bluuebunny/crossref_metadata_2025 huggingface dataset:
Procedure for lab-scale strength and failure testing of physical models of frame mine structures
Authors: Vysotin N. G. , Leizer V. I. , Eremenko V. A. , Yanbekov A. M.
Published: April 2021

Operation of any mine, including frame structured mines, alters the stress–strain behavior of enclosing rock mass. The laboratory research requires a plan and a procedure, with description of data acquisition methods (monitoring of strength and deformation characteristics of physical models of the frame mine structure). The implemented laboratory tests used the specially manufactured physical models, a hydraulic pressing machine meant for simulation of strata pressure, as well as a monitoring system including acoustic emission converters and strain gauges. The equipment allows getting an overall picture and enables the stress–strain analysis in a unit block using the theories of similarity and dimensions to understand the influence exerted by the shape, size and arrangement of mined-out stopes on enclosing rock mass stability in case of the frame mine structure.
Measures to reduce the environmental impact of the Żelazny Most Tailings Storage Facility
Authors: Zieliński S. , Stefanek P.
Published: April 2021

The Żelazny Most Tailings Storage Facility, located in south-western Poland, is one of the largest facilities of its kind in the world. Mining wastes from the processing of copper ores have been disposed continuously for over 40 years. A safe operation of TSF of this size requires the involvement of engineers, specialists and scientists from many fields of science. The article presents the latest experience in activities reducing the environmental impact of the Zelazny Most TSF, including the monitoring of groundwater, air protection and the reliability of pipe infrastructure. KGHM Polish Copper, the TSF operator, has been running the system for monitoring the quality of surface and groundwater in the foreground of dams for more than forty years. Very good diagnosis of the hydrogeological conditions in the TSF foundation allowed the research unit to develop a three-dimensional numerical model of groundwater flow. The article also describes the issues related to dust prevention. Active and passive protection methods for the beaches and slopes were presented. Slurries are pumped over a distance of up to 20 km via multiple pipelines. Due to the high abrasion properties of the rock material, KGHM runs a pipeline testing and replacement program to ensure the highest level of reliability. The issues presented in the article clearly indicate the attitude of the TSF operator to the reduction of the negative impact of waste storage in the natural environment. This is also confirmed by the presence of many rare species of wild animals in the immediate vicinity, such as deer, beavers and birds of prey.
Use of Abcd-Matrix Method For The Simulation of Laser-Ultrasonic Probing Pulse Propagation In A Layered Medium of The Optical-Acoustic Transducer
Authors: Pashkin A. I.
Published: April 2021

As a first step methods for modeling the propagation of acoustic waves in layered media was analyzed and the need to develop a new, faster method is substantiated. As a consequence, presented a method for modeling the propagation of elastic waves based on signal transformation using ABCD matrices, for the implementation of which a computer program in the Python language has been developed. For the verification of the method was analyzed the correlation between the simulated signal and the signal obtained experimentally from a medium with predetermined parameters. Further on the basis of the data obtained, the applicability of this method for modeling the propagation of acoustic signals in a plane-layered medium has been proved. As a next step modern methods of ultrasound generation and their influence on the characteristics of the probing signal was reviewed. Confirmed that laser-ultrasound techniques allow the best control over the characteristics of the probe signal. Therefore, the influence of the duration of the laser pulse, the properties of light absorption and the acoustic characteristics of the generator medium on the probing signal amplitude and bandwidth of the spectrum was estimated. To reduce the influence of the considered characteristics on the diagnostic process using the ABCD-matrix method the optimal characteristics of the optical-acoustic transducer for diagnostics at low frequencies have been determined. Finally, the main advantage of the proposed modeling method is the high speed of calculating the shape and spectrum of the signal at any point in the medium at a given time.
Areas of natural conflicts in harmonized thematic maps of the Strzelin county
Authors: Kozińska P. , Górecki A.
Published: April 2021

Recently in Poland, there has been a strong emphasis on data harmonisation, which means data coherence, mainly spatial. The reason for this is the INSPIRE Directive [1] approved in 2007 and the Spatial Information Infrastructure Act [2] implemented on the basis of this Directive in Poland in 2010. On this basis, the aim of this study was to make the data from soil-agricultural maps and geological maps coherent, so that no natural conflicts would arise. The study was based on materials concerning soil classification a nd lithology, which are soil-agricultural and geological maps, but also on isohips. The method, which was applied, consisted in combination of attributes of the maps, then natural conflicts were identified, that is lack of smooth transition from soils to lithology - a given soil would not be able to develop on the indicated geological substratum. A significant part of the identified co nflicts req uired editing, however some of them can be treated as exceptions. The reason for such discrepancies is the lack of precise information on the deposited layers at the depth of 1.5 m - 2.0 m, which results from the measurement methods of the analysed maps. The last step was to eliminate these conflicts in order to generate consistent and harmonised data. As a result, a list of attributes of full compatibility was obtained, thanks to them maps of any parameters can be generated, and also a basis for presenting soils in a different systematics.
BIPA for Business Communication Learning Model Development through MOOC
Authors: Febrianti L Y , Devina  , Ningsih R Y
Published: April 2021

The study examines to acknowledge the learning model development of MOOC-based BIPA for Business Communication. This research uses 4D learning model development (define, design, development, and dissemination). The analysis was conducted to the international students of BINUS University International, and further validated by experts and lecturers of the course itself. Based on the need analysis, BIPA for Business Communication program is an intermediate level of BIPA program aiming at preparing students to understand Indonesian actively, gain knowledge of the language and socio-cultural background for business communication purposes. Serving all that purpose, the learning model developed put its axis on the activity in business context. Taking Udemy as the platform for MOOC delivery, the development of learning model is referred to features at Udemy. The elements of learning covers; (1) Video-based learning content; (2) course content; (overview); (4) question and answer; (5) notes, and (6) announcements. In total, 10 topics BIPA for Business Communication can be accessed within the course. Expert validations indicate that BIPA for Business Communication MOOC perceives well, in which the learning model development is 3.75 with the indicator 3,4 < x ⩽ 4,2.
Turning strawberry jam into slice: a new way of consuming strawberry fruits preservation products
Authors: Wahyuningtias D , Caroline A , Adiati M P , Levyta F , Kusumawardhana I
Published: April 2021

The goal of this article is to discover an acceptance and preference of consumer towards innovative products of slice strawberry jam. While an ordinary fruit preserves often made as a jam. Sliced jam is a new way of fruit preservation to consume. Through an organoleptic study, the paper starts to examine and compare between an original product of strawberry jam to sliced jam. A quantitative tradition of research employs an experimental approach to eighty untrained respondents. Data analysis and validity were generated from SPSS statistic software to measure the result of questionnaires towards a favorite between the two and its characteristics such as texture, taste, smell, and color. The findings reveal that the new form of strawberry jam slices is favored among the major respondents. The strawberry jam slice’s texture, taste, smell, and color also attract the consumerism. Despite the limitation of the study, the article introduces a new way of consuming strawberry fruits preservation products. Thus, the research discussion would take forward business development idea, particularly on fruit preserves preparation.
Effectiveness of Media and Communication Forms to Promote a Positive Behavior of the Society around Untirta New Campus toward Environmental Preservation
Authors: Salampessy Y L A , Suherna  , Muldi A
Published: April 2021

The vision of the University of Sultan Ageng Tirtayasa (UNTIRTA) as a Green Campus shows its sensitivity to the importance of environmental quality and quick response to developing living behaviours that prioritize environmental sustainability. This study aimed to describe the issues and actions of environmental preservation that are considered important by the community around the Untirta new campus and to analyze the media and forms of effective environmental communication messages to build positive attitudes towards environmental care actions. This research used a quantitative approach with survey and quasi-experimental design. The results showed that for the community around the Untirta new campus, the main environmental issue was the environment that felt arid and maintaining trees around the home environment as the most important environmental care action considered. The community showed a pro-environmental attitude in the neighbourhood where they live, while the media and forms of environmental communication messages that are most effective in increasing this attitude were banners with positive message forms.
Sugar palm (Arenga pinnata Wurmb Merr.): a review on plant tissue culture techniques for effective breeding
Authors: Muda NA , Awal A
Published: April 2021

This review paper outlines the plant tissue culture works done on sugar palm (Arenga pinnata Wurmb Merr.); a tree under the family Arecaceae and genus Arenga cultivated mainly for its sugary sap, sweetened endosperm and highly valuable industrial black fibers. Plant tissue culture technique is a method of growing plant cells, tissues and organs on an artificial nutrient medium under controlled aseptic conditions. Plant tissue culture is a revolutionary biotechnological tool which facilitates successful breeding programs and research of many incredible plant diversity particularly of species which are facing the risks of extinction, plants of valuable economic importance and plants with morphological and physiological sterility and incompatibility. The taxonomy, botanical description, population distribution, ecology and climate requirement, horticulture practice as well as the economic contributions and challenges of sugar palm were also described.
Improving Rice Productivity Through the Implementation of Jajar Legowo Super (Jarwo Super) Technology in Jambi Province
Authors: Endrizal  , Jumakir  , Bobihoe J
Published: April 2021

Jarwo super rice cultivation is the result of the development of integrated rice cultivation technology from Indonesian Agency for Agricultural Research and Development based on the legowo row planting method. The purpose of the study was to determine the adaptation of new superior varieties of rice and increase rice production by using the Inpari 30, Inpari 32 and Inpari 33 varieties through the application of jarwo super technology. The assessment activity was carried out in Rantau Panjang Village, Batang Asai District, Sarolangun Regency, Jambi Province, cooperated with the Tanjung Harapan farmer group (involving 21 farmers) with area of 10 ha. The activity was carried out from September to December 2016. The purpose of the study was to determine the growth performance and increase in production of new superior varieties Inpari 30, Inpari 32 and Inpari 33 through the application of super jarwo technology. The components of super jarwo rice cultivation technology included new superior varieties with high yield potential, straw decomposers, biological fertilizers, balanced fertilization based on the Paddy Soil Test Tool, and control of Plant Pest Organisms with vegetable and chemical pesticides based on control thresholds, as well as agricultural machinery (transplanter and combine harvester). The results of the study showed that the innovation of super legowo row (jarwo) cultivation technology with superior varieties Inpari 30, Inpari 32 and Inpari 33 was able to increase yields by an average of 3.41 t/ha (40 - 50%), with the production of each variety was Inpari 30 (5.60 - 8.58 t/ha), Inpari 33 varieties (6.50 - 8.20 t/ha), and Inpari 32 (7.25 - 7.30 t/ha). The results were higher than the average yield of the Ciherang comparison variety (4.60 t/ha) which was commonly grown in the Rantau Panjang location. Disemination of Jarwo Super technology has been carried out through technology guidance, fields meeting, and leaflets, generally farmers can receive the introduced super jarwo technology.
The Effect of Addition Glycerol Against Nori Characterization from Gracilaria sp and Ulva sp Seaweeds
Authors: Sinurat E , Fransiska D , Livia
Published: April 2021

Nori is an edible seaweed product and is known to form a sheet. This study involves the production of nori, from a mixture of Gracilaria and Ulva Lactuca seaweeds, at a ratio of 1:1. Besides, glycerol was adopted as a plasticizing biopolymer for food packaging materials. This study, therefore, aims to evaluate the characteristics of nori, following the addition of glycerol concentration (0.4; 0.6; 0.8; 1.0 percent) as a plasticizer on the nori/edible seaweed. The parameters evaluated include elongation percentage, tensile strength, WVTR, thickness, and water content. Moreover, treatments with 0.8 percent glycerol concentration generated edible seaweed films with the following characteristics: elongation percentage of 12.15%, while the tensile strength, WVTR, thickness, and water content were 2,67 M.Pa, 2268 gr/m2 day, 328.93 μm, and 12,75 %, respectively.
Analysis of glutamine synthetase activity from Lactobacillus hilgardii LMG 7934
Authors: Zhuravleva D , Yadykova L , Iskhakova Z , Kayumov A
Published: April 2021

Lactic acid bacteria (LAB) are Gram-positive, non-spore forming, facultative anaerobic or microaerophilic bacteria living in various nutrients-rich ecological niches and are widely used for dairy food and silage production as well as probiotics for the Human and animals. While bacteria can assimilate various nitrogen-containing compounds, the glutamine and ammonium are the most preferred nitrogen sources since they could be directly involved into the nitrogen metabolism of the cell. In bacterial cells, the glutamine can be synthetized from glutamate and ammonium ions by the metalloenzyme glutamine synthetase (GS). In contrast to other bacteria which generally have one gene encoding for the glutamine synthetase, two genes encoding proteins with 53% mutual identity and predicted glutamine synthetase activity were found in the genome of Lactobacillus hilgardii LMG 7934. One gene (glnA_2) is located in the glnRA operon with the transcriptional factor GlnR gene (glnR) similarly to GS genes from other bacteria. The second GS gene (glnA_1) is monocistronic. While the biosynthetic activity glutamine synthetases could be detected in L. hilgardii cells, which protein plays the major role is still unclear.
Refinement effect of Zirconium and Samarium on Al-4Mg cast alloy
Authors: Eisawi K , Tash Mahmoud , Khalifa Waleed , El-Mahallawi Iman
Published: April 2021

This study aims at investigating the modification response of cast Al-4%Mg alloy to Zirconium or Samarium additions at high and low levels. Thermal analysis was used to evaluate the influence of Zirconium and Samarium. The solidification data represented the four main reaction peaks during solidification and had shown that both Zr and Sm play a role in refinement with a depression in solidification temperature. Moreover, Sm acts as a modifier as it had noticeable effect on retarding the recalescence temperature. Microstructure Examination was implemented by optical microscopy, image analysis software and scanning electron microscopy (SEM) with the aid of image analysis and Energy Dispersive x-ray spectroscopy (EDS). The results revealed the formation of new intermetallic phases such as agglomerates of Al38.76MgZr7.04Ti0.52Fe0.07 and Chinese script shapes of Al25.28MgFe2.77Sm1.48. Accordingly, a noticeable grain size reduction is found with respect to the level of addition of Zr and Sm where Sm showed more refinement effect.
Energy density and storage capacity of La3+ and Sc3+ co-substituted Pb(Zr0.53Ti0.47)O3 thin films
Authors: Bhattarai Mohan K , Barrionuevo Danilo , Kumar Ashok , Katiyar Ram S
Published: April 2021

We studied the energy density and storage capacity properties of rare-earth modified lead zirconate titanate thin films. Highly oriented thin films of (PbZr0.53Ti0.47)(1−y)(LaxSc1−x)yO3 wherein; [for y = 0 and x =0 viz PL0] and, [for y = 0.1 and x = 0.2, 0.4, 0.6 and 0.8 viz PL2, PL4, PL6 and PL8 respectively] abbreviated as PL10x have synthesized on MgO (100) substrate by the pulsed laser deposition technique. The higher proportion of lanthanum increased the broadening of dielectric permittivity and dielectric maxima that shifted to higher temperatures with increasing frequency, signifying the relaxor-type behavior of these films. The value of the relaxation parameter varies from γ = 1.69 for PL6 and 1.95 for PL8 that was estimated from the linear fit of the modified Curie-Weiss law indicating the relaxor nature satisfying Vogel-Fulcher relation. Furthermore, we achieved enhanced spontaneous polarization of the fabricated thin films. Slim loop hysteresis was observed on tuning lanthanum and scandium and the estimated recovered energy density (Ure) is 51.15 J cm−3 and 26.54 J cm−3 with efficiency (η) of 47.38% and 65.88% respectively for PL6 and PL8 thin films. The high dielectric permittivity, high breakdown strength, and enhanced energy storage density of thin films could make it promising materials for memory, power electronics, and energy storage applications.
Response of Beetle Assemblages (Insecta: Coleoptera) to Patch Characteristics and Habitat Complexity in an Ever-Expanding Urban Landscape in the Yucatán Peninsula, Mexico
Authors: Cortés-Arzola Silvia Ventura , León-Cortés Jorge L
Published: April 2021

Insect diversity levels and change in remnant urban habitats have been poorly examined in Neotropical regions. The aim of this study was to evaluate the diversity and composition of foliage/shrub dwelling beetles (Insecta: Coleoptera) regarding the influence of patch attributes (i.e., patch size, connectivity, and surrounding matrix) and within-patch habitat complexity, in an urban landscape at Chetumal, Yucatán peninsula, Mexico. Despite the potential species-specific responses to urban landscape pattern, our study reveals that there are effects of patch spatial features and habitat complexity on overall beetle diversity. These effects are as follows: 1) relatively larger urban patches contained higher overall beetle richness, 2) beetle species composition varied significantly regarding understory vegetation structure and tree richness, and 3) patches of intermediate vegetation age had highest beetle richness. This research provides a case study of patch and habitat features related to Neotropical insect assemblages in urban settlements, underlying the importance of using ecological information to offer management recommendations in ever-expanding urban tropical settlements.
Functional expression of the reverse transcriptase αβ heterodimer from avian myeloblastosis virus in Escherichia coli
Authors: Makino Yuriko , Sato Hiroshi , Noguchi Atsushi , Ide Teruhiko , Yatsunami Rie , Nakamura Satoshi
Published: April 2021

The α subunit of avian myeloblastosis virus reverse transcriptase (AMV-RT) is generated from the β-subunit by proteolysis, and the αβ heterodimer represents the active form. The codon-optimized gene was expressed in Escherichia coli, and an active αβ heterodimer was generated. The RNA amplification activity of the purified recombinant AMV-RT αβ heterodimer was similar to that of the native one.
GEM: scalable and flexible gene–environment interaction analysis in millions of samples
Authors: Westerman Kenneth E , Pham Duy T , Hong Liang , Chen Ye , Sevilla-González Magdalena , Sung Yun Ju , Sun Yan V , Morrison Alanna C , Chen Han , Manning Alisa K
Published: April 2021

Motivation

Gene–environment interaction (GEI) studies are a general framework that can be used to identify genetic variants that modify the effects of environmental, physiological, lifestyle or treatment effects on complex traits. Moreover, accounting for GEIs can enhance our understanding of the genetic architecture of complex diseases and traits. However, commonly used statistical software programs for GEI studies are either not applicable to testing certain types of GEI hypotheses or have not been optimized for use in large samples.

Results

Here, we develop a new software program, GEM (Gene–Environment interaction analysis in Millions of samples), which supports the inclusion of multiple GEI terms, adjustment for GEI covariates and robust inference, while allowing multi-threading to reduce computation time. GEM can conduct GEI tests as well as joint tests of genetic main and interaction effects for both continuous and binary phenotypes. Through simulations, we demonstrate that GEM scales to millions of samples while addressing limitations of existing software programs. We additionally conduct a gene-sex interaction analysis on waist-hip ratio in 352 768 unrelated individuals from the UK Biobank, identifying 24 novel loci in the joint test that have not previously been reported in combined or sex-specific analyses. Our results demonstrate that GEM can facilitate the next generation of large-scale GEI studies and help advance our understanding of the genetic architecture of complex diseases and traits.

Availability and implementation

GEM is freely available as an open source project at https://github.com/large-scale-gxe-methods/GEM.

Supplementary information

Supplementary data are available at Bioinformatics online.
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data
Authors: Markowski Julia , Kempfer Rieke , Kukalev Alexander , Irastorza-Azcarate Ibai , Loof Gesa , Kehr Birte , Pombo Ana , Rahmann Sven , Schwarz Roland F
Published: April 2021

Motivation

Genome Architecture Mapping (GAM) was recently introduced as a digestion- and ligation-free method to detect chromatin conformation. Orthogonal to existing approaches based on chromatin conformation capture (3C), GAM’s ability to capture both inter- and intra-chromosomal contacts from low amounts of input data makes it particularly well suited for allele-specific analyses in a clinical setting. Allele-specific analyses are powerful tools to investigate the effects of genetic variants on many cellular phenotypes including chromatin conformation, but require the haplotypes of the individuals under study to be known a priori. So far, however, no algorithm exists for haplotype reconstruction and phasing of genetic variants from GAM data, hindering the allele-specific analysis of chromatin contact points in non-model organisms or individuals with unknown haplotypes.

Results

We present GAMIBHEAR, a tool for accurate haplotype reconstruction from GAM data. GAMIBHEAR aggregates allelic co-observation frequencies from GAM data and employs a GAM-specific probabilistic model of haplotype capture to optimize phasing accuracy. Using a hybrid mouse embryonic stem cell line with known haplotype structure as a benchmark dataset, we assess correctness and completeness of the reconstructed haplotypes, and demonstrate the power of GAMIBHEAR to infer accurate genome-wide haplotypes from GAM data.

Availability and implementation

GAMIBHEAR is available as an R package under the open-source GPL-2 license at https://bitbucket.org/schwarzlab/gamibhear.

Supplementary information

Supplementary data are available at Bioinformatics online.
MicroCellClust: mining rare and highly specific subpopulations from single-cell expression data
Authors: Gerniers Alexander , Bricard Orian , Dupont Pierre
Published: April 2021

Motivation

Identifying rare subpopulations of cells is a critical step in order to extract knowledge from single-cell expression data, especially when the available data is limited and rare subpopulations only contain a few cells. In this paper, we present a data mining method to identify small subpopulations of cells that present highly specific expression profiles. This objective is formalized as a constrained optimization problem that jointly identifies a small group of cells and a corresponding subset of specific genes. The proposed method extends the max-sum submatrix problem to yield genes that are, for instance, highly expressed inside a small number of cells, but have a low expression in the remaining ones.

Results

We show through controlled experiments on scRNA-seq data that the MicroCellClust method achieves a high F1 score to identify rare subpopulations of artificially planted human T cells. The effectiveness of MicroCellClust is confirmed as it reveals a subpopulation of CD4 T cells with a specific phenotype from breast cancer samples, and a subpopulation linked to a specific stage in the cell cycle from breast cancer samples as well. Finally, three rare subpopulations in mouse embryonic stem cells are also identified with MicroCellClust. These results illustrate the proposed method outperforms typical alternatives at identifying small subsets of cells with highly specific expression profiles.

Availabilityand implementation

The R and Scala implementation of MicroCellClust is freely available on GitHub, at https://github.com/agerniers/MicroCellClust/ The data underlying this article are available on Zenodo, at https://dx.doi.org/10.5281/zenodo.4580332.

Supplementary information

Supplementary data are available at Bioinformatics online.
IDH knockdown alters foraging behavior in the termite Odontotermes formosanus in different social contexts
Authors: Xu (徐焕) Huan , Huang (黄求应) Qiuying , Gao (高勇勇) Yongyong , Wu (吴佳) Jia , Hassan Ali , Liu (刘昱彤) Yutong
Published: April 2021

Foraging, as an energy-consuming behavior, is very important for colony survival in termites. How energy metabolism related to glucose decomposition and adenosine triphosphate (ATP) production influences foraging behavior in termites is still unclear. Here, we analyzed the change in energy metabolism in the whole organism and brain after silencing the key metabolic gene isocitrate dehydrogenase (IDH) and then investigated its impact on foraging behavior in the subterranean termite Odontotermes formosanus in different social contexts. The IDH gene exhibited higher expression in the abdomen and head of O. formosanus. The knockdown of IDH resulted in metabolic disorders in the whole organism. The dsIDH-injected workers showed significantly reduced walking activity but increased foraging success. Interestingly, IDH knockdown altered brain energy metabolism, resulting in a decline in ATP levels and an increase in IDH activity. Additionally, the social context affected brain energy metabolism and, thus, altered foraging behavior in O. formosanus. We found that the presence of predator ants increased the negative influence on the foraging behavior of dsIDH-injected workers, including a decrease in foraging success. However, an increase in the number of nestmate soldiers could provide social buffering to relieve the adverse effect of predator ants on worker foraging behavior. Our orthogonal experiments further verified that the role of the IDH gene as an inherent factor was dominant in manipulating termite foraging behavior compared with external social contexts, suggesting that energy metabolism, especially brain energy metabolism, plays a crucial role in regulating termite foraging behavior.
Internet-based treatment of anxiety and depression in patients with ischaemic heart disease attending cardiac rehabilitation: a feasibility study (eMindYourHeart)
Authors: Helmark Charlotte , Ahm Robert , Andersen Christina M , Skovbakke Søren J , Kok Robin , Wiil Uffe K , Schmidt Thomas , Hjelmborg Jacob , Frostholm Lisbeth , Frydendal Ditte H , Hansen Tina B , Zwisler Ann-Dorthe , Pedersen Susanne S
Published: April 2021

Aims

Anxiety and depression are prevalent in 20% of patients with ischaemic heart disease (IHD); however, treatment of psychological conditions is not commonly integrated in cardiac rehabilitation (CR). Internet-based psychological treatment holds the potential to bridge this gap. To examine the feasibility of an eHealth intervention targeting anxiety and depression in patients with IHD attending CR.

Methods and results

We used a mixed-methods design, including quantitative methods to examine drop-out and change in anxiety and depression scores, and qualitative methods (thematic analysis) to evaluate patients’ and nurses’ experiences with the intervention. The therapist-guided intervention consisted of 12 modules provided via a web-based platform. The primary outcome was drop-out, with a drop-out rate <25% considered acceptable. Patients were considered as non-drop-out if they completed ≥5 modules. Out of 60 patients screened positive for anxiety and/or depression, 29 patients were included. The drop-out rate was 24% (7/29). Patients had a mean improvement in anxiety and depression scores of 5.5 and 4.6, respectively. On average, patients had 8.0 phone calls with their therapist and 19.7 written messages. The qualitative analysis of patients’ experiences identified four themes: treatment platform, intervention, communication with therapist, and personal experience. Patients were positive towards the intervention, although some found the assignments burdensome. From the nurses, we identified three themes: intervention, inclusion procedure, and collaboration with study team. The nurses were positive, however, due to limited time some struggled with the inclusion procedure.

Conclusion

Integrating an eHealth intervention in CR is feasible and the drop-out rate acceptable.
Causes, pattern, predictors, and prognostic implications of new hospitalizations after transcatheter aortic valve implantation: a long-term nationwide observational study
Authors: Nilsson Konrad , Buccheri Sergio , Christersson Christina , Koul Sasha , Nilsson Johan , Pétursson Pétur , Renlund Henrik , Rück Andreas , James Stefan
Published: April 2021

Aims

The aim of this study was to investigate the pattern, causes, and predictors of all new hospitalizations in patients who underwent transcatheter aortic valve implantation (TAVI).

Methods and results

The nationwide Swedish TAVI registry was merged with other mandatory healthcare registries, which enabled the analysis of all TAVI procedures, new hospital admissions, and death between the years 2008 and 2017. A total of 2821 patients underwent TAVI with a mean of 2.5 hospitalizations during a mean follow-up of 2.2 years. Hospitalizations were associated with worse prognosis. Heart failure (HF) was the most common cause of hospitalization with 19% having at least one hospitalization due to HF causing, 16% of all-cause admissions, and 50% of cardiovascular admissions. Male gender, age >90 years, high Charlson Comorbidity Index, atrial fibrillation, present neurologic disease, severe renal impairment, peripheral vascular disease, New York Heart Association class IV, mild or moderate mean aortic valve gradients, and pulmonary hypertension were associated with an increased risk for all-cause hospitalizations or death. For cardiovascular hospitalization or death, the pattern was similar, with the addition of impaired systolic left ventricular function as a predictor.

Conclusion

Multiple hospitalizations after TAVI are common and are often caused by HF. Reducing the rate of HF hospitalizations is important to mitigate the burden on the healthcare system due to new hospitalizations after TAVI.
Transformation of chloroplast ribosomal RNA genes in Chlamydomonas: molecular and genetic characterization of integration events.
Authors: Newman S M , Boynton J E , Gillham N W , Randolph-Anderson B L , Johnson A M , Harris E H
Published: April 2021

Transformation of chloroplast ribosomal RNA (rRNA) genes in Chlamydomonas has been achieved by the biolistic process using cloned chloroplast DNA fragments carrying mutations that confer antibiotic resistance. The sites of exchange employed during the integration of the donor DNA into the recipient genome have been localized using a combination of antibiotic resistance mutations in the 16S and 23S rRNA genes and restriction fragment length polymorphisms that flank these genes. Complete or nearly complete replacement of a region of the chloroplast genome in the recipient cell by the corresponding sequence from the donor plasmid was the most common integration event. Exchange events between the homologous donor and recipient sequences occurred preferentially near the vector:insert junctions. Insertion of the donor rRNA genes and flanking sequences into one inverted repeat of the recipient genome was followed by intramolecular copy correction so that both copies of the inverted repeat acquired identical sequences. Increased frequencies of rRNA gene transformants were achieved by reducing the copy number of the chloroplast genome in the recipient cells and by decreasing the heterology between donor and recipient DNA sequences flanking the selectable markers. In addition to producing bona fide chloroplast rRNA transformants, the biolistic process induced mutants resistant to low levels of streptomycin, typical of nuclear mutations in Chlamydomonas.
Evolutionary inferences from DNA variation at the 6-phosphogluconate dehydrogenase locus in natural populations of drosophila: selection and geographic differentiation.
Authors: Begun D J , Aquadro C F
Published: April 2021

Several allozyme-coding genes in Drosophila melanogaster show patterns suggesting that polymorphisms at these loci are targets of balancing selection. An important question is whether these genes have similar distributions of underlying DNA sequence variation which would indicate similar evolutionary processes occurring in this class of loci. One such locus, 6-phosphogluconate dehydrogenase (Pgd), has previously been shown to exhibit clinal variation for Fast/Slow electromorph variation in the United States and Australia, unusually large electromorph frequency differences between the United States and Africa, and other patterns indicative of selection. We measured four-cutter DNA restriction site and allozyme variation at Pgd among 142 D. melanogaster X chromosomes collected from several geographic regions including North Carolina, California, and Zimbabwe (Africa). We also sequenced a representative sample of 13 D. melanogaster Pgd genes collected in North Carolina and a single copy of Pgd from the sibling species, Drosophila simulans. While some population genetic models predict excess DNA polymorphism in genes which are targets of balancing selection, the D. melanogaster samples from the United States had significantly reduced levels of DNA polymorphism and extraordinarily high levels of linkage disequilibrium, providing evidence of hitchhiking effects of advantageous mutants at Pgd or at linked sites. Therefore, while selection has probably influenced the distribution of DNA variation at Pgd, the precise nature of these selective events remains obscure. Since the Pgd region appears to have low rates of crossing over, the reduced level of variation at this locus supports the idea that recombination rates are important determinants of levels of DNA polymorphism in natural populations. Furthermore, while patterns of allozyme variation are very similar at Pgd and Adh, the DNA data show that the evolutionary histories of these genes are dramatically different. We observed extensive differences in the amount and distribution of variation in D. melanogaster Pgd samples from the United States and Zimbabwe which cannot be explained by differential selection on the Fast/Slow polymorphism in these two geographic regions. Thus, genetic drift among partially isolated populations has also been an important factor in determining the distribution of variation at Pgd in D. melanogaster. Finally, we assayed four-cutter variation at Pgd in a sample of 19 D. simulans X chromosomes and observed reduced levels of DNA variability and high levels of linkage disequilibrium. These patterns are consistent with predictions of some hitchhiking models.
A genetic analysis of hermaphrodite, a pleiotropic sex determination gene in Drosophila melanogaster.
Authors: Pultz M A , Carson G S , Baker B S
Published: April 2021

Sex determination in Drosophila is controlled by a cascade of regulatory genes. Here we describe hermaphrodite (her), a new component of this regulatory cascade with pleiotropic zygotic and maternal functions. Zygotically, her+ function is required for female sexual differentiation: when zygotic her+ function is lacking, females are transformed to intersexes. Zygotic her+ function may also play a role in male sexual differentiation. Maternally, her+ function is needed to ensure the viability of female progeny: a partial loss of her+ function preferentially kills daughters. In addition, her has both zygotic and maternal functions required for viability in both sexes. Temperature sensitivity prevails for all known her alleles and for all of the her phenotypes described above, suggesting that her may participate in an intrinsically temperature-sensitive process. This analysis of four her alleles also indicates that the zygotic and maternal components of of her function are differentially mutable. We have localized her cytologically to 36A3-36A11.
Fine structure mapping and deletion analysis of the murine piebald locus.
Authors: Metallinos D L , Oppenheimer A J , Rinchik E M , Russell L B , Dietrich W , Tilghman S M
Published: April 2021

piebald (s) is a recessive mutation that affects the development of two cell types of neural crest origin: the melanocytes, responsible for pigment synthesis in the skin, and enteric ganglia, which innervate the lower bowel. As a result, mice carrying piebald mutations exhibit white spotting in the coat and aganglionic megacolon. Previously the gene had been localized to the distal half of mouse chromosome 14. To determine its precise location relative to molecular markers, an intersubspecific backcross was generated. Two anchor loci of chromosome 14, slaty and hypogonadal, in addition to simple sequence length repeat markers, were used to localize s to a 2-cM interval defined by the markers D14Mit38 and D14Mit42. The molecular markers were also used to characterize nine induced s alleles. Three of these mutations exhibited no deletions or rearrangements of the flanking markers, whereas the other six had two or more of these markers deleted. The extent of the deletions was found to be consistent with the severity of the homozygous phenotype. The location of deletion breakpoints in the induced alleles, coupled with the recombination breakpoints in the backcross progeny, provide useful molecular landmarks to define the location of the piebald gene.
Insertional mutation on mouse chromosome 18 with vestibular and craniofacial abnormalities.
Authors: Ting C N , Kohrman D , Burgess D L , Boyle A , Altschuler R A , Gholizadeh G , Samuelson L C , Jang W , Meisler M H
Published: April 2021

A dominant mutation was generated in transgenic mice as a consequence of insertional mutation. Heterozygous mice from transgenic line 9257 (Tg9257) are hyperactive with bidirectional circling behavior and have a distinctive facial appearance due to hypoplasia of the nasal bone. Morphological analysis of the inner ear revealed asymmetric abnormalities of the horizontal canal and flattening or invagination of the crista ampullaris, which can account for the circling behavior. The sensory epithelium appeared to be normal. The transgene insertion site was localized by in situ hybridization to the B1 band of mouse chromosome 18. Genetic mapping in an interspecific backcross demonstrated the gene order centromere--Tg9257--8.8 +/- 3.4--Grl-1, Egr-1, Fgf-1, Apc--14.7 +/- 4.3--Pdgfr. The phenotype and the mapping data suggest that the transgene may be inserted at the Twirler locus. Homozygosity for the transgene results in prenatal lethality, but compound heterozygotes carrying the Tw allele and the transgene are viable. The function of the closely linked ataxia locus is not disrupted by the transgene insertion. This insertional mutant will provide molecular access to genes located in the Twirler region of mouse chromosome 18.
Distribution of unlinked receptor sites for transposed Ac elements from the bz-m2(Ac) allele in maize.
Authors: Dooner H K , Belachew A , Burgess D , Harding S , Ralston M , Ralston E
Published: April 2021

We have shown before that the Ac element from the maize bz-m2(Ac) allele, located in the short arm of chromosome 9 (9S), transposes preferentially to sites that are linked to the bz donor locus. Yet, about half of the Ac transpositions recovered from bz-m2(Ac) are in receptor sites not linked to the donor locus. In this study, we have analyzed the distribution of those unlinked receptor sites. Thirty-seven transposed Ac (trAc) elements that recombined independently of the bz locus were mapped using a set of wx reciprocal translocations. We found that the distribution of unlinked receptor sites for trAs was not random. Ten trAcs mapped to 9L, i.e., Ac had transposed to sites physically, if not genetically, linked to the donor site. Among chromosomes other than 9, the Ac element of bz-m2(Ac) appeared to have transposed preferentially to certain chromosomes, such as 5 and 7, but infrequently to others, such as 1, the longest chromosome in the maize genome. The seven trAc elements in chromosome 5 were mapped relative to markers in 5S and 5L and localized to both arms of 5. We also investigated the transposition of Ac to the homolog of the donor chromosome. We found that Ac rarely transposes from bz-m2(Ac) to the homologous chromosome 9. The clustering of Ac receptor sites around the donor locus has been taken to mean that a physical association between the donor site and nearby receptor sites occurs during transposition. The preferential occurrence of 9L among chromosomes harboring unlinked receptor sites would be expected according to this model, since sites in 9L would tend to be physically closer to 9S than sites in other chromosomes. The nonrandom pattern seen among the remaining chromosomes could reflect an underlying nuclear architecture, i.e., an ordering of the chromosomes in the interphase nucleus, as suggested from previous cytological observations.
The use of mixture models to detect effects of major genes on quantitative characters in a plant breeding experiment.
Authors: Jiang C , Pan X , Gu M
Published: April 2021

An analysis based on Elston's model of mixed major locus and polygenic inheritance is extended to include populations of progeny testing such as F3, B1s and B2s families derived from F2 and backcrosses in a cross between two inbred lines. Genetic hypotheses that can be validly tested by the likelihood ratio method in the analysis of a breeding experiment include homogeneity of variances due to environment and/or polygenes with transformable scale effect by Box-Cox power function, random and independent segregation of major genes, invariance of the effects of major genes with population types and additive and dominant models for polygenes. Testing hypotheses in the order suggested here can lead to a gradual simplification of the models and increases the feasibility of the subsequent analysis, but caution must be paid to the possible bias in parameter estimation and hypotheses tests. The procedure is applied to a set of data on plant height of rice with the effects of dwarf genes in crosses among three varieties. Two recessive dwarf genes are shown to be nonallelic and unlinked. One dwarf gene is shown to reduce plant height about 36-56 cm, and another 52-61 cm. The effect of polygenes, estimated as the standard deviation among possible inbred lines derived from these crosses, is about 11.7 cm. Interactions between the dwarf genes and the polygenic background are found, especially for one of the two genes. Both the polygenic effects and the interactions are much smaller than the effects of the major dwarf genes.
Formamide sensitivity: a novel conditional phenotype in yeast.
Authors: Aguilera A
Published: April 2021

Yeast mutants unable to grow in the presence of 3% formamide have been isolated in parallel with mutants sensitive to either 37 degrees or 6% ethanol. The number of formamide-sensitive mutations that affect different genes that can be identified from yeast cells is at least as large as the number of thermosensitive or ethanol-sensitive mutations. These mutations are of two types: those that are sensitive to formamide, temperature and/or ethanol simultaneously; and those that are specific for formamide sensitivity and show no temperature or ethanol sensitivity phenotype. Those genes susceptible to giving rise to formamide-sensitive alleles include the structural gene for DNA ligase, CDC9, and the structural gene for arginine permease, CAN1. The results indicate that formamide sensitivity can be used as a novel conditional phenotype for mutations on both essential and nonessential genes. This work also confirms that ethanol-sensitivity can be used as a conditional phenotype to identify mutations in at least as many genes as those susceptible to temperature or formamide sensitive mutations.
Predicting abundance indices in areas without coverage with a latent spatio-temporal Gaussian model
Authors: Breivik Olav Nikolai , Aanes Fredrik , Søvik Guldborg , Aglen Asgeir , Mehl Sigbjørn , Johnsen Espen
Published: April 2021

A general spatio-temporal abundance index model is introduced and applied on a case study for North East Arctic cod in the Barents Sea. We demonstrate that the model can predict abundance indices by length and identify a significant population density shift in northeast direction for North East Arctic cod. Varying survey coverage is a general concern when constructing standardized time series of abundance indices, which is challenging in ecosystems impacted by climate change and spatial variable population distributions. The applied model provides an objective framework that accommodates for missing data by predicting abundance indices in areas with poor or no survey coverage using latent spatio-temporal Gaussian random fields. The model is validated, and no violations are observed.