Landslide inventory and characteristics, based on LiDAR scanning and optimised field investigations in the Kutina area, Croatia

This paper presents the preliminary results of analyses of landsliding processes derived from detailed LiDAR (Light Detection and Ranging) scans supported by field prospection on the south-western slopes of Mt. Moslavačka gora, in the wider Kutina area. This area is known for frequent landslides, but dedicated regional landslide research has not been previously undertaken. High resolution LiDAR scanning and orthophoto imaging enabled the production of a reliable landslide inventory, but also enabled research on landslide properties and the morphology of the area. Field mapping and prospection, sampling and borehole coring assisted in the collection of information about the material characteristics and specific features of typical landslides. In the research area, which covers more than 71 km2, more than 1200 very small landslides were detected. The majority of landslides were discovered in just several geological units indicating their high susceptibility: Pleistocene silts and sands with clayey interlayers, followed by M2 silty sands and gravels, and M7 sands. Nearly half of the landslides are estimated to be of recent and younger age, while other landslides may be considered as being historical implying a “long tradition” of landslide events in the research area. Preliminary terrain surface roughness analysis also supported the conclusion that the inventory contains landslides of several historical generations which are still detectable. In addition to slides (1123), this research also discovered numerous earthflow processes (143), which are more frequent in the predominantly sandy units. The landslides in this area are largely located on the banks of the gullies and are directly related to the action of water. Regarding that situation and the engineering properties of the encountered geological units, four types of bank instabilities can be differentiated: slides on top of rock masses; slides in firm soil mixtures; landslides in sands; landslides in predominantly coherent soil complexes

Rapid sample preparation and low-resource molecular detection of hepatopancreatic parvoviruses (HPV) by recombinase polymerase amplification lateral flow detection assay in shrimps (Fenneropenaeus merguiensis)

Background Viral diseases are a major problem in shrimp aquaculture facilities as these diseases reduce growth rates, which inevitably lead to production and profit losses. Hepatopancreatic parvoviruses (HPV) are common diseases in shrimp that appear to be associated with high or low levels of replication in specific genetic lineages. Selective breeding may result in resistance to HPV and improved body traits such as body weight, meat yield and shrimp colour, facilitating shrimp farming. HPV virus titre is commonly determined by quantitative PCR (qPCR), which is a time-consuming method requiring laboratory equipment unsuitable for field implementation. The aim of this study was to develop a simple, robust, rapid and reliable method to detect HPV in low-resource environments. Methods We developed a rapid shrimp HPV test that uses (1) a simple three-step sample preparation protocol, followed by (2) isothermal recombinase polymerase amplification (RPA) and lateral flow strip detection (LFD). Analytical sensitivity testing was performed in a background banana shrimp sample matrix, and retrospective testing of Fenneropenaeus merguiensis hepatopancreas tissues (n = 33) with known qPCR viral titres was used to determine diagnostic sensitivity and specificity. Results The rapid shrimp HPV test could detect as little as 35 genome-equivalent copies per reaction in homogenized F. merguiensis banana shrimp. Retrospective testing of stored tissues (n = 33) indicated 100% diagnostic sensitivity (95% confidence interval, CI: 86–100%) and 100% specificity (95% CI: 66–100%) for detection of HPV. Conclusion The rapid shrimp HPV test could be completed in only 40 minutes, and required only homogenization pestles, some pipettors, and a small heating block for single temperature incubation at 39°C. Critically, our procedure eliminated the time-consuming purification of nucleic acids from samples and when combined with RPA-LFD offers a user-friendly HPV detection format that can potentially be performed on-site. Our approach represents a major step forward in the development of a simple and sensitive end-point method for quick determination of unfavourable HPV virus numbers in shrimp, and has great potential to advance on-site management of shrimps in aquaculture

Ebolavirus diagnosis made simple, comparable and faster than molecular detection methods: preparing for the future

Background The 2014/2015 Ebolavirus outbreak resulted in more than 28,000 cases and 11,323 reported deaths, as of March 2016. Domestic transmission of the Guinea strain associated with the outbreak occurred mainly in six African countries, and international transmission was reported in four countries. Outbreak management was limited by the inability to rapidly diagnose infected cases. A further fifteen countries in Africa are predicted to be at risk of Ebolavirus outbreaks in the future as a consequence of climate change and urbanization. Early detection of cases and reduction of transmission rates is critical to prevent and manage future severe outbreaks. We designed a rapid assay for detection of Ebolavirus using recombinase polymerase amplification, a rapid isothermal amplification technology that can be combined with portable lateral flow detection technology. The developed rapid assay operates in 30 min and was comparable with real-time TaqMan™ PCR. Methods Designed, screened, selected and optimized oligonucleotides using the NP coding region from Ebola Zaire virus (Guinea strain). We determined the analytical sensitivity of our Ebola rapid molecular test by testing selected primers and probe with tenfold serial dilutions (1.34 × 1010− 1.34 × 101 copies/μL) of cloned NP gene from Mayinga strain of Zaire ebolavirus in pCAGGS vector, and serially diluted cultured Ebolavirus as established by real-time TaqMan™ PCR that was performed using ABI7500 in Fast Mode. We tested extracted and reverse transcribed RNA from cultured Zaire ebolavirus strains – Mayinga, Gueckedou C05, Gueckedou C07, Makona, Kissidougou and Kiwit. We determined the analytical specificity of our assay with related viruses: Marburg, Ebola Reston and Ebola Sudan. We further tested for Dengue virus 1–4, Plasmodium falciparum and West Nile Virus (Kunjin strain). Results The assay had a detection limit of 134 copies per μL of plasmid containing the NP gene of Ebolavirus Mayinga, and cultured Ebolavirus and was highly specific for the Zaire ebolavirus species, including the Guinea strain responsible for the 2014/2015 outbreak. The assay did not detect related viruses like Marburg, Reston, or Sudan viruses, and other pathogens likely to be isolated from clinical samples. Conclusions Our assay could be suitable for implementation in district and primary health laboratories, as only a heating block and centrifuge is required for operation. The technique could provide a pathway for rapid screening of patients and animals for improved management of outbreaks

Rapid inactivation and sample preparation for SARS-CoV-2 PCR-based diagnostics using TNA-Cifer Reagent E

RT-qPCR remains a key diagnostic methodology for COVID-19/SARS-CoV-2. Typically, nasal or saliva swabs from patients are placed in virus transport media (VTM), RNA is extracted at the pathology laboratory, and viral RNA is measured using RT-qPCR. In this study, we describe the use of TNA-Cifer Reagent E in a pre-clinical evaluation study to inactivate SARS-CoV-2 as well as prepare samples for RT-qPCR. Adding 1 part TNA-Cifer Reagent E to 5 parts medium containing SARS-CoV-2 for 10 min at room temperature inactivated the virus and permitted RT-qPCR detection. TNA-Cifer Reagent E was compared with established column-based RNA extraction and purification methodology using a panel of human clinical nasal swab samples (n = 61), with TNA-Cifer Reagent E showing high specificity (100%) and sensitivity (97.37%). Mixtures of SARS-CoV-2 virus and TNA-Cifer Reagent E could be stored for 3 days at room temperature or for 2 weeks at 4°C without the loss of RT-qPCR detection sensitivity. The detection sensitivity was preserved when TNA-Cifer Reagent E was used in conjunction with a range of VTM for saliva samples but only PBS (Gibco) and Amies Orange for nasal samples. Thus, TNA-Cifer Reagent E improves safety by rapidly inactivating the virus during sample processing, potentially providing a safe means for molecular SARS-CoV-2 testing outside traditional laboratory settings. The reagent also eliminates the need for column-based and/or automated viral RNA extraction/purification processes, thereby providing cost savings for equipment and reagents, as well as reducing processing and handling times

Sundown Syndrome in Persons with Dementia: An Update

"Sundowning" in demented individuals, as distinct clinical phenomena, is still open to debate in terms of clear definition, etiology, operationalized parameters, validity of clinical construct, and interventions. In general, sundown syndrome is characterized by the emergence or increment of neuropsychiatric symptoms such as agitation, confusion, anxiety, and aggressiveness in late afternoon, in the evening, or at night. Sundowning is highly prevalent among individuals with dementia. It is thought to be associated with impaired circadian rhythmicity, environmental and social factors, and impaired cognition. Neurophysiologically, it appears to be mediated by degeneration of the suprachiasmatic nucleus of the hypothalamus and decreased production of melatonin. A variety of treatment options have been found to be helpful to ameliorate the neuropsychiatric symptoms associated with this phenomenon: bright light therapy, melatonin, acetylcholinesterase inhibitors, N-methyl-d-aspartate receptor antagonists, antipsychotics, and behavioral modifications. To decrease the morbidity from this specific condition, improve patient's well being, lessen caregiver burden, and delay institutionalization, further attention needs to be given to development of clinically operational definition of sundown syndrome and investigations on etiology, risk factors, and effective treatment options

International Legal Protection of Sovereign Bonds as Investments in International Investment Law

Državne obveznice so dolžniški vrednostni papirji, s katerimi se država zaveže, da bo imetniku tega vrednostnega papirja ob zapadlosti izplačala periodične donose in povrnila glavnico. Obveznice predstavljajo največji vir financiranja držav in s tem prevladujočo obliko javnega dolga. Naraščanje nevzdržnih dolžniških obveznosti držav lahko povzroči težave z odplačevanjem, kar za imetnike obveznic predstavlja tveganje, da država ne bo poravnala svojih obveznosti, in da bo prišlo do prestrukturiranja javnega dolga. Magistrsko diplomsko delo naslovi vprašanje, ali mednarodno investicijsko pravo imetnikom državnih obveznic s položajem investitorja omogoča uveljavljanje zahtevkov proti državi pred mednarodno investicijsko arbitražo. Arbitražna praksa je pokazala, da jedro problematike v tovrstnih primerih predstavlja vprašanje, ali so državne obveznice zajete s pojmom investicije po mednarodnem investicijskem pravu. To je v prvi vrsti odvisno od definicije investicije, ki jo vsebuje mednarodni investicijski sporazum. Praksa tribunalov pa je pokazala, da tudi v primeru široke definicije investicije ni mogoče z zagotovostjo trditi, da so državne obveznice z njo zajete. Neusklajeni pa so tudi pristopi tribunalov k presoji obstoja investicije po ICSID Konvenciji, čemur lahko deloma pripišemo različne odločitve, deloma pa se te razhajajo zaradi nasprotujočih si stališč o enovitosti transakcij primarnega in sekundarnega trga državnih obveznic. Magistrsko diplomsko delo obravnava tudi vprašanje, ali lahko za državne obveznice štejemo, da se nahajajo na ozemlju države gostiteljice in kakšen zahtevek mora investitor uveljavljati, da tribunal o njem lahko odloča. Opredeli tudi možne kršitve investicijskih standardov, do katerih lahko pride v primeru neplačila ali prestrukturiranja javnega dolga.Sovereign bonds are financial instruments which acknowledge the indebtedness and promise a repayment of principal and interest at the maturity to the holder of the security. Bonds are the largest source of financing for governments and thus the predominant category of sovereign debt. The growth of unsustainable debt obligations of States can lead to repayment problems, which pose a risk to bondholders that a State will default on its obligations and that the sovereign debt will be restructured. The thesis addresses the question as to whether international investment law allows holders of sovereign bonds with investor status to pursue claims against the State in international investment arbitration. The arbitral practice has shown that the fundamental question is whether sovereign bonds constitute a protected foreign investment under international investment law. This depends primarily on the definition of investment contained in the international investment treaty. However, it has been established that even in the case of a non-exhaustive list of assets falling within the definition of investment, the tribunals may still conclude that government bonds cannot be considered as a protected investment. Additionally, tribunals have taken different approaches to the consideration of whether sovereign bonds correspond to the inherent meaning of investment as contemplated by the ICSID Convention. Divergent decisions of the tribunals can be attributed to the difference of approaches and conflicting views of the tribunals on the unity of the economic operation at the primary and secondary market. The thesis also addresses the question of localisation of sovereign bonds in host state and the jurisdictional issue of contract and treaty claims. It also identifies possible violations of investment standards that may arise in the event of default or sovereign debt restructuring

Multiplex Detection of Nucleic Acids Using Recombinase Polymerase Amplification and a Molecular Colorimetric 7-Segment Display

Nucleic acid analysis has become highly relevant for point-of-care (POC) diagnostics since the advent of isothermal amplification methods that do not require thermal cycling. In particular, recombinase polymerase amplification (RPA) combined with lateral flow detection offers a rapid and simple solution for field-amenable low-resource nucleic acid testing. Expanding POC nucleic acid tests for the detection of multiple analytes is vital to improve diagnostic efficiency because increased multiplexing capacity enables higher information density combined with reduced assay time and costs. Here, we investigate expanding RPA POC detection by identifying a generic multiplex RPA format that can be combined with a generic multiplex lateral flow device (LFD) to enable binary and molecular encoding for the compaction of diagnostic data. This new technology relies on the incorporation of molecular labels to differentiate nucleic acid species spatially on a lateral flow membrane. In particular, we identified additional five molecular labels that can be incorporated during the RPA reaction for subsequent coupling with LFD detection. Combined with two previously demonstrated successful labels, we demonstrate potential to enable hepta-plex detection of RPA reactions coupled to multiplex LFD detection. When this hepta-plex detection is combined with binary and molecular encoding, an intuitive 7-segment output display can be produced. We note that in all experiments, we used an identical DNA template, except for the 5' label on the forward primer, to eliminate any effects of nucleic acid sequence amplification bias. Our proof-of-concept technology demonstration is highly relevant for developing information-compact POC diagnostics where space and time are premium commodities

GeoTwinn: Twinning of the European Geological Surveys

oai:repozitorij.hgi-cgs.hr:hgi_6The GeoTwinn is the Horizon 2020 Twinning project funded by European Commission and is fully entitled: Strengthening research in the Croatian Geological Survey: Geoscience-Twinning to develop state-of-the-art subsurface modelling capability and scientific impact. The project twins the Croatian Geological Survey (HGI-CGS) with two world-leading geoscience research institutions: the Geological Survey of Denmark and Greenland (GEUS) and the British Geological Survey of the United Kingdom Research and Innovation (BGS-UKRI). The Project has started in October 2018, and is coordinated by HGI-CGS. The major aims of the project are: to significantly strengthen HGI-CGS’s research potential and capability, networking between scientists and institutions, and also development of ideas and new projects proposals. During three years of implementation, HGI-CGS experts will have the opportunity to collaborate with eminent sci-entists from other two partnering institutions. HGI-CGS will also benefit from a range of research tools, technologies, software and methods at the disposal of GEUS and BGS-UKRI. Almost thirty scientists from HGI-CGS will participate in the training programme which includes intensive training, consultations, and application of gained knowledge on test areas/data. The program involves short term visits, two-way scientific exchanges and workshops which will support HGI-CGS to strengthen research and capabilities in four important geoscience subject areas (Fig. 1): (1) 3D geological surveying and modelling (WP1) – to em-bed state-of-the-art geological surveying, interpretation and modelling. In the first activity, modern digital geological workflow and subsurface modelling capabilities including 3D virtual reconnaissance will be introduced. Also, digital field data capture, geological databases and 3D geological modelling are introduced. The second activity will reinforce these 3D visualisation and modelling skills by applying them to pilot areas using deep seismic reflection and borehole data. (2) advanced groundwater flow and contaminant transport modelling (WP2) – to understand, simulate and predict the movement of groundwater and contaminants in the subsurface. It comprises two activities, the first of which deals with strengthening HGI-CGS’s capacity to undertake cutting-edge numerical groundwater flow in porous aquifers, incorporating the robust assessment of uncertainty. The second activity deals with groundwater flow in the karst aquifers of Dinaric karst region of Croatia using advanced statistical time-series analysis methods. It will also introduce research methods to identify and analyse emerging groundwater contaminants. (3) identification and analysis of geohazards (WP3) – to introduce cutting-edge remote sensing methods for hazardous geological processes detection, monitoring and analysis. Training also includes the interpretation and visualisation of stereo imagery, processing of satellite imagery, INSAR interferometry and satellite detection of small-scale movements. The project also contains training on heuristic, statistical and geostatistical techniques to enable production of landslide susceptibility mapping. (4) geothermal energy (WP4) – scientific exchanges and training that will lead to new research into geological controls on subsurface heat flow and geochemical processes operating in hydrothermal systems. HGI-CGS staff will attend training on sampling and analytical methods of noble and dissolved gases from hydro-thermal systems. The training is also directed toward interpretation of hydrochemical data and geochemical modelling of hydrothermal systems. Second segment of the training develops fluid and heat flow modelling capability through numerical modelling of geothermal systems.The project will increase the research capacity, excellence and skill of the coordinating partner whilst fostering a network of both early career and more experienced researchers who can collaborate to produce high quality and impactful results: • a step-change in the excellence and impact of the re-search published HGI-CGS staff; • raise the reputation and the research profile of HGI-CGS scientists for novel research; • enhance research and innovation related to environmental issues, including the need for a shift to a low-carbon economy, climate change adaptation and risk management, and environmental protection and resource efficiency; • write successful bids into EU and other research grant schemes; • develop and enhance network of collaborators across the European Union; • form partnerships between the participating organisations, that outlast the project. Whilst the project focuses on supporting HGI-CGS to achieve a step-change in its research capacity, and the research profile of its scientists, it also offers significant benefits to GEUS and BGS-UKRI. By exposing GEUS and BGS-UKRI staff to a diverse range of geological set-tings within Croatia, particular environmental challenges, and to a different, large group of stakeholders, partnering institutions will also increase their level of expertise and knowledge

Repeated reuse of deoxyribozyme-based logic gates

Deoxyribozymes (DNAzymes) have demonstrated a significant capacity for biocomputing and hold promise for information processing within advanced biological devices if several key capabilities are developed. One required capability is reuse-having DNAzyme logic gates be cyclically, and controllably, activated and deactivated. We designed an oligonucleotide-based system for DNAzyme reuse that could (1) remove previously bound inputs by addition of complementary oligonucleotides via toe-hold mediated binding and (2) diminish output signal through the addition of quencher-labeled oligonucleotides complementary to the fluorophore-bound substrate. Our system demonstrated, for the first time, the ability for DNAzymes to have their activity toggled, with activity returning to 90-125% of original activity. This toggling could be performed multiple times with control being exerted over when the toggling occurs, with three clear cycles observed before the variability in activity became too great. Our data also demonstrated that fluorescent output of the DNAzyme activity could be actively removed and regenerated. This reuse system can increase the efficiency of DNAzyme-based logic circuits by reducing the number of redundant oligonucleotides and is critical for future development of reusable biodevices controlled by logical operations

Krüppel-Like Factors

Krüppel-like factors (KLFs) are deoxyribonucleic acid–binding transcriptional factors that regulate various pathways that control metabolism and other cellular mechanisms. Various KLF isoforms have been associated with cellular, organ, or systemic metabolism. Altered expression or activation of KLFs has been linked to metabolic abnormalities, such as obesity and diabetes, as well as with heart failure. This review article summarizes the metabolic functions of KLFs, as well as the networks of different KLF isoforms that jointly regulate metabolism in health and disease