bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soils of natural, arable and fallow Lands of the Selenga River delta
Authors: Belozertseva I A , Ekimovskaya O A , Lopatina D N 
Published: November 2019

Abstract
Soil-geographical investigations were made in the Selenga river delta (the southeastern coast of Lake Baikal) in the summer of 2017 and 2018. The Selenga delta developed Fluvisols aridic, Fluvisols umbric (gleyic), Fluvisols humus, Fluvisols mollicgleyic, Fluvisols Histic-gleyic, Folic-podburs, Gray (metamorphic) and Folic-gray soils. Fertile soils of the second bottom with Chernozems and Phaeozems are used as arable lands. Agricultural lands of terraces with Gray and Folic-gray soils are used as pastures. The soils of the low floodplain are put to agricultural use. It was established that the soils in most of agricultural lands are in satisfactory agricultural condition. The upper horizons of Gray soils under forest and Chernozems under steppe in natural condition have high humus concentrations. In soils permanently used in agriculture, humus content decreases. In fallow lands, its concentrations are recovering. The reaction of the medium (pH of water) in the soils is largely neutral. Gray soil under forest is distinguished by slightly acidic reaction. It was found that the soils of the Selenga delta have mostly a light granulometric composition.
ESPO oil pipeline: assessment of impact on social and economic development of municipal districts
Authors: Dets I A 
Published: November 2019

Abstract
The article presents the conducted analysis of the impact of the ESPO pipeline construction and operation on the socio-economic development of the territories along its route. The study area included municipal areas along the western part of the ESPO oil pipeline (the so-called ESPO-1): six municipal areas of Irkutsk region, four municipal areas of Yakutia and two municipal areas of Amur region. The study showed poor availability of jobs in oil pumping stations of the oil pipeline system, as well as the small amount of tax payments currently coming to the budgets of settlements and municipal districts, which is mainly explained by the existing system of redistribution of tax revenues. The change in the level of accessibility of transport infrastructure for the local population is also controversial: technological routes along the oil pipeline have departmental affiliation with limited access for third parties and individuals. As a result, despite the declared social orientation, the oil pipeline failed to bring enough positive changes for the majority of the territories, which resulted in much worse dynamics of the population relative to its regions in all municipal districts except for the Taishetsky district of Irkutsk region.
Nature management on the Arctic territories of the Russian Far East
Authors: Stepanko N G 
Published: November 2019

Abstract
The established structure of environmental management, which depends on economic activities, determines the ecological situation of a particular territory. Such studies are particularly important and relevant for areas with low ecological capacity and resistance, which include the territory of the Arctic zone of the Russian Far East (RFE). The discussed territories have a high vulnerability of the natural environment to anthropogenic impacts and a low recovery rate of the disturbed state. Analysis of information on the environmental state of the Chukotka Autonomous Region and the Republic of Sakha (Yakutia) allows us to conclude that the environmental situation is unfavorable in the regions. The established system of environmental management in certain areas of the Russian Arctic has led to the emergence of heavily modified areas as a result of economic activity, where the disturbing dynamic equilibrium of the natural environment has led to changes in the natural geochemical background, depletion of biodiversity, degradation of soil and vegetation, development of erosion processes, and environmental pollution. The paper presents the socio-economic, natural-geographical, ecological characteristics of the Arctic zone of the RFE in the context of ulus, proposed the structure of existing and possible future directions of environmental management.
Variability of vegetation index NDVI during periods of drought in the Tomsk Region
Authors: Voropay N N , Ryazanova A A , Dyukarev E A 
Published: November 2019

Abstract
Current climate changes are characterized by an increase in the frequency of occurrence of extreme natural phenomena, which include droughts and over moistening periods of the territory. The main indicator of drought / over moistening periods is the state of vegetation. Estimation of the interannual and intraseasonal variability of drought can be carried out using vegetation indicators obtained from satellite image data. In article statistical characteristics of NDVI for seven basic types of land cover, identified at the territory of the Tomsk region were studied. NDVI is most stable during the summer in wetlands, changing on average during the study period from 0.58 in May to 0.71 in July, then decreasing to September to 0.64. The variability of NDVI in dark coniferous forests is slightly greater (0.64–0.81). The greatest variability of NDVI was obtained for floodplain meadows (0.46-0.81) and croplands (0.51-0.79). VCI is used to identify drought situations and determine the onset, especially in areas where drought episodes are localized and ill defined. According to the analysis of the VCI index, in May the greatest frequency of dry periods was observed in the Tomsk region. Analysis of changes in frequency of extreme events occurrence have shown that the number of droughts decreases, and number of excessive moisture periods increases since 2000 till 2017.
An Approach to Riverine Pollutants and Water Quality of China Lake
Authors: Yang L , Li F 
Published: November 2019

Abstract
Economic growth and urbanization in the past decades have resulted in large quantity of riverine pollutants transferring to the significant lakes worldwide, giving rise to serious contamination of the water system and posing significantly harmful effects on the human environment health around the region. Hereinto, as one of the most eutrophic lakes in China, Chaohu lake riverine pollutants influenced greatly the quality of Chaohu Lake water, though it is still playing a critical role in potable water supply and environmental regulation. In this study, three rivers contaminated by agricultural rounoff (Fengle River and Hangbu River) and by urban wastewater (Nanfei River) in the Lake Chaohu watershed were selected to study the discrepancy of dissolved N2O concentrations and emissions from different types of polluted rivers. The environmental effects exploration of riverine pollutants transported by tributaries might provide useful quantitative information for policy debating to improve pollution measures for the similar lakes.
Effects of oxygen flow on properties of La2Ti2O7−x films
Authors: Li Jianchao , Su Junhong , Yang Chen , Cai Changlong , Chen Zhili 
Published: November 2019

Abstract
In order to obtain the relationship between the properties and the oxygen flow rate of La2Ti2O7−x film, the films were prepared by electron beam evaporation with various oxygen flow rates on Si and quartz substrates. The effects of oxygen flow on the properties of La2Ti2O7−x film were analyzed by XRD, XPS, optical constant and laser damage test. The result shows that the La2Ti2O7−x film lose oxygen and lead to the transition of Ti4+ to Ti3+ in oxygen-free environment. When the oxygen flow rate is greater than 4 sccm, the content of Ti4+ is stable. The refractive index of La2Ti2O7−x films decreases with the increase of oxygen flow rate and stabilizes at oxygen flow rate greater than 4 sccm. The extinction coefficient of film deposited in oxygen-free environment is less than 10−4. As the oxygen flow rate increases, the film absorption is further improved to reach 10−5 at wavelengths longer than 350 nm. The laser damage threshold of films increased with increasing oxygen flow and the maximum value is 18.35 J cm−2.
Effect of CuO modification on dielectric, ferroelectric and piezoelectric properties of lead-free SrBi4Ti4O15 ceramics
Authors: Jose Roshan , P Vineetha , S Charan Prasanth , Vijay Ammu , K Venkata Saravanan 
Published: November 2019

Abstract
We report a systematic investigation of the structure, micro-structure, dielectric, ferroelectric and piezoelectric properties of CuO added SrBi4Ti4O15 ceramics. All the samples were prepared by solid state reaction technique, where the wt% of CuO in SrBi4Ti4O15 was varied as x = 0, 0.05, 0.2, 0.5. The addition of CuO increased the density of SrBi4Ti4O15 ceramics which in turn resulted in the improvement of dielectric, ferroelectric as well as piezoelectric properties. However, no change either in the crystal structure or lattice parameter was observed with CuO addition. Further a dense micro-structure with improved electrical properties is expected to be due to liquid phase sintering. Raman spectra and specific heat measurements were also performed for getting further insight into the properties.
Workplace Emissions and Exposures During Semiconductor Nanowire Production, Post-production, and Maintenance Work
Authors: Isaxon Christina , Lovén Karin , Ludvigsson Linus , Sivakumar Sudhakar , Gudmundsson Anders , Messing Maria E , Pagels Joakim , Hedmer Maria 
Published: November 2019

Abstract

Background
Nanowires are a high-aspect-ratio material of increasing interest for a wide range of applications. A new and promising method to produce nanowires is by aerotaxy, where the wires are grown in a continuous stream of gas. The aerotaxy method can grow nanowires much faster than by more conventional methods. Nanowires have important properties in common with asbestos fibers, which indicate that there can be potential health effects if exposure occurs. No conclusive exposure (or emission) data from aerotaxy-production of nanowires has so far been published.

Methods
Different work tasks during semiconductor nanowire production, post-production, and maintenance were studied. A combination of direct-reading instruments for number concentration (0.007–20 µm) and filter sampling was used to assess the emissions (a couple of centimeter from the emission sources), the exposure in the personal breathing zone (max 30 cm from nose–mouth), and the concentrations in the background zone (at least 3 m from any emission source). The filters were analyzed for metal dust composition and number concentration of nanowires. Various surfaces were sampled for nanowire contamination.

Results
The particle concentrations in the emission zone (measured with direct-reading instruments) were elevated during cleaning of arc discharge, manual reactor cleaning, exchange of nanowire outflow filters, and sonication of substrates with nanowires. In the case of cleaning of the arc discharge and manual reactor cleaning, the emissions affected the concentrations in the personal breathing zone and were high enough to also affect the concentrations in the background. Filter analysis with electron microscopy could confirm the presence of nanowires in some of the air samples.

Conclusions
Our results show that a major part of the potential for exposure occurs not during the actual manufacturing, but during the cleaning and maintenance procedures. The exposures and emissions were evaluated pre- and post-upscaling the production and showed that some work tasks (e.g. exchange of nanowire outflow filters and sonication of substrates with nanowires) increased the emissions post-upscaling.
Seed coat development in explosively dispersed seeds of Cardamine hirsuta
Authors: Neumann Ulla , Hay Angela 
Published: November 2019

AbstractBackground and AimsSeeds are dispersed by explosive coiling of the fruit valves in Cardamine hirsuta. This rapid coiling launches the small seeds on ballistic trajectories to spread over a 2 m radius around the parent plant. The seed surface interacts with both the coiling fruit valve during launch and subsequently with the air during flight. We aim to identify features of the seed surface that may contribute to these interactions by characterizing seed coat differentiation.MethodsDifferentiation of the outermost seed coat layers from the outer integuments of the ovule involves dramatic cellular changes that we characterize in detail at the light and electron microscopical level including immunofluorescence and immunogold labelling.Key ResultsWe found that the two outer integument (oi) layers of the seed coat contributed differently to the topography of the seed surface in the explosively dispersed seeds of C. hirsuta vs. the related species Arabidopsis thaliana where seed dispersal is non-explosive. The surface of A. thaliana seeds is shaped by the columella and the anticlinal cell walls of the epidermal oi2 layer. In contrast, the surface of C. hirsuta seeds is shaped by a network of prominent ridges formed by the anticlinal walls of asymmetrically thickened cells of the sub-epidermal oi1 layer, especially at the seed margin. Both the oi2 and oi1 cell layers in C. hirsuta seeds are characterized by specialized, pectin-rich cell walls that are deposited asymmetrically in the cell.ConclusionsThe two outermost seed coat layers in C. hirsuta have distinct properties: the sub-epidermal oi1 layer determines the topography of the seed surface, while the epidermal oi2 layer accumulates mucilage. These properties are influenced by polar deposition of distinct pectin polysaccharides in the cell wall. Although the ridged seed surface formed by oi1 cell walls is associated with ballistic dispersal in C. hirsuta, it is not restricted to explosively dispersed seeds in the Brassicaceae.
SCGid: a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries of uncultured eukaryotes
Authors: Amses Kevin R , Davis William J , James Timothy Y 
Published: November 2019

Abstract

Motivation
Whole-genome sequencing of uncultured eukaryotic genomes is complicated by difficulties in acquiring sufficient amounts of tissue. Single-cell genomics (SCG) by multiple displacement amplification provides a technical workaround, yielding whole-genome libraries which can be assembled de novo. Downsides of multiple displacement amplification include coverage biases and exacerbation of contamination. These factors affect assembly continuity and fidelity, complicating discrimination of genomes from contamination and noise by available tools. Uncultured eukaryotes and their relatives are often underrepresented in large sequence data repositories, further impairing identification and separation.

Results
We compare the ability of filtering approaches to remove contamination and resolve eukaryotic draft genomes from SCG metagenomes, finding significant variation in outcomes. To address these inconsistencies, we introduce a consensus approach that is codified in the SCGid software package. SCGid parallelly filters assemblies using different approaches, yielding three intermediate drafts from which consensus is drawn. Using genuine and mock SCG metagenomes, we show that our approach corrects for variation among draft genomes predicted by individual approaches and outperforms them in recapitulating published drafts in a fast and repeatable way, providing a useful alternative to available methods and manual curation.

Availability and implementation
The SCGid package is implemented in python and R. Source code is available at http://www.github.com/amsesk/SCGid under the GNU GPL 3.0 license.

Supplementary information
Supplementary data are available at Bioinformatics online.
CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing
Authors: Cancellieri Samuele , Canver Matthew C , Bombieri Nicola , Giugno Rosalba , Pinello Luca 
Published: November 2019

ABSTRACT

Motivation
Clustered regularly interspaced short palindromic repeats (CRISPR) technologies allow for facile genomic modification in a site-specific manner. A key step in this process is the in silico design of single guide RNAs to efficiently and specifically target a site of interest. To this end, it is necessary to enumerate all potential off-target sites within a given genome that could be inadvertently altered by nuclease-mediated cleavage. Currently available software for this task is limited by computational efficiency, variant support or annotation, and assessment of the functional impact of potential off-target effects.

Results
To overcome these limitations, we have developed CRISPRitz, a suite of software tools to support the design and analysis of CRISPR/CRISPR-associated (Cas) experiments. Using efficient data structures combined with parallel computation, we offer a rapid, reliable, and exhaustive search mechanism to enumerate a comprehensive list of putative off-target sites. As proof-of-principle, we performed a head-to-head comparison with other available tools on several datasets. This analysis highlighted the unique features and superior computational performance of CRISPRitz including support for genomic searching with DNA/RNA bulges and mismatches of arbitrary size as specified by the user as well as consideration of genetic variants (variant-aware). In addition, graphical reports are offered for coding and non-coding regions that annotate the potential impact of putative off-target sites that lie within regions of functional genomic annotation (e.g. insulator and chromatin accessible sites from the ENCyclopedia Of DNA Elements [ENCODE] project).

Availability and implementation
The software is freely available at: https://github.com/pinellolab/CRISPRitzhttps://github.com/InfOmics/CRISPRitz.

Supplementary information
Supplementary data are available at Bioinformatics online.
Identification of the potential biomarkers in patients with glioma: a weighted gene co-expression network analysis
Authors: Chen Ting-Yu , Liu Yang , Chen Liang , Luo Jie , Zhang Chao , Shen Xian-Feng 
Published: November 2019

Abstract
Glioma is the most common brain tumor with high mortality. However, there are still challenges for the timely and accurate diagnosis and effective treatment of the tumor. One hundred and twenty-one samples with grades II, III and IV from the Gene Expression Omnibus database were used to construct gene co-expression networks to identify hub modules closely related to glioma grade, and performed pathway enrichment analysis on genes from significant modules. In gene co-expression network constructed by 2345 differentially expressed genes from 121 gene expression profiles for glioma, we identified the black and blue modules that associated with grading. The module preservation analysis based on 118 samples indicates that the two modules were replicable. Enrichment analysis showed that the extracellular matrix genes were enriched for blue module, while cell division genes were enriched for black module. According to survival analysis, 21 hub genes were significantly up-regulated and one gene was significantly down-regulated. What’s more, IKBIP, SEC24D, and FAM46A are the genes with little attention among the 22 hub genes. In this study, IKBIP, SEC24D, and FAM46A related to glioma were mentioned for the first time to the current knowledge, which might provide a new idea for us to study the disease in the future. IKBIP, SEC24D and FAM46A among the 22 hub genes identified that are related to the malignancy degree of glioma might be used as new biomarkers to improve the diagnosis, treatment and prognosis of glioma.
O50 DIAPHRAGMATIC HERNIA AFTER IVOR-LEWIS OESOPHAGECTOMY: ANALYSIS OF RISK FACTORS AND SURGICAL REPAIR RESULTS
Authors: Francesco Puccetti , Paolo Parise , Stefano De Pascale , Andrea Cossu , Raffaele Cerchione , Marco Palucci , Greta Olivari , Uberto Fumagalli Romario , Riccardo Rosati 
Published: November 2019

Abstract

Backgrounds and aim
oesophagectomy is the mainstay of curative treatment for oesophageal cancer and post-oesophagectomy diaphragmatic hernia (PODH) represents a potentially life-threatening complication with an underestimated occurrence rate and unclear related risk factors. Aim of this study was to identify possible risk factors of PODH and results of surgical treatment from experience of two tertiary referral centers.

Methods
all patients affected by a clinically resectable oesophageal cancer (any T, any N and M0) and submitted to Ivor-Lewis oesophagectomy, regardless of technique (open, hybrid or totally minimally invasive) between 1997 and 2017 at our Institutions were selected for this study. Demographic, clinical pre, intra, post-operative, and follow-up data were prospectively collected in an electronic database. A retrospective analysis was conducted in order to evaluate the incidence of PODH, associated risk factors and surgical repair results.

Results
414 patients underwent Ivor-Lewis oesophagectomy for cancer in the study period and 22 (5.3%) developed PODH at a median follow-up time of 16 months (6 - 177). Surgical repair was mainly conducted by laparoscopic approach (77%) with a conversion rate of 24%. Postoperative morbidity was 22.7% and mortality 4.5%. Median postoperative hospital stay was 6 days (2 - 95). 3 recurrences (13.6%) occurred at a median follow-up time of 10.1 months. A wide univariate analysis identified statistically significant associations between PODH occurrence and the administration of preoperative chemoradiation, a complete pathological response (CPR) and a harvested lymph-nodes number (HLN) larger than 33 (p-value 0.016, 0.001 and 0.024 respectively). A significant association with a large HLN number was confirmed by the multivariable analysis (0.026) along with CPR which could however be considered as a longer survival-related bias.

Conclusions
The minimally invasive surgery and the neoadjuvant chemoradiation, in contrast to results of other authors, in our experience are not associated with PODH development, while a HLN number larger than 33 resulted to be an independent risk factor, probably mirroring the extent of surgical demolition in oesophagectomy. Surgical repair can be safely and effectively performed trough laparoscopy but recurrences can frequently occur.