bluuebunny/crossref_metadata_2025 huggingface dataset:
The influence inter-day colorimetric method in quantification of chicken meat’s total cholesterol with lipid extraction -saponification pretreatment
Authors: Laila U , Putra T J
Published: October 2019

Unskinned chicken meat’s cholesterol consisting of thigh, breast, and wing meat were determined inter-daily by ferric chloride reagent spectrophotometric methods. The pretreatments before cholesterol analysis were conducted which involved with lipid extraction, saponification, and subsequent extraction of unsaponified matter. Afterwards, spectrophotometry was carried out. For understanding precision of quantification, the total cholesterol was measured inter-daily in which the difference of measurement time were one day for each same part of chicken meat. The research showed unskinned thigh meat had significantly higher total cholesterol 186.19 mg/100 g as compared to breast, and wing meat (156.05 mg/100g and 135.38 mg/100 g; p<0.01 for both). Inter-daily spectrophotometry analysis insignificantly affected on thigh, breast, and wing meat’s cholesterol content. This method can become solution for analysis time limitation problem in cholesterol spectrophotometric analysis.
Effects of health consciousness and environmental attitude on intention towards organic food purchase
Authors: Kusumaningsih D , Irianto H , Antriyandarti E
Published: October 2019

The objective of this research is to study the effect of health consciousness and environmental attitude towards intention to purchase organic food. The research is using Theory of Planned Behaviour (TPB). The study variables are health consciousness, environmental attitude, availability, subjective norm, attitude and intention to purchase organic foods. Survey method is applied, with the 150 respondents intending to purchase organic food in Surakarta. Structural equation model (SEM) is applied to analyze data. The result shows that health consciousness and environmental attitude are the determinants of an individual’s positive attitude to purchase organic food. In addition, the attitude and subjective norm are also being the determinants of intention to purchase organic food. The study suggests that increasing organic food consumption can be achieved by increasing the knowledge about the benefit of organic food on health and environmental maintenance of potential consumers.
Thermal Loading Effect During Machining of Borosilicate Glass Using ECDM Process
Authors: Arya R K , Dvivedi A
Published: October 2019

Glass has unique properties for micro fluidic, MEMS and optical applications. However, poor machinability of glass materials limit its applications. ECDM process is one of the most utilized micro machining process for fabrication of glass micro products. In ECDM thermal energy of discharges utilizes to provide thermal loading for removal of material. However, controlled thermal loading requires for machining of glass materials owing to its poor thermal conductivity. High thermal stresses may develop at high thermal loading, which leads to uncontrolled facture of glass material. Therefore, a thorough discussion is needed to understand the effect of thermal loading on glass materials. In this study, the experiments are conducted to investigate the thermal loading effect on borosilicate glass during ECDM process. Also, an analytical model is developed to estimate the induced thermal stress during ECDM process. Theses thermal stresses are discussed during drilling of micro hole on work material. After discussion three zones are identified for machining of borosilicate glass using ECDM process, wherein zone-II (i.e. from 44 V to 52 V applied voltage) is identified for safe machining.
A Novel Coupler Design and Analysis with Shielding Material Tests for a CPT System of Electric Vehicles Based on Electromagnetic Resonant Coupling
Authors: Duan J , Wang W
Published: October 2019

In this paper, a contactless power transfer (CPT) system using a novel geometrically enhanced energy transfer coupler with three different shielding materials has been built and analysed, along with the evaluations from aspects of electromagnetics and RMS power transmitting based on electromagnetic resonant coupling. A CPT system design improvement with the proposed H-shape ferromagnetic cores and the combined semi-enclosed passive electromagnetic shielding methods have been investigated in terms of generated electromagnetic field characteristics, system power transfer ratings, system efficiency optimization and performances of shielding materials. The results have shown that, across the range of operating frequency of the CPT system, aluminium shielding as a metallic material method could deliver better overall CPT system performance than other two ferromagnetic materials, steel 1010 and ferrite. In addition, the coupler prototype design limitations, misalignment tolerance and the passive shielding design considerations including distance between windings and inner surfaces of shielding shells have been discussed.
Modeling the Electrical Conductivity of Ni1-xFex-SDC Composite Anode by Using PSO-SVR
Authors: Tang J. L , Yang R. F
Published: October 2019

Studies have shown that numerous indexes affecting the electrical conductivity of Solid Oxide Fuel Cell (SOFC) anode. In order to improve performance of SOFC, it is advantageous to have a model with which one can modeling the electrical conductivity at different operating conditions. In this study, a model utilizing support vector regression (SVR) approach combined with particle swarm optimization (PSO), was proposed to modeling the electrical conductivity of Ni1-xFex(0⩽x⩽0.25)-Ce0.85Sm0.15O2-δ(SDC) composite anode. The test result by PSO-SVR show that the root mean square error (RMSE) of test samples is 3.79, mean absolute percentage error (MAPE) of test samples is 0.82%, multiplecorrelation correlation coefficients (R
2) of test samples is 1.00, which is satisfied with the engineering demand. The result of this investigation provides that PSO-SVR is an effective tool for modeling the electrical conductivity of Ni1-xFex-SDC composite anode.
Analysis of Allowable Assembly Forces for Composite Laminates
Authors: Zhang Tingyu , Zhang Chong , Zhao Jianshe , Guo Anru
Published: October 2019

Composite structures have been widely used in aerospace field due to their low density, high strength, and high stiffness to weight ratio. In the aerospace field, composite laminates are widely used in the skin of the airplane. Due to the complexity of the composite molding process, and the difficulty of machining composite laminates, the manufacturing precision of the skin is usually not very high. Hence the assembly force is applied to the skin to ensure the composite laminates fit the framework in the assembly process of an airplane. However, too large assembly force leads to the assembly out of tolerance owning to the over deformation and leads to the stress of the skin out of tolerance. Therefore, this paper proposes a method of analyzing the allowable assembly force. With the help of mechanics and physics, the mechanical relationship between the assembly forces and the deformation of a skin is modeled. On the basis of the model and the experimental date of a skin assembly process, the mathematical relationship between the assembly forces and the deformation of the skin is established. The allowable assembly forces are determined based on the mathematical relationship and the allowable deformation. This paper provides an optimization methodology of assembly force optimization.
Effects of Process Parameters on Cutting Force and Tool Temperature in Drilling Based on Finite Element Simulation
Authors: Gao Yuan , Wang Jie , Wang Qi , Li Xin , Zhang Tingyu , Zhong Yang
Published: October 2019

Cutting force and tool temperature play significant roles in the drilling process because they are strongly related to drilling performance such as surface roughness, tool wear and tool breakage etc. For difficult-to-machine materials, like titanium alloys, the drilling operation is considered to be complex due to their mechanical and thermal properties, and it is important to find suitable process parameters to avoid too large cutting force or too high tool temperature, which may deteriorate the drilling performance. This paper is dedicated to studying the effects of process parameters, including spindle speed, feed rate and helix angle, on cutting force and tool temperature in drilling based on finite element simulation. A series of drilling simulations are carried out to generate the simulated cutting force and tool temperature data under different drilling conditions. By data fitting, the steady cutting force and tool temperature are predicted. Based on the Taguchi method, the effects of process parameters on steady cutting force and tool temperature are analysed. This paper can provide a basis for suitable selection of process parameters in drilling.
Machining Grooves in Silica Glass by Using Picosecond Lasers
Authors: Jiao J K , Zhang J A , Zhang W W , Popvawe R
Published: October 2019

A picosecond laser with 1064nm wavelength was used to machine grooves in fused silica in this paper. A surface texturing method was applied to increase the laser absorption. The relationship between the width, the depth of the groove and the laser parameters such as laser power, scanning speed, number of scanning cycles was studied. The machining quality of the groove was detected by the laser scanning confocal microscopy. It showed that there were no micro-cracks on the grooving surface, and the surface roughness Ra<1.6um. The width, the depth and the shape of the groove could be controlled accurately by changing the laser parameters. And, a “V-shape” groove with 1mm width, 1mm depth was obtained with the as the frequency, the laser power, the scanning velocity and the number scanning cycle was fixed at 400KHz, 141W, 5000mm/s and 12, respectivity.
MetumpX—a metabolomics support package for untargeted mass spectrometry
Authors: Wajid Bilal , Iqbal Hasan , Jamil Momina , Rafique Hafsa , Anwar Faria
Published: October 2019

Motivation

Metabolomics is a data analysis and interpretation field aiming to study functions of small molecules within the organism. Consequently Metabolomics requires researchers in life sciences to be comfortable in downloading, installing and scripting of software that are mostly not user friendly and lack basic GUIs. As the researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines truly speeding up the learning curve to build software workstations. Therefore, this paper aims to provide MetumpX, a software package that eases in the installation of 103 software by automatically resolving their individual dependencies and also allowing the users to choose which software works best for them.

Results

MetumpX is a Ubuntu-based software package that facilitate easy download and installation of 103 tools spread across the standard metabolomics pipeline. As far as the authors know MetumpX is the only solution of its kind where the focus lies on automating development of software workstations.

Availability and implementation

https://github.com/hasaniqbal777/MetumpX-bin.

Supplementary information

Supplementary data are available at Bioinformatics online.
dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq
Authors: Huang Moli , Wang Yunpeng , Yang Manqiu , Yan Jun , Yang Henry , Zhuang Wenzhuo , Xu Ying , Koeffler H Phillip , Lin De-Chen , Chen Xi
Published: October 2019

Cancer hallmarks rely on its specific transcriptional programs, which are dysregulated by multiple mechanisms, including genomic aberrations in the DNA regulatory regions. Genome-wide association studies have shown many variants are found within putative enhancer elements. To provide insights into the regulatory role of enhancer-associated non-coding variants in cancer epigenome, and to facilitate the identification of functional non-coding mutations, we present dbInDel, a database where we have comprehensively analyzed enhancer-associated insertion and deletion variants for both human and murine samples using ChIP-Seq data. Moreover, we provide the identification and visualization of upstream TF binding motifs in InDel-containing enhancers. Downstream target genes are also predicted and analyzed in the context of cancer biology. The dbInDel database promotes the investigation of functional contributions of non-coding variants in cancer epigenome.

Availability and implementation

The database, dbInDel, can be accessed from http://enhancer-indel.cam-su.org/.

Supplementary information

Supplementary data are available at Bioinformatics online.
BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genome
Authors: Kim Eiru , Bae Dasom , Yang Sunmo , Ko Gunhwan , Lee Sungho , Lee Byungwook , Lee Insuk
Published: October 2019

Motivation

Owing to advanced DNA sequencing and genome assembly technology, the number of species with sequenced genomes is rapidly increasing. The aim of the recently launched Earth BioGenome Project is to sequence genomes of all eukaryotic species on Earth over the next 10 years, making it feasible to obtain genomic blueprints of the majority of animal and plant species by this time. Genetic models of the sequenced species will later be subject to functional annotation, and a comprehensive molecular network should facilitate functional analysis of individual genes and pathways. However, network databases are lagging behind genome sequencing projects as even the largest network database provides gene networks for less than 10% of sequenced eukaryotic genomes, and the knowledge gap between genomes and interactomes continues to widen.

Results

We present BiomeNet, a database of 95 scored networks comprising over 8 million co-functional links, which can build and analyze gene networks for any species with the sequenced genome. BiomeNet transfers functional interactions between orthologous proteins from source networks to the target species within minutes and automatically constructs gene networks with the quality comparable to that of existing networks. BiomeNet enables assembly of the first-in-species gene networks not available through other databases, which are highly predictive of diverse biological processes and can also provide network analysis by extracting subnetworks for individual biological processes and network-based gene prioritizations. These data indicate that BiomeNet could enhance the benefits of decoding the genomes of various species, thus improving our understanding of the Earth’ biodiversity.

Availability and implementation

The BiomeNet is freely available at http://kobic.re.kr/biomenet/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Overactivity of neuronal adenosine A2A receptors accelerates neurodegeneration
Authors: Cunha Rodrigo A
Published: October 2019

This scientific commentary refers to ‘Exacerbation of C1q dysregulation, synaptic loss and memory deficits in tau pathology linked to neuronal adenosine A2A receptors’, by Carvalho et al. (doi:10.1093/brain/awz288).
The Effect of Community-Based Nutritional Interventions on Children of Women Living With Human Immunodeficiency Virus in Rural India: A 2 × 2 Factorial Intervention Trial
Authors: Shin Sanghyuk S , Satyanarayana Veena A , Ekstrand Maria L , Carpenter Catherine L , Wang Qiao , Yadav Kartik , Ramakrishnan Padma , Pamujula Suresh , Sinha Sanjeev , Nyamathi Adeline M
Published: October 2019

Background

Malnutrition is a common clinical concern among children in low-income communities affected by human immunodeficiency virus (HIV). We examined the effect of a community-based nutritional intervention on anthropometric and clinical outcomes of children of women living with HIV in rural India.

Methods

We assigned women living with HIV and their child (oldest 3–8 years) to 1 of 4 programs: (1) community-based HIV care program, (2) program 1 + nutrition education, (3) program 1 + food supplement, and (4) all elements of programs 1–3. Study data were collected at baseline and months 6, 12, and 18. We applied mixed-effects modeling with restricted maximum likelihood estimation to examine changes in weight (all children) and CD4+ T-cell counts (children with HIV only).

Results

Overall, 600 mother–child pairs were enrolled (150/group) with 100% retention at follow-up visits. Approximately 20% of children were living with HIV. Children in program 4 had higher weight gain than those in programs 1, 2, and 3 at all time points (adjusted P < .001). We found a higher increase in CD4+ T cells across all time points among participants in programs 3 and 4 compared with program 1 (adjusted P < .001). Factorial analysis suggested a synergistic effect of combining nutrition education and food supplements for weight gain but not for increase in CD4+ T cells.

Conclusions

A combination of nutrition education and food supplements provided to women living with HIV significantly increased weight and CD4+ T cells, and such interventions can be integrated into HIV-care programs in low-income settings.
Prognostic implications of left ventricular global longitudinal strain in patients with bicuspid aortic valve disease and preserved left ventricular ejection fraction
Authors: Kong William K F , Vollema E Mara , Prevedello Francesca , Perry Rebecca , Ng Arnold C T , Poh Kian Keong , Almeida Ana G , González Ariana , Shen Mylène , Yeo Tiong Cheng , Shanks Miriam , Popescu Bogdan A , Galian Gay Laura , Fijałkowski Marcin , Liang Michael , Chen Ruth W , Ajmone Marsan Nina , Selvanayagam Joseph , Pinto Fausto , Zamorano Jose L , Pibarot Philippe , Evangelista Arturo , Delgado Victoria , Bax Jeroen J
Published: October 2019

Aims

In patients with bicuspid aortic valve (BAV) and preserved left ventricular (LV) ejection fraction (EF), the frequency of impaired LV global longitudinal strain (GLS) and its prognostic implications are unknown. The present study evaluated the proportion and prognostic value of impaired LV GLS in patients with BAV and preserved LVEF.

Methods and results

Five hundred and thirteen patients (68% men; mean age 44 ± 18 years) with BAV and preserved LVEF (>50%) were divided into five groups according to the type of BAV dysfunction: (i) normal function BAV, (ii) mild aortic stenosis (AS) or aortic regurgitation (AR), (iii) ≥moderate isolated AS, (iv) ≥moderate isolated AR, and (v) ≥moderate mixed AS and AR. LV systolic dysfunction based on 2D speckle-tracking echocardiography was defined as a cut-off value of LVGLS (−13.6%). The primary outcome was aortic valve intervention or all-cause mortality. The proportion of patients with LVGLS ≤−13.6% was the highest in the normal BAV group (97%) and the lowest in the group with moderate and severe mixed AS and AR (79%). During a median follow-up of 10 years, 210 (41%) patients underwent aortic valve replacement and 17 (3%) died. Patients with preserved LV systolic function (LVGLS ≤ −13.6%) had significantly better event-free survival compared to those with impaired LV systolic function (LVGLS > −13.6%). LVGLS was independently associated with increased risk of events (mainly aortic valve replacement): hazard ratio 1.09; P < 0.001.

Conclusion

Impaired LVGLS in BAV with preserved LVEF is not infrequent and was independently associated with increased risk of events (mainly aortic valve replacement events).
Sex-related differences in risk factors, outcome, and quality of life in patients with permanent atrial fibrillation: results from the RACE II study
Authors: Kloosterman Mariëlle , Crijns Harry J G M , Mulder Bart A , Groenveld Hessel F , Van Veldhuisen Dirk J , Rienstra Michiel , Van Gelder Isabelle C
Published: October 2019

Aims

Atrial fibrillation (AF) risk factors translate into disease progression. Whether this affects women and men differently is unclear. We aimed to investigate sex differences in risk factors, outcome, and quality of life (QoL) in permanent AF patients.

Methods and results

The Rate Control Efficacy in Permanent Atrial Fibrillation (RACE II) randomized 614 patients, 211 women and 403 men, to lenient or strict rate control. In this post hoc analysis risk factors, cardiovascular events during 3-year follow-up (cardiovascular death, heart failure hospitalization, stroke, systemic embolism, bleeding, and life-threatening arrhythmic events), outcome parameters, and QoL were compared between the sexes. Women were older (71 ± 7 vs. 66 ± 8 years, P < 0.001), had more hypertension (70 vs. 57%, P = 0.002), and heart failure with preserved ejection fraction (36 vs. 17%, P < 0.001), but less coronary artery disease (13 vs. 21%, P = 0.02). Women had more risk factors (3.7 ± 1.2 vs. 2.9 ± 1.4, P < 0.001) Cardiovascular events occurred in 46 (22%) women and 59 (15%) men (P = 0.03). Women had a 1.52 times [95% confidence interval (CI) 1.03–2.24] higher yearly cardiovascular event-rate [8.2% (6.0–10.9) vs. 5.4% (4.1–6.9), P = 0.03], but this was no longer significant after adjusting for the number of underlying risk factors. Women had reduced QoL, irrespective of age and heart rate but negatively influenced by their risk factors.

Conclusion

In this permanent AF population, women had more accumulation of AF risk factors than men. The observed higher cardiovascular event rate in women was no longer significant after adjusting for the number of risk factors. Further, QoL was negatively influenced by the higher number of risk factors in women. This suggests that sex differences may be driven by the greater risk factor burden in women.
Net benefit of oral anticoagulants in patients with atrial fibrillation and active cancer: a nationwide cohort study
Authors: Atterman Adriano , Friberg Leif , Asplund Kjell , Engdahl Johan
Published: October 2019

Aims

To estimate the net cerebrovascular benefit of prophylactic treatment with oral anticoagulants (OACs) in patients with atrial fibrillation (AF) and active cancer.

Methods and results

We included all Swedish patients who had been diagnosed with AF in a hospital or in a hospital-associated outpatient unit between 1 July 2005 and 1 October 2017. Patients with active cancer (n = 22 596) and without cancer (n = 440 848) were propensity score matched for the likelihood of receiving OACs at baseline. At baseline, 38.3% of cancer patients with AF and high stroke risk according to CHA2DS2-VASc score received OACs. There was a net benefit of OACs, assessed by the composite outcome of ischaemic stroke, extracranial arterial thromboembolism, all major bleedings, and death, both among patients with active cancer [hazard ratio (HR): 0.81, confidence interval (CI): 0.78–0.85] and among patients without cancer (HR: 0.81, CI: 0.80–0.82). When limiting follow-up to 1 year to minimize the effects of possible treatment cross-over and additionally accounting for death as a competing risk in cancer patients, a net cerebrovascular benefit regarding ischaemic stroke or intracranial bleeding was observed for OACs [subhazard ratio (sHR): 0.67, CI: 0.55–0.83]. A net cerebrovascular benefit was also seen for non-vitamin K antagonist OACs over warfarin after competing risk analyses in cancer patients (sHR: 0.65, CI: 0.48–0.88).

Conclusion

Patients with AF and active cancer benefit from OAC treatment.
The Dutch Public Health Foresight Study 2018: an example of a comprehensive foresight exercise
Authors: Verschuuren Marieke , Hilderink Henk B M , Vonk Robert A A
Published: October 2019

Background

The use of foresight studies is common in some policy fields, but not in public health. Interest in such studies is growing. This paper gives a general overview of the Dutch Public Health Foresight Study (PHFS) 2018, providing insight into what performing a broad scenario exercise in the field of public health entails and its societal impacts.

Methods

The aim of the PHFS-2018 was: (a) to show how public health and healthcare in the Netherlands will develop over the next 25 years if we pursue our current course and detect ‘new’ developments; (b) to give options for dealing with the major future societal challenges. Part a was addressed by means of a quantitative business-as-usual scenario exercise complemented with qualitative thematic studies, and part b by elaborating courses of action for three key challenges, based on stakeholder consultation. Typical aspects of the PHFS methods are a multidisciplinary, participatory and conceptual approach and using a broad definition of health.

Results

The PHFS-2018 is the basis for the upcoming National Health Policy Memorandum and the Trend Scenario is the baseline for the National Prevention Agreement. Unexpectedly, the findings about increasing mental pressure in young people received most attention. There still is room for expanding use of the study to its full potential.

Conclusions

Long-term thinking could be stimulated by using back casting techniques and stronger involvement of policy-makers in the elaboration of options for action. Lessons learned from developing intersectoral policy at the local level could be applied at the national level.
On the Function of Trans-Splicing: No Evidence for Widespread Proteome Diversification in Trypanosomes
Authors: Soulette Cameron M , Oliverio Oliver , Roy Scott W
Published: October 2019

A long-standing mystery of genomic/transcriptomic structure involves spliced leader trans-splicing (SLTS), in which short RNA “tags” transcribed from a distinct genomic locus is added near the 5′ end of RNA transcripts by the spliceosome. SLTS has been observed in diverse eukaryotes in a phylogenetic pattern implying recurrent independent evolution. This striking convergence suggests important functions for SLTS, however no general novel function is known. Recent findings of frequent alternative SLTS (ALT-TS) suggest that ALT-TS could impart widespread functionality. Here, we tested the hypothesis that ALT-TS diversifies proteomes by comparing splicing patterns in orthologous genes between two deeply diverged trypanosome parasites. We also tested proteome diversification functions of ALT-TS by utilizing ribosome profiling sequence data. Finally, we investigated ALT-TS as a mechanism to regulate the expression of unproductive transcripts. Although our results indicate the functional importance of some cases of trans-splicing, we find no evidence for the hypothesis that proteome diversification is a general function of trans-splicing.
Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach
Authors: Edsall Lee E , Berrio Alejandro , Majoros William H , Swain-Lenz Devjanee , Morrow Shauna , Shibata Yoichiro , Safi Alexias , Wray Gregory A , Crawford Gregory E , Allen Andrew S
Published: October 2019

Changes in transcriptional regulation are thought to be a major contributor to the evolution of phenotypic traits, but the contribution of changes in chromatin accessibility to the evolution of gene expression remains almost entirely unknown. To address this important gap in knowledge, we developed a new method to identify DNase I Hypersensitive (DHS) sites with differential chromatin accessibility between species using a joint modeling approach. Our method overcomes several limitations inherent to conventional threshold-based pairwise comparisons that become increasingly apparent as the number of species analyzed rises. Our approach employs a single quantitative test which is more sensitive than existing pairwise methods. To illustrate, we applied our joint approach to DHS sites in fibroblast cells from five primates (human, chimpanzee, gorilla, orangutan, and rhesus macaque). We identified 89,744 DHS sites, of which 41% are identified as differential between species using the joint model compared with 33% using the conventional pairwise approach. The joint model provides a principled approach to distinguishing single from multiple chromatin accessibility changes among species. We found that nondifferential DHS sites are enriched for nucleotide conservation. Differential DHS sites with decreased chromatin accessibility relative to rhesus macaque occur more commonly near transcription start sites (TSS), while those with increased chromatin accessibility occur more commonly distal to TSS. Further, differential DHS sites near TSS are less cell type-specific than more distal regulatory elements. Taken together, these results point to distinct classes of DHS sites, each with distinct characteristics of selection, genomic location, and cell type specificity.
Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp
Authors: Matthey-Doret Cyril , van der Kooi Casper J , Jeffries Daniel L , Bast Jens , Dennis Alice B , Vorburger Christoph , Schwander Tanja
Published: October 2019

Sex determination has evolved in a variety of ways and can depend on environmental and genetic signals. A widespread form of genetic sex determination is haplodiploidy, where unfertilized, haploid eggs develop into males and fertilized diploid eggs into females. One of the molecular mechanisms underlying haplodiploidy in Hymenoptera, the large insect order comprising ants, bees, and wasps, is complementary sex determination (CSD). In species with CSD, heterozygosity at one or several loci induces female development. Here, we identify the genomic regions putatively underlying multilocus CSD in the parasitoid wasp Lysiphlebus fabarum using restriction-site associated DNA sequencing. By analyzing segregation patterns at polymorphic sites among 331 diploid males and females, we identify up to four CSD candidate regions, all on different chromosomes. None of the candidate regions feature evidence for homology with the csd gene from the honey bee, the only species in which CSD has been characterized, suggesting that CSD in L. fabarum is regulated via a novel molecular mechanism. Moreover, no homology is shared between the candidate loci, in contrast to the idea that multilocus CSD should emerge from duplications of an ancestral single-locus system. Taken together, our results suggest that the molecular mechanisms underlying CSD in Hymenoptera are not conserved between species, raising the question as to whether CSD may have evolved multiple times independently in the group.
Environmental Genome-Wide Association Reveals Climate Adaptation Is Shaped by Subtle to Moderate Allele Frequency Shifts in Loblolly Pine
Authors: De La Torre Amanda R , Wilhite Benjamin , Neale David B
Published: October 2019

Understanding the genomic basis of local adaptation is crucial to determine the potential of long-lived woody species to withstand changes in their natural environment. In the past, efforts to dissect the genomic architecture in gymnosperms species have been limited due to the absence of reference genomes. Recently, the genomes of some commercially important conifers, such as loblolly pine, have become available, allowing whole-genome studies of these species. In this study, we test for associations between 87k SNPs, obtained from whole-genome resequencing of loblolly pine individuals, and 270 environmental variables and combinations of them. We determine the geographic location of significant loci and identify their genomic location using our newly constructed ultradense 26k SNP linkage map. We found that water availability is the main climatic variable shaping local adaptation of the species, and found 821 SNPs showing significant associations with climatic variables or combinations of them based on the consistent results of three different genotype–environment association methods. Our results suggest that adaptation to climate in the species might have occurred by many changes in the frequency of alleles with moderate to small effect sizes, and by the smaller contribution of large effect alleles in genes related to moisture deficit, temperature and precipitation. Genomic regions of low recombination and high population differentiation harbored SNPs associated with groups of environmental variables, suggesting climate adaptation might have evolved as a result of different selection pressures acting on groups of genes associated with an aspect of climate rather than on individual environmental variables.
Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias
Authors: Acosta Armando , Martínez-Pacheco Mónica L , Díaz-Barba Karina , Porras Niccole , Gutiérrez-Mariscal Mariana , Cortez Diego
Published: October 2019

The age of sex chromosomes is commonly obtained by comparing the substitution rates of XY gametologs. Coupled with phylogenetic reconstructions, one can refine the origin of a sex chromosome system relative to specific speciation events. However, these approaches are insufficient to determine the presence and duration of ancestral sex chromosome systems that were lost in some species. In this study, we worked with genomic and transcriptomic data from mammals and squamates and analyzed the effect of male mutation bias on X-linked sequences in these groups. We searched for signatures indicating whether monotremes shared the same sex chromosomes with placental mammals or whether pleurodonts and acrodonts had a common ancestral sex chromosome system. Our analyses indicate that platypus did not share the XY chromosomes with placental mammals, in agreement with previous work. In contrast, analyses of agamids showed that this lineage maintained the pleurodont XY chromosomes for several million years. We performed multiple simulations using different strengths of male mutation bias to confirm the results. Overall, our work shows that variations in substitution rates due to male mutation bias could be applied to uncover signatures of ancestral sex chromosome systems.
Sarcopenia Characteristics Are Associated with Incident Mobility Limitations in African Caribbean Men: The Tobago Longitudinal Study of Aging
Authors: Santanasto Adam J , Miljkovic Iva , Cvejkus Ryan K , Wheeler Victor W , Zmuda Joseph M
Published: October 2019

Background

Sarcopenia varies by ethnicity, and has a major impact on health in older adults. However, little is known about sarcopenia characteristics in African ancestry populations outside the United States. We examined sarcopenia characteristics in 2,142 African Caribbean men aged 59.0 ± 10.4 years (range: 40–92 years) in Tobago, and their association with incident mobility limitations in those aged 55+ (n = 738).

Methods

Body mass index (BMI), grip strength, dual-x-ray absorptiometry (DXA) appendicular lean mass (ALM), and self-reported mobility limitations were measured at baseline, and 6 years later. Change in sarcopenia characteristics, including grip strength, grip strength/BMI, ALMBMI, and ALM/ht2, were determined. Foundations for the National Institutes of Health Sarcopenia Project (FNIH) and European Working Group for Sarcopenia in Older People 2 (EWGSOP2) cut-points were also examined. Odds ratios (OR) and 95% confidence intervals (CI) for mobility limitation were calculated using multivariable linear regression models adjusted for covariates.

Results

Overall, sarcopenia prevalence was quite low using the FNIH (0.3%) and EWGSOP2 (0.6%) operational cut-points, but was higher in those aged 75+ (2.1% [FNIH] and 3.7% [EWGSOP2]). Prevalence was also higher when based on “weakness”, versus “low ALM.” When sarcopenia markers were examined separately, baseline levels, but not changes, were associated with incident mobility limitations. Baseline grip strength/BMI was a particularly strong risk factor for incident mobility limitations (OR per SD: 0.50; 95% CI: 0.37–0.68).

Conclusions

Our findings suggest that grip strength normalized to body mass, measured at one time point, may be a particularly useful phenotype for identifying African Caribbean men at risk for future mobility limitations.
Are You Saving for Retirement? Racial/Ethnic Differentials in Contributory Retirement Savings Plans
Authors: Tamborini Christopher R , Kim Changhwan
Published: October 2019

Objectives: How individuals and families accumulate retirement resources during working years is a key aspect of aging with implications for later life. This study examines how much, and by what mechanisms, savings in retirement plans vary by race/ethnicity.

Method: Using representative survey data and linked W-2 tax records, we estimate the probability of participation in employer-sponsored defined contribution (DC) retirement plans with probit regression, and contribution levels with ordinary least squares (OLS) models. We use Heckman models to adjust for potential sample selection.

Results: Black and Hispanic workers have lower participation and contributions in employer-sponsored DC retirement plans than do white workers, while Asian Americans have higher levels. The bulk of racial/ethnic differences is attributed to socioeconomic position, especially education and labor market circumstances like earnings. Differentials are also associated with family circumstances, namely for black workers. After accounting for education, labor market, and family covariates, social-psychological factors appear to explain only small portions of differences, especially for black and Hispanic.

Discussion: This study clarifies how racial/ethnic disparities in socioeconomic circumstances generate advantages and disadvantages in retirement wealth accumulation. Lower DC retirement plan participation and contributions among minorities in work life represent an underappreciated earlier-life channel through which racial inequalities in income and wealth in later life are generated.
A Scoping Review of the Evidence About the Nurses Improving Care for Healthsystem Elders (NICHE) Program
Authors: Squires Allison , Murali Komal Patel , Greenberg Sherry A , Herrmann Linda L , D’amico Catherine O
Published: October 2019

Background and Objectives

The Nurses Improving Care for Healthsystem Elders (NICHE) is a nurse-led education and consultation program designed to help health care organizations improve the quality of care for older adults. To conduct a scoping review of the evidence associated with the NICHE program to (a) understand how it influences patient outcomes through specialized care of the older adult and (b) provide an overview of implementation of the NICHE program across organizations as well as its impact on nursing professionals and the work environment.

Research Design and Methods

Six databases were searched to identify NICHE-related articles between January 1992 and April 2019. After critical appraisal, 43 articles were included.

Results

Four thematic categories were identified including specialized older adult care, geriatric resource nurse (GRN) model, work environment, and NICHE program adoption and refinement. Specialized older adult care, a key feature of NICHE programs, resulted in improved quality of care, patient safety, lower complications, and decreased length of stay. The GRN model emphasizes specialized geriatric care education and consultation. Improvements in the geriatric nurse work environment as measured by perceptions of the practice environment, quality of care, and aging-sensitive care delivery have been reported. NICHE program adoption and refinement focuses on the methods used to improve care, implementation and adoption of the NICHE program, and measuring its impact.

Discussion and Implications

The evidence about the NICHE program in caring for older adults is promising but more studies examining patient outcomes and the impact on health care professionals are needed.
Constraints on the location, depth and yield of the 2017 September 3 North Korean nuclear test from InSAR measurements and modelling
Authors: Sreejith K M , Agrawal Ritesh , Rajawat A S
Published: October 2019

The Democratic People's Republic of Korea (North Korea) conducted its sixth and largest affirmed underground nuclear test on 2017 September 3. Analysis of Interferometric Synthetic Aperture Radar (InSAR) data revealed detailed surface displacements associated with the nuclear explosion. The nuclear explosion produced large-scale surface deformation causing decorrelation of the InSAR data directly above the test site, Mt. Mantap, while the flanks of the Mountain experienced displacements up to 0.5 m along the Line-of-Sight of the Satellite. We determined source parameters of the explosion using the Bayesian inversion of the InSAR data. The explosive yield was estimated as 245–271 kiloton (kt) of TNT, while the previous yield estimations range from 70–400 kt. We determined the nuclear source at a depth of 542 ± 30 m below Mt. Mantap (129.0769°E, 41.0324°N). We demonstrated that the Bayesian modelling of the InSAR data reduces the uncertainties in the source parameters of the nuclear test, particularly the yield and source depth that are otherwise poorly resolved in seismic methods.
Ovarian stimulation for freeze-all IVF cycles: a systematic review
Authors: Mizrachi Yossi , Horowitz Eran , Farhi Jacob , Raziel Arieh , Weissman Ariel
Published: October 2019

BACKGROUND

Freeze-all IVF cycles are becoming increasingly prevalent for a variety of clinical indications. However, the actual treatment objectives and preferred treatment regimens for freeze-all cycles have not been clearly established.

OBJECTIVE AND RATIONALE

We aimed to conduct a systematic review of all aspects of ovarian stimulation for freeze-all cycles.

SEARCH METHODS

A comprehensive search in Medline, Embase and The Cochrane Library was performed. The search strategy included keywords related to freeze-all, cycle segmentation, cumulative live birth rate, preimplantation genetic diagnosis, preimplantation genetic testing for aneuploidy, fertility preservation, oocyte donation and frozen-thawed embryo transfer. We included relevant studies published in English from 2000 to 2018.

OUTCOMES

Our search generated 3292 records. Overall, 69 articles were included in the final review. Good-quality evidence indicates that in freeze-all cycles the cumulative live birth rate increases as the number of oocytes retrieved increases. Although the risk of severe ovarian hyperstimulation syndrome (OHSS) is virtually eliminated in freeze-all cycles, there are certain risks associated with retrieval of large oocyte cohorts. Therefore, ovarian stimulation should be planned to yield between 15 and 20 oocytes. The early follicular phase is currently the preferred starting point for ovarian stimulation, although luteal phase stimulation can be used if necessary. The improved safety associated with the GnRH antagonist regimen makes it the regimen of choice for ovarian stimulation in freeze-all cycles. Ovulation triggering with a GnRH agonist almost completely eliminates the risk of OHSS without affecting oocyte and embryo quality and is therefore the trigger of choice. The addition of low-dose hCG in a dual trigger has been suggested to improve oocyte and embryo quality, but further research in freeze-all cycles is required. Moderate-quality evidence indicates that in freeze-all cycles, a moderate delay of 2–3 days in ovulation triggering may result in the retrieval of an increased number of mature oocytes without impairing the pregnancy rate. There are no high-quality studies evaluating the effects of sustained supraphysiological estradiol (E2) levels on the safety and efficacy of freeze-all cycles. However, no significant adverse effects have been described. There is conflicting evidence regarding the effect of late follicular progesterone elevation in freeze-all cycles.

WIDER IMPLICATIONS

Ovarian stimulation for freeze-all cycles is different in many aspects from conventional stimulation for fresh IVF cycles. Optimisation of ovarian stimulation for freeze-all cycles should result in enhanced treatment safety along with improved cumulative live birth rates and should become the focus of future studies.
The rapid expansion of yellowtail (Seriola quinqueradiata) spawning ground in the East China Sea is linked to increasing recruitment and spawning stock biomass
Authors: Sassa Chiyuki , Takahashi Motomitsu , Konishi Yoshinobu , Yoshimasa Aonuma , Tsukamoto Youichi
Published: October 2019

Biomass of the yellowtail Seriola quinqueradiata, an important fishery resource in Japan, has increased about threefold over the past 20 years to ∼300 thousand metric tons. We examined the interannual variations in distribution and abundance of S. quinqueradiata larvae [4.2–7.9 mm body length (BL), ∼7 to 18 days after hatching], based on sampling surveys over a broad area of the shelf-break region of the East China Sea (ECS) in April, the main spawning period, over 15 years (2001–2015). High abundances of larvae were found in the northern ECS off the southwestern coast of Kyushu Island throughout the survey period. After 2010, the larvae began to occur abundantly also in the southern ECS south of 29°30′N, indicating a southward expansion of the spawning ground. There has been a significant positive trend of larval abundance over the whole ECS during the 15 years, which was mainly due to the sharp increase in larval abundance in the southern ECS after 2010. Although interannual variation in larval abundance was not related to environmental conditions (temperature, salinity, and chlorophyll a concentration), it was closely correlated with the spawning stock biomass. This indicates that the increasing trend of larvae was related to the increase in egg production in the ECS. Also, the larval abundance showed a weak positive correlation with recruitment, suggesting that the increased larval abundance has, in part, contributed to high recruitment.
Does regulation of illegal content need reconsideration in light of blockchains?
Authors: Schellekens Maurice
Published: October 2019

Blockchains are increasingly being used for content distribution, sometimes as an unwanted side effect of blockchain applications that have other primary purposes, sometimes as intended content distribution. The typical characteristics of a blockchain such as its claimed immutability raise new questions as to what preventive measures can reasonably be demanded from blockchain intermediaries, and managers of nodes in particular. The article asks whether the exemptions introduced in the Directive on e-Commerce can be applied, what mitigating or preventive measures other than Notice-and-Takedown can be applied and how governmental regulators should react.
Mauritian Courts and the Protection of the Rights of Asylum Seekers in the Absence of Dedicated Legislation
Authors: Mujuzi Jamil Ddamulira
Published: October 2019

Mauritius became a party to the 1951 Refugee Convention through succession but is yet to accede to the 1967 Protocol relating to the Status of Refugees. It has signed but not yet ratified the OAU Convention Governing the Specific Aspects of Refugee Problems in Africa and has not signed the African Union Convention for the Protection and Assistance of Internally Displaced Persons in Africa. Unlike many other countries in Africa, Mauritius has not yet enacted domestic legislation dealing with the issue of refugees. However, international human rights obligations and domestic legislation allow the rights of asylum seekers to be protected in Mauritius. This article argues that the principle of non-refoulement bars Mauritius from extraditing or deporting an asylum seeker to a country where he or she will be persecuted or where his or her rights will be violated, and that asylum seekers and citizens are equally protected by the Constitution with regard to absolute rights. However, limitations may be imposed on asylum seekers in their enjoyment of non-absolute rights. For such limitations to be lawful, they must aim to achieve the objectives stipulated in section 3 of the Constitution.