bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractInferring 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

Abstract

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

ABSTRACTComplex 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

Abstract
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

AbstractATP 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

AbstractRoberts 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.