bluuebunny/crossref_metadata_2025 huggingface dataset:
Signals of electromagnetic tool with toroidal coils in highly deviated wells
Authors: Mikhaylov I , Surodina I , Glinskikh V , Nikitenko M
Published: December 2021

The research is aimed at expanding the applicability of the logging tool with toroidal coils from vertical to highly deviated wells. Its electromagnetic signals are computed with a three-dimensional finite-difference simulation algorithm on the computing resources of the Siberian Supercomputer Center of SB RAS, which is accompanied by a multi-aspect numerical analysis of the signals. We consider a wide range of geoelectric models with various resistivity contrasts: those of oil-, gas- and water-saturated reservoirs having a different number of horizontal boundaries and varying thicknesses, including the case of fine layering.
Monte Carlo method for solving the problem of predicting the computer network resistance against DoS attacks
Authors: Voevodin V A , Burenok D S , Cherniaev V S
Published: December 2021

The application of the Monte Carlo method to solving the problem of identifying and assessing the protection against DDoS attacks of weak nodes is considered. The field of research is of practical and theoretical interest, since the methods developed by the classical theory of reliability are focused on simple, stationary flows. Under the conditions of DDoS attacks, the flow of attacking requests is not stationary, so the known analytical models give an unacceptable error. For the reliability of the results, the freedom to choose the distribution function, the moments of arrival of the attacking requests, their duration and the response of the attacked node is required. The method is applicable for modelling a computer network when organizing an information security audit.
Monte Carlo method for predicting the stability of the functioning of the informatization object in the conditions of massive computer attacks
Authors: Voevodin V A
Published: December 2021

The application of the Monte Carlo method for solving the problem of predicting the functioning stability of the object of informatization in the conditions of massive computer attacks (MCA) is considered. The field of research represents practical and theoretical interests, since the methods developed by the theory of reliability are focused on simple, stationary, failure flows, which cannot be applied to the MCA conditions. In the conditions of the MCA, the period of normal functioning is commensurate with the recovery time, therefore, the application of the Poisson flow model leads to a significant error. To ensure the reliability of modeling, it is necessary to use an alternating process model, where the recovery time is commensurate with the period of operation and has a finite value, while analytical models of the real functioning processes are cumbersome, difficult to interpret and have no practical application.
Spatial-temporal variation of CO2emissions from private vehicle use in Japan
Authors: Long Yin , Yoshida Yoshikuni , Li Yuan , Gasparatos Alexandros
Published: December 2021

The transport sector is a major contributor to anthropogenic climate change through the emissions of large amounts of greenhouse gases from fossil fuel combustion. Private vehicles account for almost half of the transport energy demand, and are thus a major target for climate change mitigation efforts. However, emissions from private vehicles can have large variability due to various geographic, demographic and socioeconomic factors. This study aims to understand how such factors affect private vehicle emissions in Japan using a nationally representative survey of household energy consumption (n= 7370) for 2017. The results indicate a large temporal and spatial variability in private vehicle emissions. Annual emissions show three peaks associated with major holiday seasons in winter and summer. Some of the more noteworthy spatial patterns are the higher emissions in prefectures characterized by low population density and mountainous terrain. Income, city size and the fuel-saving driving behavior all have a significant effect on emissions. The results indicate the need for sub-regional and socioeconomically-sensitive mitigation efforts that reflect the very different emission patterns, and the factors affecting them. The strong effect of city size, which is often much more clear-cut than between prefectures, suggests that it is more appropriate to approach transport decarbonization in Japan at the city level.
Lectures on the superconformal index
Authors: Gadde Abhijit
Published: December 2021

In these lectures, we give a pedagogical introduction to the superconformal index. This is the writeup of the lectures given at the Winter School ‘YRISW 2020’ and is to appear in a special issue of J. Phys. A. The lectures are at a basic level and are geared towards a beginning graduate student interested in working with the superconformal index.
Basic properties of the mangrove tree branches as a raw material of wood pellets and briquettes
Authors: Nuryawan A , Syahputra R S , Azhar I , Risnasari I
Published: December 2021

In order to sustain mangrove forests, only branches part of the mangrove trees have been utilized. In this context, these parts have been used as the raw material of wood pellets and briquettes. These solid biofuels are produced by compressing pulverized woody biomass with or without additives in cubic-form or cylindrical units. In this study, five predominant mangrove trees, namelyAvicennia marina, Bruguiera sexangula, Excoecaria agallocha, Rhizopora apiculata,andR. mucronata, have been harvested their branches. Wood with and without bark derived from branches has been investigated for their fundamental properties, namely percentage of bark, ash-content, and physical properties (moisture content, density, and specific gravity). These properties will determine the quality class of the resulted wood pellets and briquettes considering pre-treatment or the nature of the branches’ wood.
Washing and Chopping Pre-treatment Effect of Vetiver Roots on Vetiver Oil Yield and Distillation Time
Authors: Sabila G M , Sephia C , Karliati T , Suhaya Y , Dungani R
Published: December 2021

Vetiver is a type of grass mainly used for its roots to be extracted into vetiver oil. Despite the increasing market demand, the productivity of vetiver oil in Indonesia still consider low. One of the determinant factors of the extraction yield is the pre-treatment before distillation. This study aimed to determine the best pre-treatment method to improve the vetiver oil extraction using water and steam distillation by looking at the yield, distillation rate, and forecasted distillation duration. The distillation process was using water and steam distillation method for 9 hours. The data analysis method used Durbin-Watson autocorrelation analysis. The feasibility test of polynomial regression was modelled with the F test and ANOVA variance test. The result showed that the combination of washing 2-3 times and chopping pre-treatments of vetiver roots with a size of ± 5 cm could significantly increase the extracted vetiver oil by producing the highest yield (0.36% (wet-based) and 0.47% (dry based)), the highest extraction rate (0.057%/h) and the fastest forecasted duration of the distillation (10.5 hours). The combination of washing and chopping pre-treatments of vetiver roots was the best method and could be an economical solution for low productivity problems of vetiver oil in Indonesia.
Community knowledge and involvement in mangrove ecosystem management in the coastal of Muara Gembong Bekasi
Authors: Salampessy M L , Febryano I G , Ichsan A C
Published: December 2021

Mangrove ecosystems have experienced pressure and decreased function due to abrasion and high land conversion activities for pond expansion. The government has tried to increase the role of the community for mangrove conservation but this effort has not obtained optimal results. This study aims to determine the understanding of coastal communities about Mangroves and community involvement in Mangrove ecosystem management. Methods of data collection using a questionnaire instrument, field observations, and in-depth interviews. Data analysis was done descriptively tabulated. The selection of respondents using purposive sampling. The results of the study stated that 60% of the community understood the importance of mangroves for their lives. The community understands that mangroves are a source of livelihood for the community and protect the coast from waves and abrasion. The community is actively involved in Mangrove planting program activities (53%) but based on activities initiated by the government in certain groups. Knowledge and community involvement in mangrove forest management are closely related to important community decisions to participate actively in mangrove forest management. Therefore, efforts to increase knowledge need to be increased through outreach activities and development of community empowerment programs.
Geodynamic risks of developing rockburst-hazardous deposits in the Far Eastern region
Authors: Fedotova Yu V , Anikin P A , Potapchuk M I
Published: December 2021

Geodynamic activity of the Earth’s crust depends on the parameters of the movement of lithospheric plates and stress fields, both inherited in aseismic areas and modified in seismic active ones. Geomechanical processes occur in rock mass under the influence of various natural (endogenous and exogenous) and man-made (anthropogenic) factors. The degree of influence of these factors on the change in the energy saturation of blocks of various ranks will depend on various factors. In the geological environment of natural and man-made systems, there are dynamic phenomena of various energy levels from acoustic noise (microseismic) to rockburst and mining-induced earthquakes, that is, there is always a geodynamic risk in the geological environment of natural and man-made systems, especially in mining ones. The conditions of the geodynamic risks occurrence at specific deposits are considered on the example of rockburst hazardous deposits in the Far Eastern region of the Russian Federation. The influence of natural seismic activity on the realization of mining-induced seismicity is shown.
Results of reinterpretation of marine geochemical survey on the Sakhalin shelf
Authors: Kostrov Yu V , Kamenev P A
Published: December 2021

Geochemical survey of hydrocarbons (HC) all over the world is a reliable tool of the complex of geological exploration, which allows to localize hydrocarbon saturation in structures exposed by seismic exploration, as well as to identify non-structural deposits. In 2011, a marine geochemical survey of the sorbed gases of bottom sediments was carried out on the shelf section of the northwest of Sakhalin Island. Based on the results of geochemical studies, 12 maps of the distribution of hydrocarbon and non-hydrocarbon gases in the work area and 7 maps of the distribution of metals in bottom sediments were constructed. Promising areas were distinguished by anomalies with the maximum content of parameters. The research area is characterized by a complex structure, located within the Baikal synclinal zone of the North Sakhalin oil and gas basin, which is part of the rift system of the Cenozoic sedimentary basins the Sea of Okhotsk. In 2019, the authors began to re-process and reinterpret the data in order to clarify the results. The work was based on modern theoretical foundations and methodological approaches of oil and gas prospecting geochemistry. The interpretation of the results was carried out on the basis of the model of interpretation of geochemical anomalies developed by the authors. Maps of anomalies were constructed according to 11 geochemical criteria and two geological and geochemical sections. The complex interpretation of geological and geochemical data was carried out taking into account the results of seismic exploration and drilling in a single project. According to the results of the complex interpretation, 6 promising sites were identified, which are ranked according to the degree of prospects.
Probability assessment of possible ice encounters during the petroleum hydrocarbons transportation in the Sea of Okhotsk
Authors: Romanyuk V A , Pishchal’nik V M , Nikulina I V
Published: December 2021

The increase in freight traffic along the Northern Sea Route necessitates the study of the ice regime of the freezing seas of Russia, including the Far Eastern ones (Bering Sea, the Sea of Okhotsk and the Sea of Japan). This paper, on the basis of the analysis of the Sea of Okhotsk’s ice cover and the location of the edges of the Sea of Okhotsk’s ice massif, evaluates the probability of an encounter with ice for the ships in transit during cargo transportation on the Northern Sea Route through the Far Eastern seas along two basic routes from the southern tip of the Kamchatka Peninsula: 1) traverse Cape Lopatka–Sea of Okhotsk–La Perouse Strait; 2) traverse Cape Lopatka–Sangarsky Strait. It was shown that at the stage of ice cover maximum development in the Sea of Okhotsk (February-March), route No. 2 was the most adequate and the safest for ships of ice class Arc4 and below. The section of route No. 1 with a 70 % ice encounter probability was 421 km long in February and 382 km long in March. That section of the route was dominated by very cohesive first-year thin ice up to 70 cm thick with inclusions of first-year ice of average thickness (up to 120 cm).
Comparison of forecast estimates of seabed subsidence of the Yuzhno-Kirinskoye field
Authors: Zhukov V S , Kuzmin D K , Kuzmin Yu O , Pleshkov I V
Published: December 2021

The geodynamic consequences of the field development process include the subsidence of the earth’s surface. Monitoring of deformations in offshore fields is difficult and it is necessary to evaluate them by various methods. It is important to investigate how much the calculated amplitude of the seabed subsidence is reduced by taking into account changes in the porosity and compressibility of the pore space with a decrease in reservoir pressure. The analysis of changes in the petrophysical parameters of the reservoirs of the Daginsky horizon during the projected development of the Yuzhno-Kirinskoye hydrocarbon field for depletion and a decrease in formation pressure by 10 MPa showed that the porosity decrease will be 0.038 absolute percent, the compressibility of the pore space will decrease by 0,08 10-3 1/MPa. With the help of the Petrel software, changes in the thickness of the productive layer from 80 to 120 cm were obtained, which can be taken as an estimate of the seabed subsidence in the area of the field. The application of the genetic model of the deformable formation by Kuzmin Yu showed that the maximum amplitude of the seabed subsidence to be 101 cm. Comparison of these estimates of the seabed subsidence indicates their proximity. Taking into account the dynamics of tectonophysical and petrophysical characteristics due to the long-term development of hydrocarbon deposits significantly changes the intensity of the deformation state of the rock mass and the earth’s surface above the field.
Hydroacoustic study of the basin of Biryuzovoe Karyernoe lake (Korsakovsky district, Sakhalin Island)
Authors: Kozlov D N , Romanyuk F A , Zharkov R V
Published: December 2021

For the first time, the paper presents the results of a detailed hydroacoustic study of the basin of the Biryuzovoe Karyernoe Lake (Novikovo village, Korsakovsky District, Sakhalin Region), formed after the conservation of the germaniferous coal deposit of the same name. On the basis of 12 hydroacoustic profiles, a detailed bathymetric scheme of the lake was compiled, its main morphometric parameters were calculated, and the morphological appearance was described. Preliminary conclusions have been made about the rates of sedimentation within the basin of the lake, and perspective points for monitoring the dynamics of bottom and slope sedimentation have been established. Based on the results of the chemical analysis of the lake waters, a conclusion was made on the prospects of its use for tourist and recreational purposes.
On the issue of the impact of adverse and dangerous natural processes on the use of coastal recreational areas of the Russian Federation
Authors: Yu Sanin A , Kulakovskaya V
Published: December 2021

Adverse and dangerous natural processes are a deterrent factor in the economic, in particular, recreational use of the coastal territories of Russia. They significantly reduce their tourist potential. At the same time, a decrease in the recreational value of territories is one of the consequences of human impact on the natural landscapes of the coastal zone. It seems important to consider the impact of adverse and dangerous natural processes specifically for coastal recreational areas due to their exceptional importance for domestic tourism. It, in turn, plays a huge role both for the economy of Russia and certain regions of our country, and for Russians themselves: tourists and local residents.

As a result of the research, for each of the seaside recreational areas available in Russia, the study revealed the most characteristic adverse and dangerous natural processes. Some of them are more or less manifested everywhere, for example, abrasion processes or storms. Others, in particular, seismic threat, are characteristic only for certain coastal territories. Measures to counteract dangerous natural processes are also somewhat similar for all the regions considered. However, when developing measures to counteract adverse and dangerous natural processes, the peculiarities of coastal regions should also be taken into account. Such features include climatic and relief characteristics, the landscapes of the region, the existing structure of human activity and the intensity of economic development of the region, the types of tourism that are characteristic of it, and the level of popularity of the region among recreants, as well as its recreational potential.
Toxic element concentrations in lichen Platismatia interrupta around the geothermal power station on Kunashir Island
Authors: Ezhkin A K , Kordyukov A V
Published: December 2021

The results of the study of the gross content of 14 chemical elements in lichen Platismatia interrupta collected around the geothermal power station “Mendeleevskaya” on Kunashir Island are presented. The highest exceedance was noted for As in the research area. The gross content of As varies from 0.8–2.6 mg/kg in control areas and up to 5–9 mg/kg in the impact zone, i.e. the maximum excess in lichen is noted by 11.6 times. For other elements, there were no strong exceedances in the impact zone compared to the control areas. According to the results of regression analysis, a statistically reliable inverse exponential relationship between the content of As and the distance to the power station (adjusted R2: 0.86, p-value: 0.001) is traced. The average value of the enrichment coefficient for As exceeds 100, which indicates the non-substrate origin of this element.
Epiphytic mosses in urban sites and the possibility of their use in biomonitoring (Yuzhno-Sakhalinsk)
Authors: Kaganov V V
Published: December 2021

The article presents the study results on epiphytic mosses. The research area is Yuzhno-Sakhalinsk and its surroundings. To assess the epiphytic cover the method of occurrence measuring on the tree trunks with the help of a frame 10×40 cm (400 cm2) was used at 15 locations within the study region. 15 species of epiphyte moss and their distribution characteristics were identified. Populus maximowiczii A. Henri was selected as a substrate because it predominates in urban vegetation and grows naturally in floodplain areas where control plots were set up.
A generic model for the study of supercontinuum generation in graphene-covered nanowires
Authors: Linale N , Fierens P I , Vermeulen N , Grosz D F
Published: December 2021

We study supercontinuum (SC) generation in graphene-covered nanowires based on a generic model that correctly accounts for the evolution of the photon number under Kerr and two-photon absorption processes, and the influence of graphene is treated within the framework of saturable photoexcited-carrier refraction. We discuss the role of the various effects on the generation of SC by a thorough analysis of short-pulse propagation in two different kinds of graphene-covered nanowires, one made of silicon nitride and the other made of silicon. Finally, we discuss the effect of stacking graphene layers as a means to enhance SC generation with pulse powers compatible with those in integrated optical devices.
Instability, index theorem, and exponential trichotomy for Linear Hamiltonian PDEs
Authors: Lin Zhiwu , Zeng Chongchun
Published: December 2021

Consider a general linear Hamiltonian system∂tu=JLu\partial _{t}u=JLuin a Hilbert spaceXX. We assume that L:X→X∗\ L:X\rightarrow X^{\ast }induces a bounded and symmetric bi-linear form⟨L⋅,⋅⟩\left \langle L\cdot ,\cdot \right \rangleonXX, which has only finitely many negative dimensionsn−(L)n^{-}(L). There is no restriction on the anti-self-dual operatorJ:X∗⊃D(J)→XJ:X^{\ast }\supset D(J)\rightarrow X. We first obtain a structural decomposition ofXXinto the direct sum of several closed subspaces so thatLLis blockwise diagonalized andJLJLis of upper triangular form, where the blocks are easier to handle. Based on this structure, we first prove the linear exponential trichotomy ofetJLe^{tJL}. In particular,etJLe^{tJL}has at most algebraic growth in the finite co-dimensional center subspace. Next we prove an instability index theorem to relaten−(L)n^{-}\left ( L\right )and the dimensions of generalized eigenspaces of eigenvalues of JL\ JL, some of which may be embedded in the continuous spectrum. This generalizes and refines previous results, where mostlyJJwas assumed to have a bounded inverse. More explicit information for the indexes with pure imaginary eigenvalues are obtained as well. Moreover, when Hamiltonian perturbations are considered, we give a sharp condition for the structural instability regarding the generation of unstable spectrum from the imaginary axis. Finally, we discuss Hamiltonian PDEs including dispersive long wave models (BBM, KDV and good Boussinesq equations), 2D Euler equation for ideal fluids, and 2D nonlinear Schrödinger equations with nonzero conditions at infinity, where our general theory applies to yield stability or instability of some coherent states.
TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences
Authors: Dahal-Koirala Shiva , Balaban Gabriel , Neumann Ralf Stefan , Scheffer Lonneke , Lundin Knut Erik Aslaksen , Greiff Victor , Sollid Ludvig Magne , Qiao Shuo-Wang , Sandve Geir Kjetil
Published: December 2021

T-cell receptor (TCR) sequencing has enabled the development of innovative diagnostic tests for cancers, autoimmune diseases and other applications. However, the rarity of many T-cell clonotypes presents a detection challenge, which may lead to misdiagnosis if diagnostically relevant TCRs remain undetected. To address this issue, we developed TCRpower, a novel computational pipeline for quantifying the statistical detection power of TCR sequencing methods. TCRpower calculates the probability of detecting a TCR sequence as a function of several key parameters: in-vivo TCR frequency, T-cell sample count, read sequencing depth and read cutoff. To calibrate TCRpower, we selected unique TCRs of 45 T-cell clones (TCCs) as spike-in TCRs. We sequenced the spike-in TCRs from TCCs, together with TCRs from peripheral blood, using a 5′ RACE protocol. The 45 spike-in TCRs covered a wide range of sample frequencies, ranging from 5 per 100 to 1 per 1 million. The resulting spike-in TCR read counts and ground truth frequencies allowed us to calibrate TCRpower. In our TCR sequencing data, we observed a consistent linear relationship between sample and sequencing read frequencies. We were also able to reliably detect spike-in TCRs with frequencies as low as one per million. By implementing an optimized read cutoff, we eliminated most of the falsely detected sequences in our data (TCR α-chain 99.0% and TCR β-chain 92.4%), thereby improving diagnostic specificity. TCRpower is publicly available and can be used to optimize future TCR sequencing experiments, and thereby enable reliable detection of disease-relevant TCRs for diagnostic applications.
A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data
Authors: Zhao Mengyuan , He Wenying , Tang Jijun , Zou Quan , Guo Fei
Published: December 2021

Inferring gene regulatory networks (GRNs) based on gene expression profiles is able to provide an insight into a number of cellular phenotypes from the genomic level and reveal the essential laws underlying various life phenomena. Different from the bulk expression data, single-cell transcriptomic data embody cell-to-cell variance and diverse biological information, such as tissue characteristics, transformation of cell types, etc. Inferring GRNs based on such data offers unprecedented advantages for making a profound study of cell phenotypes, revealing gene functions and exploring potential interactions. However, the high sparsity, noise and dropout events of single-cell transcriptomic data pose new challenges for regulation identification. We develop a hybrid deep learning framework for GRN inference from single-cell transcriptomic data, DGRNS, which encodes the raw data and fuses recurrent neural network and convolutional neural network (CNN) to train a model capable of distinguishing related gene pairs from unrelated gene pairs. To overcome the limitations of such datasets, it applies sliding windows to extract valuable features while preserving the direction of regulation. DGRNS is constructed as a deep learning model containing gated recurrent unit network for exploring time-dependent information and CNN for learning spatially related information. Our comprehensive and detailed comparative analysis on the dataset of mouse hematopoietic stem cells illustrates that DGRNS outperforms state-of-the-art methods. The networks inferred by DGRNS are about 16% higher than the area under the receiver operating characteristic curve of other unsupervised methods and 10% higher than the area under the precision recall curve of other supervised methods. Experiments on human datasets show the strong robustness and excellent generalization of DGRNS. By comparing the predictions with standard network, we discover a series of novel interactions which are proved to be true in some specific cell types. Importantly, DGRNS identifies a series of regulatory relationships with high confidence and functional consistency, which have not yet been experimentally confirmed and merit further research.
Real-World Effectiveness of Remdesivir in Adults Hospitalized With Coronavirus Disease 2019 (COVID-19): A Retrospective, Multicenter Comparative Effectiveness Study
Authors: Garibaldi Brian T , Wang Kunbo , Robinson Matthew L , Betz Joshua , Caleb Alexander G , Andersen Kathleen M , Joseph Corey S , Mehta Hemalkumar B , Korwek Kimberly , Sands Kenneth E , Fisher Arielle M , Bollinger Robert C , Xu Yanxun
Published: December 2021

Background

There is an urgent need to understand the real-world effectiveness of remdesivir in the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Methods

This was a retrospective comparative effectiveness study. Individuals hospitalized in a large private healthcare network in the United States from 23 February 2020 through 11 February 2021 with a positive test for SARS-CoV-2 and ICD-10 diagnosis codes consistent with symptomatic coronavirus disease 2019 (COVID-19) were included. Remdesivir recipients were matched to controls using time-dependent propensity scores. The primary outcome was time to improvement with a secondary outcome of time to death.

Results

Of 96 859 COVID-19 patients, 42 473 (43.9%) received at least 1 remdesivir dose. The median age of remdesivir recipients was 65 years, 23 701 (55.8%) were male, and 22 819 (53.7%) were non-White. Matches were found for 18 328 patients (43.2%). Remdesivir recipients were significantly more likely to achieve clinical improvement by 28 days (adjusted hazard ratio [aHR] 1.19, 95% confidence interval [CI], 1.16–1.22). Remdesivir patients on no oxygen (aHR 1.30, 95% CI, 1.22–1.38) or low-flow oxygen (aHR 1.23, 95% CI, 1.19–1.27) were significantly more likely to achieve clinical improvement by 28 days. There was no significant impact on the likelihood of mortality overall (aHR 1.02, 95% CI, .97–1.08). Remdesivir recipients on low-flow oxygen were significantly less likely to die than controls (aHR 0.85, 95% CI, .77–.92; 28-day mortality 8.4% [865 deaths] for remdesivir patients, 12.5% [1334 deaths] for controls).

Conclusions

These results support the use of remdesivir for hospitalized COVID-19 patients on no or low-flow oxygen. Routine initiation of remdesivir in more severely ill patients is unlikely to be beneficial.
Ecology and potential functions of plant-associated microbial communities in cold environments
Authors: Marian Malek , Licciardello Giorgio , Vicelli Bianca , Pertot Ilaria , Perazzolli Michele
Published: December 2021

Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.
Plasticity as a Link Between Spatially Explicit, Distance-Independent, and Whole-Stand Forest Growth Models
Authors: García Oscar
Published: December 2021

Models at various levels of resolution are commonly used for both forest management and ecological research. They all have comparative advantages and disadvantages, making desirable a better understanding of the relationships between various approaches. Accounting for crown and root morphological plasticity in the limit where equilibrium among neighbors is reached (perfect plasticity) transforms spatial models into nonspatial, distance-independent versions. The links between spatial and nonspatial models obtained through a perfect plasticity assumption are more realistic than ignoring spatial structure by a mean field approximation. This article also reviews the connection between distance-independent models and size distributions and how distributions evolve over time and relate to whole-stand descriptions. In addition, some ways in which stand-level knowledge feeds back into detailed individual-tree formulations are demonstrated. This presentation is intended to be accessible to nonspecialists.
ATP Synthase K+- and H+-Fluxes Drive ATP Synthesis and Enable Mitochondrial K+-“Uniporter” Function: I. Characterization of Ion Fluxes
Authors: Juhaszova Magdalena , Kobrinsky Evgeny , Zorov Dmitry B , Nuss H Bradley , Yaniv Yael , Fishbein Kenneth W , de Cabo Rafael , Montoliu Lluis , Gabelli Sandra B , Aon Miguel A , Cortassa Sonia , Sollott Steven J
Published: December 2021

ATP synthase (F1Fo) synthesizes daily our body's weight in ATP, whose production-rate can be transiently increased several-fold to meet changes in energy utilization. Using purified mammalian F1Fo-reconstituted proteoliposomes and isolated mitochondria, we show F1Fo can utilize both ΔΨm-driven H+- and K+-transport to synthesize ATP under physiological pH = 7.2 and K+ = 140 mEq/L conditions. Purely K+-driven ATP synthesis from single F1Fo molecules measured by bioluminescence photon detection could be directly demonstrated along with simultaneous measurements of unitary K+ currents by voltage clamp, both blocked by specific Fo inhibitors. In the presence of K+, compared to osmotically-matched conditions in which this cation is absent, isolated mitochondria display 3.5-fold higher rates of ATP synthesis, at the expense of 2.6-fold higher rates of oxygen consumption, these fluxes being driven by a 2.7:1 K+: H+ stoichiometry. The excellent agreement between the functional data obtained from purified F1Fo single molecule experiments and ATP synthase studied in the intact mitochondrion under unaltered OxPhos coupling by K+ presence, is entirely consistent with K+ transport through the ATP synthase driving the observed increase in ATP synthesis. Thus, both K+ (harnessing ΔΨm) and H+ (harnessing its chemical potential energy, ΔμH) drive ATP generation during normal physiology.
Genetically induced redox stress occurs in a yeast model for Roberts syndrome
Authors: Mfarej Michael G , Skibbens Robert V
Published: December 2021

Roberts syndrome (RBS) is a multispectrum developmental disorder characterized by severe limb, craniofacial, and organ abnormalities and often intellectual disabilities. The genetic basis of RBS is rooted in loss-of-function mutations in the essential N-acetyltransferase ESCO2 which is conserved from yeast (Eco1/Ctf7) to humans. ESCO2/Eco1 regulate many cellular processes that impact chromatin structure, chromosome transmission, gene expression, and repair of the genome. The etiology of RBS remains contentious with current models that include transcriptional dysregulation or mitotic failure. Here, we report evidence that supports an emerging model rooted in defective DNA damage responses. First, the results reveal that redox stress is elevated in both eco1 and cohesion factor Saccharomyces cerevisiae mutant cells. Second, we provide evidence that Eco1 and cohesion factors are required for the repair of oxidative DNA damage such that ECO1 and cohesin gene mutations result in reduced cell viability and hyperactivation of DNA damage checkpoints that occur in response to oxidative stress. Moreover, we show that mutation of ECO1 is solely sufficient to induce endogenous redox stress and sensitizes mutant cells to exogenous genotoxic challenges. Remarkably, antioxidant treatment desensitizes eco1 mutant cells to a range of DNA damaging agents, raising the possibility that modulating the cellular redox state may represent an important avenue of treatment for RBS and tumors that bear ESCO2 mutations.
A reference-quality, fully annotated genome from a Puerto Rican individual
Authors: Zimin Aleksey V , Shumate Alaina , Shinder Ida , Heinz Jakob , Puiu Daniela , Pertea Mihaela , Salzberg Steven L
Published: December 2021

Until 2019, the human genome was available in only one fully annotated version, GRCh38, which was the result of 18 years of continuous improvement and revision. Despite dramatic improvements in sequencing technology, no other genome was available as an annotated reference until 2019, when the genome of an Ashkenazi individual, Ash1, was released. In this study, we describe the assembly and annotation of a second individual genome, from a Puerto Rican individual whose DNA was collected as part of the Human Pangenome project. The new genome, called PR1, is the first true reference genome created from an individual of African descent. Due to recent improvements in both sequencing and assembly technology, and particularly to the use of the recently completed CHM13 human genome as a guide to assembly, PR1 is more complete and more contiguous than either GRCh38 or Ash1. Annotation revealed 37,755 genes (of which 19,999 are protein coding), including 12 additional gene copies that are present in PR1 and missing from CHM13. Fifty-seven genes have fewer copies in PR1 than in CHM13, 9 map only partially, and 3 genes (all noncoding) from CHM13 are entirely missing from PR1.
The Copyrightability of Opera Direction
Authors: Iaia Vincenzo
Published: December 2021

A judgment of the Italian Court of Cassation – No. 17565 of 18 June 2021 – offers an opportunity to investigate the legal protection options applicable to the direction of opera. As this issue is not addressed by EU law, EU Member States have adopted different approaches, from awarding copyright, to neighboring rights, to a mixture of the two. This opinion aims at finding the most consistent solution within the Italian legal framework. After an assessment of the alternative legal options, it argues that opera direction should be eligible for copyright protection via an analogical application of Art. 44 of the Italian copyright law, which indirectly includes cinematic direction within the area of copyrightable works. This conclusion is based on the fact that there are no substantial differences between the two types of direction justifying a diverse treatment. Otherwise, it would result in blatant and unsubstantiated discrimination because both categories of directors set out to convert a text – the dramatic text or the film script – to the medium of theatre or film respectively. Finally, this opinion suggests that even if the other creative roles involved in opera making are not addressed by the law, they too should qualify as co-authors if they make a creative contribution.
Cormorant predation mortality of perch (Perca fluviatilis) in coastal and archipelago areas, northern Baltic Sea
Authors: Heikinheimo Outi , Marjomäki Timo J , Olin Mikko , Rusanen Pekka
Published: December 2021

Perch (Perca fluviatilis) is an important prey species of the great cormorant (Phalacrocorax carbo sinensis) in the coastal waters of the northern Baltic Sea. The annual predation mortality caused by cormorants was estimated based on the consumed numbers of perch in relation to the abundance of perch in vulnerable age groups in the sea. We used existing stock assessment data (Archipelago Sea) or a simple population model in other areas (Gulf of Finland, Bothnian Sea, and Quark), based on commercial and recreational perch catches, and estimated fishing and natural mortalities, with distributions describing our understanding about the likelihood of different values for every variable. The median predation mortality was 4–10% annually, depending on the sea area. The area-specific 80% likelihood limits ranged from 3 to 21% annually. Compared to a recent perch tagging study in the Quark, the cormorant-induced mortality estimates were considerably lower, but the likelihood distributions partly overlapped. The results were sensitive to the estimated number of vulnerable perch in the population, which in turn largely depends on the natural mortality in young perch age groups.
A Detection Assay to Identify Alternative Food Sources of the Two-Spotted Stink Bug, Bathycoelia distincta (Hemiptera: Pentatomidae)
Authors: Fourie Arista , Venter Stephanus N , Slippers Bernard , Fourie Gerda
Published: December 2021

The two-spotted stink bug, Bathycoelia distincta Distant (Hemiptera: Pentatomidae), is a serious pest in South African macadamia orchards. This pest is predominantly controlled using insecticides, thus alternative control methods are essential. The stink bugs arrive as adults in the orchards, during the early nut set season, but little is known about their alternative plant hosts before their arrival. The aim of this study was to develop a PCR-based metabarcoding assay to identify plant material in the gut of B. distincta. Thereafter, the persistence of plant DNA in the gut, after switching food sources, was determined by rearing the stink bugs on Zea mays L. (Cyperales: Poaceae), transferring them to Macadamia sp. and then collecting insects at different time points. As a proof of concept, the assay was tested on insects collected from commercial macadamia orchards to determine if it can identify alternative food sources. The chloroplast gene markers, trnL and trnF, were most successful for plant DNA amplification. The time trial suggested that plant material can be detected 24 h after switching to the alternate food source and one of the samples still contained Z. mays DNA after five days. Various plant species were detected from the orchard collected samples, including known food sources of other stink bugs, such as tea plants (Camellia sinensis L. (Ericales:Theaceae)) and sunflowers (Helianthus annuus L. (Asterales: Asteraceae)). This study provides the first indication of potential alternative food sources of B. distincta. The assay developed in this study can now be implemented for large-scale field surveys to contribute to future integrated pest management strategies.
Feasibility of combining oncology surgery with bariatric surgery; a two-patient case series of sleeve gastrectomy with cytoreductive surgery and HIPEC
Authors: Aburahmah Mohammad , Hijji Talal M , Saif Lama Tareq , Kalagi Dana , Azzam Ayman Zaki , Amin Tarek
Published: December 2021

Patients with an oncologic disease requiring cytoreductive surgery and hyperthermic intraperitoneal chemotherapy may also present with morbid obesity. In some patients, it may be possible to offer bariatric surgery such as sleeve gastrectomy in combination with their cancer resection to treat both diseases concurrently. Two such cases are described where sleeve gastrectomy was done alongside the primary oncologic surgery in the same procedure. Our patients had long-term follow-ups and their overall outcomes were favorable. They achieved remission and acceptable levels of weight loss over their several years of follow-up appointments. The added benefit of bariatric surgery may decrease long-term morbidity and mortality in carefully selected patients. More studies are indicated to fully understand the risks of benefits of this combined procedure in order to offer it on a wider scale.
Vitamin D receptor expression in SLE peripheral blood CD4+T cells is associated with disease activity and cell apoptosis
Authors: Zhang Ying , Niu Lingying , Wang Fan , Tang Xiaojun , Wang Chun , Zhu Yun
Published: December 2021

Objectives

Systemic lupus erythematosus (SLE) is characterised by accumulated cell apoptosis. Vitamin D receptor (VDR) has immunomodulatory effect and potent anti-apoptosis activities. The aim of this study was to examine the correlation between CD4+T cells VDR expression, cell apoptosis, and disease activity in patients with SLE.

Methods

Forty-five SLE patients were recruited and 50 healthy individuals served as controls. The expression of VDR in CD4+T cells and their subsets were determined by flow cytometry. The correlations between VDR expression and cell apoptosis or disease parameters in SLE patients were analysed.

Results

VDR expression in CD4+T cells and their subsets were upregulated in SLE patients, especially in help T (Th)1, regulatory T (Treg), and follicular helper T (Tfh) cells. Frequency of VDR-positive CD4+T cells was positively associated with SLE disease activity index (SLEDAI)-2K values and inversely correlated with serum C3 concentration. The frequency of VDR-positive CD4+T cells, Th1 cells, Th2 cells, Th17 cells, Treg cells, and Tfh cells was positively correlated with cells apoptosis.

Conclusion

VDR expression in CD4+T cells and their subsets were increased in SLE. VDR expression was positively associated with disease activity and cell apoptosis in SLE patients.
Relationship between locomotive syndrome and frailty in rheumatoid arthritis patients by locomotive syndrome stage
Authors: Sobue Yasumori , Suzuki Mochihito , Ohashi Yoshifumi , Koshima Hiroshi , Okui Nobuyuki , Funahashi Koji , Ishikawa Hisato , Asai Shuji , Terabe Kenya , Yokota Yutaka , Kishimoto Kenji , Takahashi Nobunori , Imagama Shiro , Kojima Toshihisa
Published: December 2021

Objectives

This study aimed to evaluate the association between locomotive syndrome (LS) and frailty in rheumatoid arthritis (RA) patients.

Methods

Subjects were 538 RA patients (female, 72.9%; mean age ± standard deviation, 66.8 ± 13.4 years). LS and frailty were defined as ≥16 points on the 25-question Geriatric Locomotive Function Scale (Stage ≥2) and ≥8 points on the Kihon Checklist (KCL), respectively.

Results

There were 214 subjects with Stage ≥2 LS (39.8%) and 213 subjects with frailty (39.6%). Among subjects with Stage 0, 1, 2, and 3 LS, 11.0%, 21.9%, 48.3%, and 84.6% had frailty, respectively. The KCL points for cognitive and psychosocial factors had no significant differences across LS stages. Multivariable logistic regression analysis revealed that the Health Assessment Questionnaire was independently associated with frailty and LS stage, and the Clinical Disease Activity Index was associated with LS stage but not frailty.

Conclusions

As LS worsens in RA patients, the likelihood of developing physical frailty increases. RA patients with a low LS stage can still develop frailty, and suppressing disease activity may not be sufficient to prevent frailty. These findings highlight the need to screen for frailty in RA patients and consider appropriate interventions based on each patient’s condition, focusing on nonphysical factors.
Structural equation modelling provides insights to understand the construct of chronic pain in women with rheumatoid arthritis
Authors: Vendrusculo-Fangel Leticia Meda , Fangel Renan , Vieira de Sousa Neto Ivo , Nobrega Otavio Toledo , dos Reis Felipe José Jandre , Durigan João Luiz Quaglioti , de Cassia Marqueti Rita
Published: December 2021

Objectives

We aimed to adopt a multidimensional approach and investigate the interconnections between biomarkers (cytokines, matrix metalloproteinases, and cortisol) and psychosocial aspects considering pain acceptance, the individual construct of pain perception in terms of blood inflammation biomarkers, anxiety, self-efficacy, and functional performance and to define the quality of life (QoL) in women with rheumatoid arthritis (RA).

Methods

An observational cross-sectional study with a total of 42-RA participants, with chronic pain and 42-women without rheumatic diseases or chronic pain were included. A structural equation model was used to investigate the association between independent variables.

Results

Women with RA presented high blood biomarker levels, representing an intense inflammatory process. The participants with RA reported moderate pain most of the time, a worsening QoL, functionality, engagement in activities, and a willingness to live with pain and self-efficacy. It was found that the higher the chronic pain, the greater the intensity of pain perceived by these women with RA, as well as, the worse the functionality, the higher the perceived pain.

Conclusions

The exacerbation of pain perception leads to worsening of the experience of chronic pain. The new construct of pain experience should include functionality as a crucial factor in understanding the mechanisms underlying pain.