhibition at the POT1 DNA binding site. The second is indirect and is by stabilization of G-quadruplex formation within the normal POT1 single-stranded DNA sequence to prevent POT1 binding.

Proteins undergo changes in their partial volumes in numerous biological processes such as enzymatic catalysis, unfolding–refolding, and ligand binding. The change in the protein volume upon ligand binding—a parameter termed the protein–ligand binding volume—can be extensively studied by high-pressure NMR spectroscopy. In this study, we developed a method to determine the protein–ligand binding volume from a single two-dimensional (2D) 1H–15N heteronuclear single quantum coherence (HSQC) spectrum at different pressures, if the exchange between ligand-free and ligand-bound states of a protein is slow in the NMR time-scale. This approach required a significantly lower amount of protein and NMR time to determine the protein–ligand binding volume of two carbonic anhydrase isozymes upon binding their ligands. The proposed method can be used in other protein–ligand systems and expand the knowledge about protein volume changes upon small-molecule binding.

A standard operating procedure for a fluorescence-based thermal shift assay (FTSA) is provided describing its typical applications, advantages and limitations. FTSA is a simple, robust, universal and quick assay to determine protein–ligand binding affinities and protein stabilities in the presence of various excipients and solution conditions. Therefore, the assay is very useful for the straightforward characterization of new recombinantly produced proteins. The assay has a wide dynamic range enabling simultaneous determination of affinities in the milimolar to picomolar range. The assay could be used for essentially any protein that is sufficiently soluble and stable in the studied aqueous solution. Here we provide examples and typical experimental protocols for both affinity and stability determinations.

According to the 3D printing technology, individual connecting modules of prostheses and limbs - sockets -are manufactured. Nowadays, there are currently no objective data on the compliance of such modules with the requirements of national regulatory documents in Russia. The purpose of the study was to develop a system for assessing the strength of the below knee (BK) and above knee (AK) prosthetic socket under static loading. The test method was selected in accordance with the requirements of international GOST 10328. As a result of the work, a test bench was created for conducting static tests of printed sockets. The stand design integrates real-time applied force monitoring systems, inertial measuring devices, bend and extension sensors, and a controller. The stand is used in research work on individual 3D-printed socket testing. As a result of work at the bench, objective data on the analysis of strength under static loading were obtained.

In this chapter we describe the model that quantifies interactions between proteins and ligands applying the thermal shift assay. When combined with fluorescence-based measurements of protein thermal unfolding, this model forms the basis of the fluorescent thermal shift assay—a widely applicable and cost-effective technique to quantify ligand affinity towards proteins. Most ligands stabilize proteins against thermal denaturation and shift their melting points towards higher temperatures. Equations that relate the shift in protein melting temperature with the ligand concentration are presented. The assay has been used to determine affinities of various sulfonamide inhibitor binding to carbonic anhydrase isoforms. The results illustrate applicability and limitations of the fluorescent thermal shift assay.

High-pressure studies of protein–ligand system in aqueous solution provide volumetric information about the increase or decrease in compactness of the interacting counterparts. Volumetric parameters complement the thermodynamic picture of protein–ligand interaction. Here we describe fluorescent pressure shift assay—a technique that addresses volume-related parameters of protein–ligand system. Carbonic anhydrase (CA) and their ligands were useful objects that extended our knowledge about the applicability of this method.

Quarterly reviews of biophysics 51(e10), 1 - 48 (2018). doi:10.1017/S0033583518000082, The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure–thermodynamics and structure–kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy $(ΔG_{int})$, enthalpy $(ΔH_{int})$, entropy $(ΔS_{int})$, volume $(ΔV_{intr})$, heat capacity $(ΔC_{p,int})$, association rate $(k_{a,int})$, and dissociation rate $(k_{d,int}))$ between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure–energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure–thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design., Published by Cambridge Univ. Press, Cambridge

Biophysical methods have emerged as attractive screening techniques in drug discovery both as primary hit finding methodologies, as in the case of weakly active compounds such as fragments, and as orthogonal methods for hit validation for compounds discovered through conventional biochemical or cellular assays. Here we describe a dual method employing fluorescent thermal shift assay (FTSA), also known as differential scanning fluorimetry (DSF) and surface plasmon resonance (SPR), to interrogate ligands of the kinase p38α as well as several known pan-assay interference compounds (PAINs) such as aggregators, redox cyclers, and fluorescence quenchers. This combinatorial approach allows for independent verification of several biophysical parameters such as K D , k on , k off , Δ G , Δ S , and Δ H , which may further guide chemical development of a ligand series. Affinity values obtained from FTSA curves allow for insight into compound binding compared with reporting shifts in melting temperature. Ligand–p38 interaction data were in good agreement with previous literature. Aggregators and fluorescence quenchers appeared to reduce fluorescence signal in the FTSAs, causing artificially high shifts in T m values, whereas redox compounds caused either shifts in affinity that did not agree between FTSA and SPR or a depression of FTSA signal.

Human heat shock protein 90 (Hsp90) is a key player in the homeostasis of the proteome and plays a role in numerous diseases, such as cancer. For the design of Hsp90 ATPase activity inhibitors, it is important to understand the relationship between an inhibitor structure and its inhibition potential. The volume of inhibitor binding is one of the most important such parameters that are rarely being studied. Here, the volumes of binding of several ligands to recombinant Hsp90 were obtained by three independent experimental techniques: fluorescent pressure shift assay, vibrating tube densitometry, and high-pressure NMR. Within the error range, all techniques provided similar volumetric parameters for the investigated protein-ligand systems. Protein-ligand binding volumes were negative, suggesting that the protein-ligand complex, together with its hydration shell, occupies less volume than the separate constituents with their hydration shells. Binding volumes of tightly binding, subnanomolar ligands were significantly more negative than those of weakly binding, millimolar ligands. The volumes of binding could be useful for designing inhibitors with desired recognition properties and further development as drugs.

Monte Carlo simulation of phase transitions to antiferromagnetic stripe phases are performed for square and triangular lattices. We employed Ising model with competing ferromagnetic nearest neighbour and antiferromagnetic dipolar interactions and calculated phase diagram for different values of exchange and dipolar interaction ratio. The order of transitions to stripe phases with different interaction ratio (stripe width) was determined. We have shown by using histogram method that for transition to the stripe phase AF1 with the smallest stripe width h = a (a is lattice constant) the order is different for square and triangular lattices. For a square lattice the first order phase transition is found only for transitions to AF2 (h = 2a) phase, the transitions to AF1 and AF3 (h = 3a) phases being continuous. For triangular lattice we determined first order phase transitions to AF1 and AF2 phases and second order phase transitions to AF3 and AF4 phases.

The oxygen and hydrogen atoms co-adsorption experiment on Pd(111) is modelled using kinetic Monte Carlo method. We consider O–O, H–H, and O–H interactions and several kinetic processes (diffusion, surface and subsurface H-atoms exchange and water-formation reaction) leading to the phase transition (2×2)O → ( √ 3×3)O with increase in H-coverage. We also demonstrate how reverse phase transition ( √ 3×3)O → (2×2)O occurs due to hydrogen dissolution into subsurface in the absence of hydrogen gas. At higher temperature we observe the disappearance of (2× 2)O oxygen islands due to water-formation reaction.

The structural, electrical and magnetic properties of ultra-thin La 0.83 Sr 0.17 MnO 3 (LSMO) films, deposited on NdGaO 3 substrate by using the MOCVD technique, were studied. The film thickness d varied in the range from 4 to 140 nm. X-ray and RHEED measurements demonstrated that the films had a two-phase structure. One phase had an orthorhombic face centred structure ( a = 0.406 nm and c = 0.46 nm), while the other one had a cubic perovskite-like structure with a = 0.388 nm. Low field dc resistance and magnetization vs. temperature dependences were investigated in the temperature range from 5 to 300 K using a conventional four-probe method and a SQUID magnetometer. It was found that the temperature of the resistivity maximum, T m , increases with increasing film thickness and that the value of the Curie temperature T C estimated from the temperature dependence of magnetization is very close to T m . Modelling of the remanent magnetization vs. temperature dependence based on a two-phase model was in agreement with experimental results. This model also explains the T m shift to lower temperatures with decreasing film thickness.

The model has been proposed to simulate numerically the reaction O + CO → CO2 and occurring phase transitions on Pd(1 1 1) surface. We calculate the phase diagram for this system by kinetic Monte Carlo method. It shows the phase transitions p ( 2 × 2 ) O → 3 × 3 R 30 O ° and p ( 2 × 2 ) O → 3 × 3 R 30 O ° → p ( 2 × 1 ) O with increase of CO coverage for room and intermediate temperatures, respectively, while in the low temperature limit the direct p(2 × 2)O → p(2 × 1)O phase transition is observed. We demonstrate that the reaction rate is the crucial factor determining the occurrence of the p(2 × 1)O phase and vanishing of the 3 × 3 R 30 O ° with decrease of temperature. The results indicate that the reaction proceeds inside both the p(2 × 2)O and 3 × 3 R 30 O ° phases, but on the perimeter of the domains of p(2 × 1)O structure.

Using the interaction parameters up to the third neighbors and activated form of O and CO diffusion and their reaction, the model has been proposed for Monte-Carlo simulations describing the catalytic O + CO → CO2 reaction and occurring phase transitions on Pd(1 1 1) surface. Upon adsorption of CO the pre-adsorbed oxygen transforms from p(2 × 2)O phase into 3 × 3 R 30 O ° and 3 × 3 R 30 O ° → p ( 2 × 1 ) O phases in the limit of room and moderate temperatures, respectively. We demonstrate that the kinetic effects determine both the occurrence of the p(2 × 1)O and disappearance of the 3 × 3 R 30 O ° phases at moderate and low temperatures, respectively. Using reaction rate as a fit parameter, we show that at room temperature the start of the reaction can be synchronized with the occurrence of 3 × 3 R 30 O ° phase.

We present two phenomenological models to calculate the grain boundary resistance in polycrystalline and two-phase lanthanum manganites. Using the rst model we demonstrate that it is not the total magnetization, but rather the difference in magnetization of neighboring magnetic grains that plays the most important role in temperature dependences of resistance and magnetoresistance of doped polycrystalline lanthanum manganites with grain boundaries. Our calculations show that, in order to obtain the maximum in temperature dependence of resistance at Tm, grain boundary layers have to be, at least, weakly ferromagnetic. Increase of the ferromagneticity of these layers leads to decrease of resistance, increase of Tm, and decrease of the difference between Tm and Curie temperature TC. Increase in the number of grain boundaries also leads to increase of resistance, but does not affect the value of Tm. The second model is devoted to relation of resistivity and magnetization in two-phase thin lms of lanthanum manganites. Every plane is asumed to be a mixture of two ferromagnetic phases with different magnetizations and concentrations. Thin lm, represented as the system of such planes, is reduced to a circuit of resistances connected in parallel. The grain boundary resistivity is expressed as the difference in magnetization of phases. For such a system we have found that the peak of resistivity Tm decreases and shifts towards higher values of temperature with increase of lm thickness, the result which qualitatively agrees with experimental data.

The ordering of subphthalocyanine molecules into honeycomb and hexagonal close packed patterns on Ag(111) is described using complex Lennard–Jones-type intermolecular potential. We rescale Ag(111) lattice, and take into account an infinite exclusion of first, second, and third neighbours, attraction — of fourth and fifth, and repulsion — of sixth and seventh. The phase diagram is obtained by the lattice gas model using Monte Carlo simulations. Very strong first order phase transitions, causing the two-phase co-existence, are found between disordered and honeycomb as well as between disordered and hexagonal closed packed phases.

The magnetic properties of core-shell-type nanoparticles with non-magnetic core and ferromagnetic shell are modeled using Monte Carlo simulation. The influence of the surface spin disorder on the magnetization and Curie temperature of magnetic states is studied. Due to competition between exchange coupling and surface anisotropy, rotation of the magnetization axis is observed, as the surface anisotropy of the ferromagnetic shell is increased. It is shown that the exchange coupling at the core-shell interface can influence the shape of the temperature dependence of total magnetization. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

The potentiodynamic anodic behavior of zinc, nickel, and their alloy is studied depending on the compositions of both the electrolyte for dissolution and electroplates to be dissolved. Zinc deposits are indifferent to the presence of chloride ions in solutions. However, the latter ions strongly affect the anodic behavior of Ni and Zn–Ni alloy. The curves of increasing the polarization of the alloys containing more than 70% Ni demonstrate peaks corresponding to the dissolution of both the Zn–Ni solid solution in a range from –0.2 to +0.2 V and nickel in a range from 0.6 to 0.9 V. For alloys containing less than 31% Ni, no peak of its anodic dissolution is observed, because all Ni is bound with Zn.

The change in protein volume observed upon protein-ligand interaction (termed as the binding volume) is an important but largely neglected thermodynamic parameter from the perspective of both fundamental science and potential applications in the development of specific protein ligands. The binding volume is the pressure derivative of the Gibbs energy, thus elevated pressure is required to determine the volumetric properties of proteins. Here we describe the use of high-pressure spectrofluorimetry to determine both unfolding and ligand binding- induced volume changes of a protein. The degree of protein unfolding at elevated pressures was monitored by an intrinsic tryptophan fluorescence. Different approaches of experimental fluorescence spectra analysis are described and the impact on the quality of thermodynamic parameters is discussed.

Human carbonic anhydrase IX (CA IX) is highly expressed in tumor tissues, and its selective inhibition provides a potential target for the treatment of numerous cancers. Development of potent, highly selective inhibitors against this target remains an unmet need in anticancer therapeutics. A series of fluorinated benzenesulfonamides with substituents on the benzene ring was designed and synthesized. Several of these exhibited a highly potent and selective inhibition profile against CA IX. Three fluorine atoms significantly increased the affinity by withdrawing electrons and lowering the pKa of the benzenesulfonamide group. The bulky ortho substituents, such as cyclooctyl or even cyclododecyl groups, fit into the hydrophobic pocket in the active site of CA IX but not CA II, as shown by the compound's co-crystal structure with chimeric CA IX. The strongest inhibitor of recombinant human CA IX's catalytic domain in human cells achieved an affinity of 50 pM. However, the high affinity diminished the selectivity. The most selective compound for CA IX exhibited 10 nM affinity. The compound that showed the best balance between affinity and selectivity bound with 1 nM affinity. The inhibitors described in this work provide the basis for novel anticancer therapeutics targeting CA IX.

It is found that, at a certain Zn++concentration in the electrolyte, the cathodic current (i c) peaks are observed in the potentiodynamic curves; the peak's height depends on the electrolyte composition and the cathodic potential sweep rate. At an elevated electrolyte temperature, no i cpeaks are observed in the potentiodynamic curves. It is found that high-quality Zn–Ni alloy coatings are plated under the conditions, when the i cpeaks are present in the potentiodynamic curves. Acetates negatively affect the quality of alloy electroplates.

We propose the model with two interaction constants (nearest neighbour pair repulsion of SiO complexes and their trio attraction in a line) which demonstrates stripe formation during silane decomposition on oxidized Pd(111) surface. The simplest (2 × 1) stripe phase is obtained by kinetic Monte Carlo simulation in absence of longer-range attractive interactions which are usually necessary for stripe structure formation. Despite higher energy, this phase is shown to be very stable. Phase diagram for this model is obtained, and (2 × 1) phase stability is analyzed varying coverage and reaction rate parameters (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

We investigated the relationship between IGF-I, gender, height, weight, body composition and birth size in 260 healthy 7- and 8-year-old children (139 females). All children were born term at Nepean Hospital, Western Sydney. Body composition was measured using dual energy X-ray absorptiometry. IGF-I levels were determined by radioimmunoassay. Girls had higher IGF-I levels than boys (20.2 ± 6.5 nmol/l compared to 15.9 ± 6.1 nmol/l, p < 0.001) but there was no correlation between age and IGF-I. IGF-I was positively correlated with height SDS (R2 = 0.12), weight SDS (R2 = 0.19), BMI SDS (R2 = 0.18), total body fat (%) (R2 = 0.14), and fat-free tissue/cm (R2 = 0.03). After adjusting for gender and current weight, IGF-I-levels were inversely related to birth size – children with the lowest birth size and heaviest current weight had the highest IGF-I levels. This correlation between birth weight and IGF-I supports the hypothesis that the IGF-I axis is altered in babies who are small for gestational age.

Depth perception of two point-like stimuli presented dixoptically was studied as a function of luminance distribution within the pair of stimuli in each half-field. The dots subtended approximately l arcminute and were separated by 3, 4, 5 or 6 arcminutes. The depth changed gradually unless the separation between the stimuli exceeded 4 arcminutes. The depth change cannot be derived solely on the basis of disparity change. The results may be accounted for if assumed that disparity is evaluated by the difference in the weighted mean (centroid) of luminance distribution over corresponding left and right retinal regions.

The volume changes accompanying ligand binding to proteins are thermodynamically important and could be used in the design of compounds with specific binding properties. Measuring the volumetric properties could yield as much information as the enthalpic properties of binding. Pressure-based methods are significantly more laborious than temperature methods and are underused. Here we present a pressure shift assay (PressureFluor, analogous to the ThermoFluor thermal shift assay) that uses high pressure to denature proteins. The PressureFluor method was used to study the ligand binding thermodynamics of heat shock protein 90 (Hsp90). Ligands stabilize the protein against pressure denaturation, similar to the stabilization against temperature denaturation. The equations that relate the ligand dosing, protein concentration, and binding constant with the volumes and compressibilities of unfolding and binding are presented.

The paper presents a new approach to fuzzy knowledge management and provides fuzzy expert maps (FEM) as a tool. FEM is a systematic extension for a well-known paradigm of fuzzy cognitive maps combined with open fuzzy control systems. Transparent examples from international politics are presented to illustrate the entire extension chain. Recommendations for further research are given as well.

After widely known implementations of perfect ideas, expressed by researchers R. Axelrod, L. Zadeh and B. Kosko, the fuzzy cognitive map (FCM) became an important tool for decision makers in various practical areas, such as business evaluation, risk management, international policy making, medical diagnostics and others. The principle possibility of FCM involvement into a regional oceanic modeling system (ROMS) was presented during the US/EU Baltic International Symposium in Klaipeda in May 2006. Todaypsilas experience permits to extend the concept of FCM nodes, including additional fuzzy expert knowledge and enriching the representation of real situations under consideration. This paper presents a systematic approach, based on the authorspsila research, to the idea of FCM extension and its transformation into a rule-based fuzzy expert map (FEM), presents a simplified fragment of FEM use for a port security system, and discusses further perspectives of developing new tools for decision makers in risk management systems in general.