bluuebunny/crossref_metadata_2025 huggingface dataset:
Species Composition, and Diversity of Mataram University Green Open Space, West Nusa Tenggara
Authors: Latifah S , Valentino N , Permata Sari D , Sari BSA
Published: December 2021

Mataram university green open space (GOS) is one of the partial green open spaces (GOS) approaches that can be used to conserve endemic germplasm as well to fulfil the proportion and distribution of urban forests. This research aims to describe the species composition, and diversity including the authenticity of Flora Malesiana in this area. We used a census method (100% measurement) to identify the species and measured the diameter and height of all tree species with the diameter of more than 2 cm. The results showed that the 99 species belonged to 85 Genera, 39 families with a composition of 61 species (61.62%) including the flora Malesiana and 38 species (38.38%) including exotic species. Based on IVI analysis showed thatPtychosperma macarthuriidominated at the sapling level whileSwietenia mahagonidominated at the pole and tree levels. The H’ of diversity is in the medium category with the sapling level has the highest value (3.42).
Diagnostics of changes in the stress-strain state of the massif after earthquakes by geodetic methods
Authors: Panzhin A A , Koptiakov D A
Published: December 2021

The results of diagnostics of changes in the stress-strain state of the massif during the earthquake in the region of Katav-Ivanovsk in September 2018 are presented. The data were obtained as a result of a study of regional geodynamics using permanent stations of the Global Navigation Satellite System (GNSS) of the Urals. The numerical values of the amplitudes of changes in coordinates, the distribution of displacements and deformations of the rock mass have been determined.
The short-term tsunami forecast
Authors: Korolev Yu P
Published: December 2021

A brief overview of the methods of a tsunami early warning in the Kuril Islands, which turned out to be ineffective during recent events, is presented. A hydrophysical method for short-term tsunami forecasting based on information about a tsunami in the ocean, used in the United States, and an express method, also using information about a tsunami in the ocean, are briefly described. The results of the retrospective forecast of the tsunami that occured on March 11, 2011, by the express method are presented.
The hindcast of recent tsunamis in Northern Pacific
Authors: Korolev P , Korolev Yu , Loskutov A
Published: December 2021

Three earthquakes occurred in the North Pacific in 2020, causing observable tsunamis. The tsunamis were not devastating. Numerical modelling of tsunami propagation was performed to reproduce operational forecasting (retrospective analysis) of waveforms at deep-water stations. Direct calculation of tsunami using USGS finite-fault source data on GPU was carried out. The leap-frog (Arakawa staggered grid) scheme calculation over the Pacific Ocean on a regular grid with a spatial step of 0.5 arc minutes of 1440 min (1 day) tsunami propagation was performed in approximately 90 min of computer time. With use of a hybrid cluster with several GPU accelerators and proper optimization of the simulation algorithm, this time can be reduced by tens of times. Consequently, the time for estimating the transfer function will be comparable to the travel time of a tsunami to the stations, where the forecasts data is. It will make possible to forecast the shape of a tsunami at any point with a lead time enough to decide for tsunami alert at sites where a tsunami poses a real danger. The calculation results are in good agreement with the real data of deep-ocean measurements. The quality of the forecast is comparable to the quality of calculations by other methods.
Comparative analyses of changes in the ice cover of the Tatar Strait in relation to 1961-1990 and 1991-2020 climate normals
Authors: Zarubina D V , Pishchalnik V M , Romanyuk V A
Published: December 2021

Current warming in the Northern Hemisphere has encompassed not only the surface atmosphere, but also manifested itself in a change in the state of the sea ice cover, as an integral part of the climate system. One of the indicators of the warming was a reduction in ice cover observed in the water area of the Far Eastern seas since the late 1980s. The prospective areas of hydrocarbon deposits discovered in the Tatar Strait, as well as the existing needs for the transportation of hydrocarbons along the shipping routes in the strait, led to the emerging interest in researching the ice regime of the Sea of Japan in the modern climatic era. The proposed paper analyses the changes in ice cover of the Tatar Strait in relation to 1961–1990 and 1991–2020 climate normals. The regularities of the long-term variability of ice cover within non-overlapping 30-year periods were revealed. The analysis of the dynamics of ice cover anomalies, calculated for each normal separately, was carried out. An assessment of the distribution of winter types in the periods under study was carried out. The characteristic features of variations in the intra-seasonal course of ice cover and the dates of the onset of ice phases in different types of winters were identified.
Search for hydrogeochemical indicators of the genetic relation between mud volcanism and oil and gas fields
Authors: Nikitenko O A , Ershov V V
Published: December 2021

The paper reports the results of a comparative analysis of the chemical and isotope composition (δ180 and δD) of mud volcanic waters and formation waters from oil and gas fields. Studies show that the waters discharged by mud volcanoes in most cases are very similar to formation waters. The most characteristic geochemical traits of both waters are elevated concentrations of hydrocarbonate ions, iodine, boron, bromine, and a low content of sulfate ions.
Specificity of the products of Tyatya volcano eruption in 1973
Authors: Veselov O V , Kazakov A I , Kozlov D N
Published: December 2021

Based on 198 determinations of the complete silicate analysis of Tyatya volcano (Kunashir Island), we compared the data of the latter (1973) and all previous eruptions to reveal their differences and determine the evolution of Tyatya volcanism in the Holocene. The application of the estimation of the thermobaric parameters of the upper mantle magma chamber of the volcano made it possible to determine the temperature decrease in the magma chamber in 1973. An assumption was made about the polycyclic magmatic activity of the Tyatya volcano. The results of statistical processing of data on the thickness of tephra and the size of its fragments from the 1973 eruption are presented. Polynomial regressions of various degrees are applied. Models of tephra distribution based on three-dimensional trend analysis have been constructed. The results of the study are recommended for the creation of information databases on the petrochemistry of eruption products and the distribution of pyroclastics from volcanoes in the Kuril Island arc.
The shores of the contact zone of the Subarctic and moderately cold seas
Authors: Afanasev V V , Uba A V
Published: December 2021

Longitude sectorality and latitudinal zonality of morpholithogenesis on the coast of Sakhalin is the result of the unique geographical position of the island, which is a zone of mutual influences and interactions of neighboring geosystems of the subarctic Sea of Okhotsk and the moderately cold northern part of the Sea of Japan – a contact geographical structure. Based on the digitizing of maps of morphogenetic types of shores, modern morpholithodynamic settings and lithological complexes of the coast, geomorphological and morphodynamic differences of the shores of Sakhalin Island are shown, the eastern shores of which have a subarctic appearance, and the western shores are washed by the temperate sea.
Coastal dynamics of the Gulf of Kalamita (Western Crimea)
Authors: Agarkova-Lyakh I V
Published: December 2021

The performed research showed that since the first third of the 20th century until today the beach width at various sections of the Gulf of Kalamita has decreased two-to fourfold, and at some of them beaches have totally disappeared. The average coast erosion rate for the last 100 years has been 1.3 m/yr, with the maximum being 7.8 m/yr. These processes are accompanied with depletion of debris on the beach and underwater slope, erosion of bench deposits, and destruction of coastal structures. This is due to deficiency of beach-forming material resulted from intense economic management in the coastal area. Implementation of scientifically and technically sound coastal protection projects is essential to preserve the beaches of the Gulf of Kalamita.
Integrity of risk indicators of hazardous natural processes (on the example of the Krasnodar Krai)
Authors: Lyubimova T V , Bondarenko N A
Published: December 2021

The problem of assessing risk indicators of hazardous natural processes as the basis for sustainable development of the region arises due to the peculiarities of the geological structure of the territory of Krasnodar Krai. The work is based on a comprehensive assessment of the geological conditions of the territory of Krasnodar Krai with the use of a systematic approach. A list of characteristic natural processes that pose the greatest danger to capital constructions was determined: in the mountainous part – erosion processes, on the plain – soil subsidence and associated landforms. Then, schematic maps were compiled and the geological component of the risk (its spatial-areal indicator) was determined. Subsequently, to compare these maps, overlay operations were performed, as a result of which the spatial characteristics of ARC/INFO layers were combined into a new layer and relational join of their attribute data was carried out. Adding the risks of each parameter made it possible to rank the territory into 4 zones according to the degree of integral risk of manifestation of natural processes.
Adventive component flora of the southern part of Sakhalin Island
Authors: Lozhnikova O O
Published: December 2021

The article is devoted to the adventive flora of the southern part of Sakhalin Island. Nowadays, 274 species of adventive plants, belonging to 192 genera and 57 families, have been identified here. Five families (Amaranthaceae, Cannabaceae, Commelinaceae, Linaceae, and Malvaceae) are represented by invasive species only. The structure of the leading families and genera is analyzed, the participation of adventive species information of plant communities is indicated. Adventive species are classified into life forms, method of entering and degree of naturalization.
Steppe communities within the coast of the Taman Peninsula
Authors: Pikalova N A , Krylenko S V , Volkova T A
Published: December 2021

The article presents the results of field research in 2019–2020 of plant communities of the abrasive coast of the Taman Peninsula. The biomorphological structure of populations is dominated by annual species, which indicates a high dynamism associated with exogenous processes. Ecologically, the dominant species are xerophytes and xeromesophytes, as well as species with a wide eco-amplitude. The process of unification of the studied flora is low and amounted to 17 %. The generalized floristic list includes 231 plant species from 48 families. In the study area, 7 species of Red Book plants were found, of which 2 species were included in the Red Book of the Russian Federation.
Biodiversity of the flora of vascular plants of the Makarovsky Nature Reserve on Sakhalin Island
Authors: Sabirova N D , Sabirov R N
Published: December 2021

The article is devoted to the research results concerning the flora of vascular plants of the Makarovsky Nature Reserve situated in the middle part of Sakhalin Island. Nowadays, 407 species of vascular plants have been identified on its territory, and 26.8 % of the total number of taxa known on the island. Among them, 13 species of rare plants included in the Red Data Book of the Sakhalin Region have been identified. The structure of the leading families and genera is indicated, the flora is analyzed by life forms, geographical elements and ecological-cenotic groups.
Structural deviations in secondary phloem of young shoots of Spiraea beauverdiana near magma volcanoes
Authors: Vatserionova E O , Kopanina A V , Vlasova I I
Published: December 2021

We performed a comparative analysis of the internal structure of the secondary phloem of one, two and three-year-old stems of Spiraea beauverdiana growing in extreme conditions of solfataric fields of Golovnin Volcano caldera and Mendeleyev Volcano and in normal conditions. The combination of environmental factors in conditions of solfataric activity, such as high temperatures in the soil and in the near-surface air, as well as saturation with gases toxic to plants, rare elements accumulating in the nearby substrate, and lack of soil moisture, interfere with normal phellogen and cambium activity. Deviations from the normal structure involve changes in the following parameters of the internal structure of a year-old stem of S. beauverdiana. Secondary phloem parameters in the studied habitats are normal, except for the length of the segments of sieve tubes, the height of single-row rays, the length of parenchymal girder; these are shorter in S. beauverdiana stems from volcanos. At two and three years of age in volcanic conditions we see reduction in the width of the secondary phloem (both conductive and non-conductive) and the diameter of the segments of sieve tubes. In samples from Golovnin Volcano we see reduction in tangential diameter, while in the samples from Mendeleyev Volcano it’s the radial diameter. We also see reduction in the height of multiple-row rays. At that age we see changes in the structure of the radial parenchyma; namely, we find no double-row rays in samples from Golovnin Volcano caldera. One of the signs of impact of volcanic activity on the bark structure is development of non-specific anomalies in the internal structure of the S. beauverdiana bark, namely, in the outer bark, or in deeper levels, such as the secondary phloem. That causes sclerification and dilatation of parenchyma, and multiple layers in some tissues.
A Monte Carlo investigation of some important radiation parameters and tissue equivalency for photons below 1 keV in human tissues
Authors: Mohammad Rafiei Mustafa , Parsaei Sara , Kaur Parminder , Singh K J , Büyükyıldız Mehmet , Kurudirek Murat
Published: December 2021

The attenuation coefficients are important input values in estimating not only the dose and exposure in radiotherapy and medical imaging, but also in the proper design of photon shields. While studies are widely available above 1 keV, the attenuation coefficients of human tissues for photon energies less than 1 keV have not been studied yet. In this study, the attenuation coefficients of water and some human tissues were estimated for low energy photons using the MCNP6.1 code in the energy region 0.1 keV–1 keV. Mass attenuation coefficients were estimated at photon energies of 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950 and 1000 eV for water and ten human tissues (Soft, Breast, Lung, Bone, Brain, Eye lens, Ovary, Skin, Thyroid and Prostate). Results were compared with those available in literature and a fairly good agreement has been obtained. These data were then used to calculate the mean free path, half value layer, tenth value layer, effective atomic number and specific gamma-ray constant (useful for calculation of dose rate) as well. Moreover, for comparison the effective atomic number of the water has been obtained using the results of this work and using the data available in NIST database from 0.1 to 1 keV. In addition, the human tissues were compared with some tissue equivalent materials in terms of effective atomic number and specific gamma-ray constant to study the tissue equivalency from the results, the muscle-equivalent liquid with sucrose has been found to be the best tissue equivalent material for soft tissue, eye lens and brain with relative difference below 4.1%.
Influence of Cenosphere on Compression After Impact Strength of Glass Epoxy Laminates
Authors: Rajendran Balaji , Kumar P K Dinesh
Published: December 2021

Under controlled lab settings, two distinct laminates, one containing cenosphere and the other with neat resin, were evaluated for impact strength using a Fractovis impact machine, compression, and Compression After Impact (CAI) strengths through Tinus Olsen UTM. The GFRP laminates were prepared with 16 layers of glass fiber    combined with epoxy resin reinforced Cenospheres at concentrations of 1, 3 and 5 wt%, according to ASTM specifications. The dominant failure mode controlling the specimen’s compression ultimate load resistance, and other failure modes of impacted specimens such like fiber pull-out and debonding, were found to be the effects of delamination using coupled coustic emission (AE) monitoring and compression tests. On specimens with a 3 wt% filler additive, there was a noticeable increase in strength. Both impacted and non-impacted samples exhibited significant compression ultimate load resistances, with the 3 wt% filler impregnated specimen having the maximum.
Comparison of a Novel Silicone Gel Wound Dressing vs Bacitracin After Follicular Unit Extraction Hair Transplantation
Authors: James Isaac B , Turer David M , DiBernardo Barry E
Published: December 2021

Background

Follicular unit extraction (FUE) hair transplantation subjects are excellent candidates to assess wound dressings. The wound surface area is large and adequately delineated to allow randomization, while in-patient split scalp designs allow patients to serve as their own controls.

Objectives

This randomized, single-blinded, split-scalp comparison trial compares a novel, film-forming silicone gel—Stratamed (SM; Stratpharma AG, Basel, Switzerland)—to Bacitracin (Bac; McKesson Medical-Surgical Inc., Richmond, VA) in subjects undergoing FUE.

Methods

Twenty subjects were randomized to receive SM and Bac on alternating sides of the scalp. Primary outcome measures included blinded clinician assessments of edema, erythema, crusting, healing response and outcome preference. Secondary measures included subject-reported assessments of pain and pruritis as well as FaceQ scores taken at post-FUE days two through six.

Results

Twenty subjects were enrolled. Nineteen completed the trial. All subjects were non-smokers, and none had medical comorbidities expected to impact wound healing. An average of 1778 follicles per subject were harvested. No adverse events were reported, and all subjects healed by day 7. Healing response and outcome preference were significantly higher at day 1 in the SM group and by day 7, both groups were similar. There were no significant differences between groups for edema, erythema, or crusting. There were no significant differences between groups for subject-reported outcomes of pain, pruritis, or FACE-Q scores. When asked which product they preferred using, 44% of subjects preferred using SM versus 22% who preferred Bac.

Conclusions

The SM wound dressing was well-tolerated in patients undergoing FUE. SM may speed the healing response in the early phase of wound healing.

Level of Evidence: 2
Rare variant association tests for ancestry-matched case-control data based on conditional logistic regression
Authors: Cheng Shanshan , Lyu Jingjing , Shi Xian , Wang Kai , Wang Zengmiao , Deng Minghua , Sun Baoluo , Wang Chaolong
Published: December 2021

With the increasing volume of human sequencing data available, analysis incorporating external controls becomes a popular and cost-effective approach to boost statistical power in disease association studies. To prevent spurious association due to population stratification, it is important to match the ancestry backgrounds of cases and controls. However, rare variant association tests based on a standard logistic regression model are conservative when all ancestry-matched strata have the same case-control ratio and might become anti-conservative when case-control ratio varies across strata. Under the conditional logistic regression (CLR) model, we propose a weighted burden test (CLR-Burden), a variance component test (CLR-SKAT) and a hybrid test (CLR-MiST). We show that the CLR model coupled with ancestry matching is a general approach to control for population stratification, regardless of the spatial distribution of disease risks. Through extensive simulation studies, we demonstrate that the CLR-based tests robustly control type 1 errors under different matching schemes and are more powerful than the standard Burden, SKAT and MiST tests. Furthermore, because CLR-based tests allow for different case-control ratios across strata, a full-matching scheme can be employed to efficiently utilize all available cases and controls to accelerate the discovery of disease associated genes.
Virtifier: a deep learning-based identifier for viral sequences from metagenomes
Authors: Miao Yan , Liu Fu , Hou Tao , Liu Yun
Published: December 2021

Motivation

Viruses, the most abundant biological entities on earth, are important components of microbial communities, and as major human pathogens, they are responsible for human mortality and morbidity. The identification of viral sequences from metagenomes is critical for viral analysis. As massive quantities of short sequences are generated by next-generation sequencing, most methods utilize discrete and sparse one-hot vectors to encode nucleotide sequences, which are usually ineffective in viral identification.

Results

In this article, Virtifier, a deep learning-based viral identifier for sequences from metagenomic data is proposed. It includes a meaningful nucleotide sequence encoding method named Seq2Vec and a variant viral sequence predictor with an attention-based long short-term memory (LSTM) network. By utilizing a fully trained embedding matrix to encode codons, Seq2Vec can efficiently extract the relationships among those codons in a nucleotide sequence. Combined with an attention layer, the LSTM neural network can further analyze the codon relationships and sift the parts that contribute to the final features. Experimental results of three datasets have shown that Virtifier can accurately identify short viral sequences (<500 bp) from metagenomes, surpassing three widely used methods, VirFinder, DeepVirFinder and PPR-Meta. Meanwhile, a comparable performance was achieved by Virtifier at longer lengths (>5000 bp).

Availability and implementation

A Python implementation of Virtifier and the Python code developed for this study have been provided on Github https://github.com/crazyinter/Seq2Vec. The RefSeq genomes in this article are available in VirFinder at https://dx.doi.org/10.1186/s40168-017-0283-5. The CAMI Challenge Dataset 3 CAMI_high dataset in this article is available in CAMI at https://data.cami-challenge.org/participate. The real human gut metagenomes in this article are available at https://dx.doi.org/10.1101/gr.142315.112.

Supplementary information

Supplementary data are available at Bioinformatics online.
InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses
Authors: Ferguson James M , Gamaarachchi Hasindu , Nguyen Thanh , Gollon Alyne , Tong Stephanie , Aquilina-Reid Chiara , Bowen-James Rachel , Deveson Ira W
Published: December 2021

Motivation

InterARTIC is an interactive web application for the analysis of viral whole-genome sequencing (WGS) data generated on Oxford Nanopore Technologies (ONT) devices. A graphical interface enables users with no bioinformatics expertise to analyze WGS experiments and reconstruct consensus genome sequences from individual isolates of viruses, such as SARS-CoV-2. InterARTIC is intended to facilitate widespread adoption and standardization of ONT sequencing for viral surveillance and molecular epidemiology.

Results

We demonstrate the use of InterARTIC for the analysis of ONT viral WGS data from SARS-CoV-2 and Ebola virus, using a laptop computer or the internal computer on an ONT GridION sequencing device. We showcase the intuitive graphical interface, workflow customization capabilities and job-scheduling system that facilitate execution of small- and large-scale WGS projects on any common virus.

Availability and implementation

InterARTIC is a free, open-source web application implemented in Python that executes best-practice command line workflows from the ARTIC network. The application can be downloaded as a set of pre-compiled binaries that are compatible with all common Linux distributions, Windows with Linux subsystems, MacOSX and ARM systems. All code can be found on GitHub at https://github.com/Psy-Fer/interARTIC/ and documentation can be found at https://github.com/Psy-Fer/interARTIC/.

Supplementary information

Supplementary data are available at Bioinformatics online.
ZDHHC19 localizes to the cell membrane of spermatids and is involved in spermatogenesis
Authors: Wu Yangyang , Zhang Xin , Zhang Xi , Liu Siyu , Zhang Jintao , Sun Shuya , Zhao Shuqin , Wang Zerui , Cui Yiqiang , Huang Xiaoyan , Liu Mingxi
Published: December 2021

Sperm is the ultimate executor of male reproductive function. Normal morphology, quantity, and motility of sperm ensure the normal reproductive process. Palmitoylation is a posttranslational modification mediated by palmitoyltransferases whereby palmitoyl is added to proteins. Seven palmitoyltransferases have been identified in Saccharomyces cerevisiae and 23 in humans (including ZDHHC1–9 and ZDHHC11–24), with corresponding homologs in mice. We identified two testis-specific palmitoyltransferases ZDHHC11 and ZDHHC19 in mice. The Zdhhc11 and Zdhhc19-knockout mouse models were constructed, and it was found that the Zdhhc11 knockout males were fertile, while Zdhhc19 knockout males were sterile. ZDHHC19 is located in the cell membrane of step 4–9 spermatids in the mouse testis, and phenotypic analysis showed that the testicular weight ratio in the Zdhhc19−/− mice decreased along with the number and motility of the sperm decreased, while sperm abnormalities increased, mainly due to the “folded” abnormal sperm caused by sperm membrane fusion, suggesting the involvement of ZDHHC19 in maintaining membrane stability in the male reproductive system. In addition, Zdhhc19−/− mice showed abnormal sperm morphologies and apoptosis during spermatogenesis, suggesting that spermatogenesis in the Zdhhc19−/− mice was abnormal. These results indicate that ZDHHC19 promotes membrane stability in male germ cells.
A Sensitive Liquid Chromatography-Mass Spectrometry Method for Determination of Toosendanin in Rat Plasma and its Application to Pharmacokinetic Study
Authors: Shen Chuangpeng , Pan Zhisen , Wu Xiaojie , Zhong Chong , Li Qiao , Si Yuqi , Liu Changhui , Tu Haitao , Deng Zhijun , Zhu Zhangzhi , Guo Jiewen , Xin Xiaoyi , Liu Min
Published: December 2021

A simple, rapid and sensitive analytical method was developed for the determination of toosendanin in rat plasma using liquid chromatography tandem mass spectrometry (LC–MS/MS). Andrographolide was selected as the internal standard, and the plasma samples were extracted by liquid–liquid extraction with diethyl ether. Chromatographic separation was performed on a Dikma Spursil C18, 3.5 μm (150 × 2.1 mm i.d) analytical column with 85% methanol:water (v/v) containing 0.025% formic acid (pH = 3.9) as mobile phase. The flow rate was 0.25 mL/min, and the total run time was 3 min. Detection was performed with a triple-quadrupole tandem mass spectrometer using negative ion mode electrospray ionization (ESI) in the multiple reaction monitoring (MRM) mode. The MS/MS ion transitions monitored were m/z 573.1 → 531.1 and 349.0 → 287.0 for toosendanin and andrographolide, respectively. Good linearity was observed over the concentration range of 3.125–500 ng/mL in 100 μL of rat plasma with a correlation coefficient ˃0.9997. Intra- and inter-assay variabilities were ˂8.5% in plasma. The recovery and the matrix effect were in the range 71.8–73.5% and 96.4–103.8%, respectively. The analyte was stable under various conditions (at room temperature, during freeze–thaw settings, in the autosampler, and under deep-freeze conditions). The method was successfully applied to a pharmacokinetic study of toosendanin after its oral administration in rats at a dose of 10 mg/kg.
The last pre-pandemic European Renal Association Registry report: age at start of kidney replacement therapy in Europe
Authors: Carriazo Sol , Ortiz Alberto
Published: December 2021

The European Renal Association (ERA) Registry Annual Report 2019 will be its last pre-pandemic report. From 2020 on, registry data will incorporate any potential impact of coronavirus disease 2019 (COVID-19) on kidney replacement therapy (KRT) practices in Europe. The 2019 report focussed on age comparisons and found substantial differences in the distribution of primary renal disease, treatment modality, kidney donor type and the survival probabilities for different age categories. The report presents data that support a correlation (R2 = 0.43, P < 0.00001) between the incidence of KRT per million population (pmp) and the median age at the start of KRT in the different regions and countries, suggesting that initiating KRT at an older median age may be a determinant of KRT incidence. The causes of the lower age at KRT in some countries should be explored. These may include, but are not limited to, KRT not being offered to the elderly or the elderly refusing KRT. In this regard, there was a correlation between the median age at the start of KRT and per capita gross domestic product (GDP) (R2 = 0.26, P < 0.0046), suggesting that the availability of resources may be a factor that limits the offer of KRT to the elderly. The UK may represent a case to study these issues. Both age at initiation of KRT and KRT incidence are below the European median and lower than that expected for GDP. Furthermore, there are differences between the various countries within the UK, as well as documented racial differences, the latter being a piece of information missing for most European countries.
Percutaneous versus surgical femoral access in minimally invasive cardiac operations
Authors: El-Sayed Ahmad Ali , Bayram Ali , Salamate Saad , Sirat Sami , Amer Mohamed , Bakhtiary Farhad
Published: December 2021

OBJECTIVES

Both surgical and percutaneous femoral accesses for the establishment of extracorporeal circulation are used in minimally invasive cardiac surgeries. The goal of this study was to compare the outcomes with the MANTA vascular closure device after percutaneous arterial decannulation via the surgical approach.

METHODS

Between November 2018 and January 2021, a total of 490 consecutive patients underwent minimally invasive cardiac operations at our institution. Cannulation and decannulation of femoral vessels were under direct vision surgically or percutaneously. The MANTA system was used to close the femoral artery in all patients with percutaneous cannulation. Demographic, clinical and procedural data were collected retrospectively.

RESULTS

Surgical cut-down and suture closure of the femoral artery was performed in 222 patients (45.3%); percutaneous access and closure with the MANTA system was used in 268 patients (54.7%). The surgical group presented a significantly higher incidence of any access site complication compared to the percutaneous group [18 patients (8.1%) vs 6 patients (2.2%); P = 0.003]. Lymph fistula and wound healing disorders occurred more frequently in the surgical group (3.2% vs 0% [P = 0.004] and 3.6% vs 0% [P = 0.002], respectively). Median procedural duration and stays in the intensive care unit were significantly lower in the percutaneous group {127 [interquartile range (IQR) 97–158] min vs 150 (IQR 117–185) min (P < 0.001) and 1 (IQR 1–2) day vs 2 (IQR 1–3) days (P = 0.008), respectively}.

CONCLUSIONS

Percutaneous access and closure with the MANTA system are feasible, safe and associated with lower incidences of all-cause access site complications and shorter stays in the intensive care unit compared to surgical access and closure in minimally invasive cardiac surgeries.
Genotyping-by-sequencing and genomic selection applications in hexaploid triticale
Authors: Ayalew Habtamu , Anderson Joshua D , Krom Nick , Tang Yuhong , Butler Twain J , Rawat Nidhi , Tiwari Vijay , Ma Xue-Feng
Published: December 2021

Triticale, a hybrid species between wheat and rye, is one of the newest additions to the plant kingdom with a very short history of improvement. It has very limited genomic resources because of its large and complex genome. Objectives of this study were to generate dense marker data, understand genetic diversity, population structure, linkage disequilibrium (LD), and estimate accuracies of commonly used genomic selection (GS) models on forage yield of triticale. Genotyping-by-sequencing (GBS), using PstI and MspI restriction enzymes for reducing genome complexity, was performed on a triticale diversity panel (n = 289). After filtering for biallelic loci with more than 70% genome coverage, and minor allele frequency (MAF) > 0.05, de novo variant calling identified 16,378 single nucleotide polymorphism (SNP) markers. Sequences of these variants were mapped to wheat and rye reference genomes to infer their homologous groups and chromosome positions. About 45% (7430), and 58% (9500) of the de novo identified SNPs were mapped to the wheat and rye reference genomes, respectively. Interestingly, 28.9% (2151) of the 7430 SNPs were mapped to the D genome of hexaploid wheat, indicating substantial substitution of the R genome with D genome in cultivated triticale. About 27% of marker pairs were in significant LD with an average r2 > 0.18 (P < 0.05). Genome-wide LD declined rapidly to r2 < 0.1 beyond 10 kb physical distance. The three sub-genomes (A, B, and R) showed comparable LD decay patterns. Genetic diversity and population structure analyses identified five distinct clusters. Genotype grouping did not follow prior winter vs spring-type classification. However, one of the clusters was largely dominated by winter triticale. GS accuracies were estimated for forage yield using three commonly used models with different training population sizes and marker densities. GS accuracy increased with increasing training population size while gain in accuracy tended to plateau with marker densities of 2000 SNPs or more. Average GS accuracy was about 0.52, indicating the potential of using GS in triticale forage yield improvement.
The genome of the zebra mussel,Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol
Authors: McCartney Michael A , Auch Benjamin , Kono Thomas , Mallez Sophie , Zhang Ying , Obille Angelico , Becker Aaron , Abrahante Juan E , Garbe John , Badalamenti Jonathan P , Herman Adam , Mangelson Hayley , Liachko Ivan , Sullivan Shawn , Sone Eli D , Koren Sergey , Silverstein Kevin A T , Beckman Kenneth B , Gohl Daryl M
Published: December 2021

The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate a high-quality chromosome-scale genome assembly. Through comparative analysis and transcriptomics experiments, we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact steamer-like elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.
Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions
Authors: Salavati Mazdak , Woolley Shernae A , Cortés Araya Yennifer , Halstead Michelle M , Stenhouse Claire , Johnsson Martin , Ashworth Cheryl J , Archibald Alan L , Donadeu Francesc X , Hassan Musa A , Clark Emily L
Published: December 2021

There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the “Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)” to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.
Sea level instantaneous budget for 2003–2015
Authors: Mu Dapeng , Xu Tianhe , Guan Meiqian
Published: December 2021

Most studies of sea level budget only indicate the stationary causes for the global mean sea level (GMSL) rise over the course of a time span of interest, providing limited information on temporary changes in the GMSL budget. In this contribution, we present an instantaneous budget of the GMSL for the period of 2003–2015, which offers new insights on the time evolution of the GMSL budget. We use a space-state model to compute the instantaneous rates of GMSL and their contributing sources (barystatic and steric contributions), to investigate the causes of the GMSL instantaneous budget, which accounts for and quantifies low-frequency variations in GMSL rise. Combining the barystatic GMSL instantaneous rates (estimated from satellite gravimetry) along with a particular choice of steric GMSL instantaneous rates (inferred from an Argo product) achieves closure of the GMSL instantaneous budget with a standard deviation of 0.4 mm yr−1. We find that the barystatic GMSL rate is primarily responsible for the striking fluctuations in the GMSL instantaneous rates between 2009 and 2015. For example, over only 20 months (July 2010 to February 2012), the GMSL (barystatic) rate increases from 0.32 (0.71) to 6.12 (4.55) mm yr−1. These strong fluctuations mainly result from hydrology and mountain glacier mass variations rather than mass loss in ice sheet, for instance, Australia slowed ∼1.2 mm yr−1 equivalent contribution to GMSL rise over the year 2010, which is approximately four times the linear rate of Antarctica mass loss.
Innovative actions in oceans and human health for Europe
Authors: Pellens Noortje , Boelee Eline , Veiga Joana M , Fleming Lora E , Blauw Anouk
Published: December 2021

Innovative actions are local initiatives which leverage the interactions between the ocean and human health to reduce the risks and enhance the benefits for the stakeholders and the natural environment. These initiatives can have strong positive effects on human health and wellbeing as well as on the marine environment. We analysed 150 such innovative actions in Europe. Using a combined case study and survey approach, innovative actions were identified using interviews and content analysis of websites and compiled into a database. Quantitative data were analysed according to the Drivers, Pressures, State, Impact and Response (DPSIR) framework, guided by selected in-depth interviews. Overall, the innovative actions provided a positive impact on the health of both the ocean and humans through increasing food provision, water quality and tourism opportunities; and addressing environmental issues such as commercial fish stock depletion, pollution and climate change. Innovative actions contributed to meeting various targets of the Sustainable Development Goals (SDGs) 3, 13 and 14. These actions played a potential role ahead of and alongside policy. Some of the innovative actions may have potential to be put in place elsewhere. Such up-scaling would need to be adapted to local circumstances and could be facilitated by an innovative action exchange platform.
A retrospect of the structure determination of Taka-amylase A
Authors: Kusunoki Masami
Published: December 2021

The 3D structure of Taka-amylase A was determined by X-ray crystal analysis at 3 Å resolution by Masao Kakudo’s laboratory at the Institute for Protein Research, Osaka University, in 1980. Seven kinds of heavy atom derivatives were used for phase determination. There are three copies of Taka-amylase molecules in the asymmetric unit, which improved the quality of electron density maps, leading to the completion of a molecular model with 478 amino acids. The structure determination process in those days is described briefly.
The Hidden Danger of Lithium Battery-Powered Electric Bicycles and Scooters: A Case Series of the Israeli National Burn Center Experience
Authors: Segalovich Matan , Berl Ariel , Aviv Uri , Jaffe Eli , Shelef Ran , Haik Josef , Cleary Michelle , Kornhaber Rachel , Harats Moti
Published: December 2021

Electric-powered bicycles and scooters that use rechargeable lithium batteries are an urban transportation alternative and have become increasingly popular. However, in recent years, there has been an increase in patient admissions to the Israeli National Burn Center with burns associated with their use. In this case series of all patients (n = 9) referred to the Emergency Department (February 2016–October 2020) with lithium-related battery burns from electric-powered bicycles and scooters, we present burn depth, size, treatment, inhalation injuries, and hospitalization. All patients were admitted to the Israeli National Burn Center for treatment. The average TBSA was 27.5% (range 3%–57%). All but one patient had a combination of partial to full-thickness burns affecting the upper and lower limbs. Three patients sustained inhalation injuries and a total of four patients required intubation. Seven patients required surgery that included debridement and, in most cases, skin grafting. The availability and increase in the use of battery-powered bicycles and scooters may lead to an increase in injuries and death if consumers are not aware of the potential dangers related to the safe use of lithium batteries.
Resistance of Lepidopteran Egg Parasitoids,Trichogramma japonicumandTrichogramma chilonis, to Insecticides Used for Control of Rice Planthoppers
Authors: Xie Lian-Cheng , Jin Lin-Hong , Lu Yan-Hui , Xu Hong-Xing , Zang Lian-Sheng , Tian Jun-Ce , Lu Zhong-Xian
Published: December 2021

Trichogramma wasps are commonly used as biocontrol agents to manage lepidopteran rice pests in rice fields. However, lepidopteran pests synergistically occur with rice planthoppers which are not targeted by Trichogramma. The use of Trichogramma parasitoids in field-based pest control efforts is greatly affected by the application of insecticides targeting planthoppers. As such, insecticide-resistant strains of Trichogramma are urgently needed for the incorporation of these beneficial natural enemies into integrated pest management programs in rice agroecosystems. In the present study, Trichogramma japonicum Ahmead (Hymenoptera: Trichogrammitidae) and Trichogramma chilonis Ishii (Hymenoptera: Trichogrammitidae) were treated with sublethal doses of four insecticides which target rice planthoppers, to generate tolerant strains in the laboratory. The resistance rate of T. japonicum to imidacloprid was the highest (17.8-folds) after 10 successive treatments and experienced 2.5, 4.72, and 7.41-fold increases in tolerance to thiamethoxam, buprofezin, and nitenpyram, respectively. Tolerance of T. chilonis to imidacloprid, thiamethoxam, buprofezin, and nitenpyram were 8.8, 6.9, 4.43, and 5.67-fold greater, respectively. The emergence and deformity (without spreading wings or short wings) rates of T. japonicum and T. chilonis gradually recovered with an increased exposure time of treatments. The fecundity of T. japonicum treated with thiamethoxam was significantly higher than that of the control and T. chilonis treated with thiamethoxam and nitenpyra. Our results demonstrate that screening for insecticide-tolerant/resistant Trichogramma strains was feasible, especially in the pairing of T. japonicum and imidacloprid, which could provide a valuable biological control tool that can be combined with traditional chemical control strategies for use in IPM of rice agroecosystems.
Two Perspectives on Fanie du Toit’s When Political Transitions Work: Reconciliation as Interdependence
Authors: Deng Francis Mading , Hamber Brandon
Published: December 2021

This review essay offers two complementary perspectives on Fanie du Toit’s When Political Transitions Work: Reconciliation as Interdependence—each reflecting on the book’s assessment of the transitional justice process in South Africa to date and underlining some of the key lessons learned from that history for contemporary human rights and peacebuilding practitioners.
Cancer-derived C-terminus-extended p53 mutation confers dominant-negative effect on its wild-type counterpart
Authors: Huang Shibo , Cao Bo , Wang Jieqiong , Zhang Yiwei , Ledet Elisa , Sartor Oliver , Xiong Yuqin , Zeng Shelya X , Lu Hua
Published: December 2021

The vast majority of p53 missense mutants lose the wild-type (wt) function and/or exert ‘dominant-negative’ effects on their wt counterpart. Here, we identify a novel form of p53 mutation with an extended C-terminus (p53 long C-terminus, p53LC) in a variety of human cancers. Interestingly, the two representative mutants (named ‘p53-374*48’ and ‘p53-393*78’) as tested in this study show both loss-of-function and dominant-negative phenotypes in cell proliferation and colony formation assays. Mechanistically, p53LCs interact with and retain wt p53 in the cytoplasm and prevent it from binding to the promoters of target genes, consequently inhibiting its transcriptional activity. Also, p53LCs are very stable, though not acetylated in cells. Remarkably, the p53LCs can desensitize wt p53-containing cancer cells to p53-activating agents. Together, our results unveil a longer form of p53 mutant that possesses a dominant-negative effect on its wt counterpart, besides losing its wt activity.