bluuebunny/crossref_metadata_2025 huggingface dataset:
IT Governance Audit at Lampung University Using COBIT 5 Framework Focus on EDM Domain
Authors: Tristiyanto  , Octaria C
Published: October 2019

The competitiveness of an organization depends on IT governance because it enables organizations to optimize the benefits of implementing IT. The process of IT governance in the university’s answer to the needs of the organization which will guarantee the certainty of value creation of information technology as well as an assurance of the return of information technology investments that have been invested. Currently, IT governance and implementation at the University of Lampung has been run fairly well, but there are some steep obstacles in its business processes. COBIT 5 is a standard for IT governance processes that can help an organization to manage, develop, and retain its assets. In this study, an information technology governance audit was conducted based on the focal framework of COBIT 5 EDM domains with case studies at the University of Lampung. Data collection methods used are data analysis, interviews, and questionnaires. From the audit process, it was found that Lampung University’s ability to manage information technology at EDM generally focuses on level 4, but the achievement in each process has not been fulfilled yet and has not achieved the expected results by University of Lampung.
A New Approach of Steganography Using Center Sequential Technique
Authors: Darwis D , Junaidi A , Wamiliana
Published: October 2019

The quality of steganographic images can be determined from several aspects. One of the testing techniques on steganography is cropping which is part of robustness testing. Under cropping process, it is possible that the secret message cannot be extracted from the stego-image. This happen because the pixels values on the stego-image embedded message changed and the message content on the stego-image will be lost. In this research we propose a new approach for solving that problem by using the algorithm based on Sequential Technique where the input process starts from the center of the cover. The secret information in the form of image and the cover image is also an image. By using this method, the secret image is safe although the cropping is done from left, right, above or bottom of the stego image.
Learning Activities to Promote the Concept of Engineering Design Process for Grade 10 Students’ Ideas about Force and Motion through Predict-Observe-Explain (POE)
Authors: Bunprom Somsak , Tupsai Jiraporn , Yuenyong Chokchai
Published: October 2019

The purpose of this study was to learning activities for promoted the concept of engineering design Grade 10 students’ ideas of engineering design process on the problem based about force and motion. The force and motion unit provided the problem based activities through predict-observe-explain (POE). Participants included 60 Grade 10 students who were studying in Khon Kaen University Demonstration Secondary School (suksasart). Methodology regarded interpretive paradigm. The Hynes et.al. (2011) framework of engineering design process (EPD) was applied as reference of students’ existing ideas of engineering design process. The Hynes et.al. (2011) EPD consists of 9 steps including (1) identify need or problem, 2) research need or problem, 3) develop possible solutions, 4) select the best possible solution, 5) construct a prototype, 6) test and evaluate solution, 7) communicate the solution, 8) redesign, and 9) completion decision. The force and motion POE problem based was provided in order to allow students to design the possible solutions of inclined plane problem based. The 13 students’ tasks of solutions were interpreted to clarify students’ existing ideas of EPD. The findings revealed that all group could be interpreted that they held 9 steps of Hynes et.al. (2011) EPD to design their solutions. The paper will discuss the details of students’ existing ideas of engineering design process. The paper may have implication for STEM education teaching and learning.
Local Wisdom Related to STEM Education
Authors: Saeng-Xuto Virapong
Published: October 2019

This study aimed to clarify plausibility of developing STEM education learning activities based on Thai local wisdom. Research method regarded document analysis. The author previous research about toys and local wisdom were analysed for STEM education. The local toys in northern part of Thailand were selected to represent how they could be used in classroom for STEM education. Two kinds of toys were explained. These included (1) Bunbeu and (2) E-plor. The paper clarified the components of toys, how to play the toys, and STEM knowledge behind playing the toys. This study may have implications for STEM education learning activities.
Localization study of CHD7 protein expressed in HeLa and HEK293 cells
Authors: Brajadenta G S , Kitzis A , Thoreau V
Published: October 2019

CHARGE syndrome is a rare genetic disease characterized by numerous congenital abnormalities caused by de novo alterations of the CHD7 gene. It encodes a chromo domain protein, involved in the ATP-dependent remodelling of chromatin. It has been described that CHD7 protein plays a role as a positive regulator of the nucleolar expression of the 45S ribosomal RNA precursor. The aim of this research was to study where the CHD7 protein is localized. Knowledge of the subcellular localization of the CHD7 protein is essential for understanding its physiological function. This study was conducted by transfection of two plasmids encoding CHD7-HA or FLAG-CHD7 into HeLa (human cervix carcinoma) and HEK293 (human embryonic kidney) cells. Protein expression and localization of the CHD7 protein was demonstrated by western blot and immunofluorescence. CHD7 protein was expressed in both cell models, and localization of the protein was found in the nucleoplasm, but not in the nucleolus.
The effect of micro-climate to quality and existence of Gedong Gincu Mango
Authors: Jaenudin A , Suradinata T , Maryuliyanna M
Published: October 2019

Indonesia as tropical country has various of agro-climate that affected to spread of plants, of course for mango plant. Gedong Gincu mango as a competitive commodities in west java, spread. In three district of west java, Cirebon, Majalengka and Indramayu district. The aims of this research was to analyze the effect of physical environmental components to Gedong Gincu mango characteristics in three districts of west Java, Indonesia. The research was performed in Indramayu, Cirebon, and Majalengka in January-June 2017. The methods of this research was descriptive qualitative. The results showed that the difference of micro-climate, including (rainfall, temperature, and humidity), effected Gedong Gincu mango characteristics, especially size, shape, color and texture of fruit flesh. Gedong Gincu mango from Indramayu has spherical shape, a small size, a strong red color, a hard and thin flesh, a fragrant flavor, and very sweet taste. Gedong Gincu mango from Cirebon has oval shape, a medium size, red color, medium and rather thick flesh, a fragrant flavour and sweet taste. Gedong Gincu mango from Majalengka has a sprawl, large size, yellowish red color, fine meat and thick flesh, a medium flavour and less sweet taste.
Communication in agricultural extension services toward farmer empowerment
Authors: Faqih A , Aisyah S
Published: October 2019

This research was conducted to find out the influence of agents on the results of empowerment of farmers, the effect of recipients on the results of the farmer empowerment, the effect of agricultural extension on the results of the farmer empowerment, and the influence of agents, recipients, and agricultural extension on the results of farmer empowerment. This research was carried out in May to July 2017. Quantitative descriptive method was applied by using primary and secondary data. Primary data obtained from interviews with 24 respondents who applied integrated crop management technology (PTT) on paddy fields. Technique of interview was guided with questionnaires while secondary data was taken from some literature work and relevant agencies. The results showed that: there is positive and significant influence between the agents and farmer empowerment, there is positive and significant influence between the recipients on the farmer empowerment, there is positive and significant influence between agricultural extension on the results of the farmer empowerment, and there is positive and significant influence between the agents, recipients, and agricultural extension on the results of farmer empowerment.
Aerial pathogenic micro fungi in medical classes on medical faculty
Authors: Amanah A , Kusmawan D , Sutisna A
Published: October 2019

Microbiological air pollution consists of micro fungi and bacteria. Micro fungi are indoor air pollutant because its spores widely spread, floats in the air, surface, dust, and water, and can be pathogenic. Isolation and identification of aerial pathogenic micro fungi in study rooms in Medical Faculty attempted to find whether there was difference of micro fungi number in every study room. The research design is experimental descriptive research, using 8 samples with 3 repetitions. Data analyzed using Kruskal-Walls test. The research result showed the successfully identified 10 aerial pathogenic micro fungi which were: Aspergillus Niger, Aspergillus flavus, Aspergillus glaucus, Rhizopus sp., Mucor sp., Penicillium sp., Trichoderma sp., Syncephalastrum sp., Scopulariopsis sp., and Cladophialophorabantiana. The research also showed that there was difference of aerial pathogenic micro fungi number in every study rooms ranging between 16,490-73,026 CFU m3, but statistically there wasn’t significant difference. (P Value = 0,459). The result was still considered as normal based on the regulation of ministry of health Republic of Indonesia.
Analysis of added value in dry sea fish agroindustry in Gebang Sub District, Cirebon Regency
Authors: Wachdijono W , Julhan R
Published: October 2019

It has been recognized by agricultural economists that the biggest added value to the agribusiness system lies in its agro-industrial sub-system. This is because in the sub-system, agricultural products experience additional benefits so that the selling price becomes higher. High selling prices will increase profits for the perpetrators and on a wider scale will be a source of new economic growth. This study aims to analyze the added value of dry sea fish agroindustry in Gebang Sub District, Cirebon Regency. The research location was determined intentionally and carried out during May - June 2018. The research method was quantitative and survey data collection techniques. The population is 18 processors of wet sea fish into dry sea fish and census sampling techniques. Data analysis uses Hayami Model calculation method. The results showed that the added value of dry sea fish agroindustry was Rp 681, - / kg (8 %). Based on this analysis it can be concluded that the value added of dry sea fish is still relatively small so the opportunity to increase the added value is still open. For this reason, it is suggested to the Cirebon Regency Government to make policies to increase the added value of dry sea fish through the application of appropriate technology.
Learning Management System (LMS) schoology: Why it’s important and what it looks like
Authors: Ferdianto F , Dwiniasih
Published: October 2019

E-learning becomes one of the concepts deriving learning management system (LMS) which is designed to identify the gaps in teaching learning process, analyzing and reporting the data received automatically. One of the upgrading platforms of this learning management system recently is Schoology. It serves collaborative blended learning units which is form used in revolution 4.0 era. In investigating the reason of why Schoology is important and try to dig more information of its look, interview and documentation are applied in this research to be described clearly. Two teachers from one of the private universities in Cirebon are willing to participate in this research. By its interactive features that Schoology has, it changes teacher’s perspective to be a must using Schoology since it allows teachers to collaborate not only with their students, but also with other teachers, coaches, and parents. Four aspects of features involve content delivery, test and quizzes, discussion, and video viewing/link sources which allowed teachers sharing material discussed with students, searching new article with other teachers, and grading students test result, quizzes and attendance offered by Schoology as the reason of both teachers that Schoology should be one of learning management system conducted.
Informal caregiving for dementia patients: the contribution of patient characteristics and behaviours to caregiver burden
Authors: Allen Andrew P , Buckley Maria M , Cryan John F , Ní Chorcoráin Aoife , Dinan Timothy G , Kearney Patricia M , O’Caoimh Rónán , Calnan Mareeta , Clarke Gerard , Molloy D William
Published: October 2019

Objectives

The burden often associated with informal caregiving for patients with dementia is associated with negative effects on health, both physiologically and in terms of caregiver cognition. There is wide variation in the level of burden experienced by dementia caregivers. To better understand caregiver burden, it is thus important to understand the factors associated with level of burden.

Methods

In the current study, we collected carer burden and putative associated factors at baseline, 6 and 12 months. Hierarchical regression was used to assess the impact of these factors on caregiver burden. We assessed self-reported carer burden, patient behavioural and safety issues, and level of difficulty associated with providing assistance with activities of daily living (ADL). Patients’ age was also recorded, and trained nurses assessed patient cognitive performance using the quick mild cognitive impairment screen.

Results

At baseline, patients’ age, cognition and ADLs were associated with burden, and safety and challenging behaviour were both significantly associated with burden independent of the other factors. Change in burden was associated with change in carer-reported safety at 6-month follow-up, and with change in safety and change in carer-reported challenging behaviours at 12-month follow-up.

Conclusions

Safety issues and challenging behaviours are associated with carer burden, even after accounting for cognitive and functional impairment in the person with dementia. As dementia progresses, monitoring these factors may help to inform stress-management strategies for caregivers.
Vancomycin volume of distribution estimation in adults with class III obesity
Authors: Dunn Ryan D , Crass Ryan L , Hong Joseph , Pai Manjunath P , Krop Lynne C
Published: October 2019

Purpose

To compare methods of estimating vancomycin volume of distribution (V) in adults with class III obesity.

Methods

A retrospective, multicenter pharmacokinetic analysis of adults treated with vancomycin and monitored through measurement of peak and trough concentrations was performed. Individual pharmacokinetic parameter estimates were obtained via maximum a posteriori Bayesian analysis. The relationship between V and body weight was assessed using linear regression. Mean bias and root-mean-square error (RMSE) were calculated to assess the precision of multiple methods of estimating V.

Results

Of 241 patients included in the study sample, 159 (66.0%) had a BMI of 40.0–49.9 kg/m2, and 82 (34.0%) had a BMI of ≥50.0 kg/m2. The median (5th, 95th percentile) weight of patients was 136 (103, 204) kg, and baseline characteristics were similar between BMI groups. The mean ± S.D. V was lower in patients with a BMI of 40.0–49.9 kg/m2 than in those with a BMI of ≥50.0 kg/m2 (72.4 ± 19.6 L versus 79.3 ± 20.6 L, p = 0.009); however, body size poorly predicted V in regression analyses (R2 < 0.20). A fixed estimate of V (75 L) or use of 0.52 L/kg by total body weight yielded similar bias and error in this population.

Conclusion

Results of the largest analysis of vancomycin V in class III obesity to date indicated that use of a fixed V value (75 L) and use of a TBW-based estimate (0.52 L/kg) for estimation of vancomycin V in patients with a BMI of ≥40.0 kg/m2 have similar bias. Two postdistribution vancomycin concentrations are needed to accurately determine patient-specific pharmacokinetic parameters, estimate AUC, and improve the precision of vancomycin dosing in this patient population.
Blindness After Facial Filler Injections: The Role of Extravascular Hyaluronidase on Intravascular Hyaluronic Acid Embolism in the Rabbit Experimental Model
Authors: Zhang Lei , Feng Xiao , Shi Hangyan , Wu Woffles T L , Wu Sufan
Published: October 2019

Background

Blindness caused by ophthalmic artery embolism is the most catastrophic complication of facial hyaluronic acid (HA) injections. Extravascular (retrobulbar) injection of hyaluronidase has been suggested as a salvage in this calamitous situation. However, the effectiveness of this treatment still lacks consensus.

Objectives

The aim of this study was to investigate the role of extravascular hyaluronidase in dissolving intravascular HA occlusion.

Methods

Two different animal experiments were performed: (1) isolated rabbit abdominal aorta segments filled with HA were treated with extravascular immersion of highly concentrated hyaluronidase for 90 minutes, followed by gross observation, microscopic examination, particle size analysis, and immunohistochemical staining; and (2) live rabbit auricular arteries were first occluded with HA and then immediately treated with extravascular injection of hyaluronidase. The ears were then evaluated by gross observation, microscopic examination, and perfusion studies after 60 minutes and again after 90 minutes.

Results

The HA within the aorta segments showed no gross or microscopic changes after treatment with extravascular hyaluronidase. Hyaluronidase could only be detected in adventitia of the aortae, instead of in vascular smooth muscle, tunica intima, or vascular lumen. The occluded auricular arteries showed no reperfusion after extravascular injection of hyaluronidase.

Conclusions

In this rabbit model, extravascular hyaluronidase was unable to penetrate into the arterial lumen of the isolated abdominal aorta nor the live auricular artery of the rabbit to dissolve intravascular HA within a 90-minute time limit, thus casting doubt on whether extravascular (retrobulbar) hyaluronidase injection has a role in treating ophthalmic artery embolism caused by HA injections.
Intralesional Electrocoagulation With Insulated Microneedle for the Treatment of Periorbital Syringomas: A Retrospective Analysis
Authors: Ahn Ga Ram , Jeong Guk Jin , Kim Jae Min , Hong Ji Yeon , Li Kapsok , Lee Chang Kyun , Kim Beom Joon
Published: October 2019

Background

Conventional treatment options for periorbital syringomas are often unsatisfactory because of inevitable surface damage from the procedure and frequent recurrence rate of the tumors.

Objectives

The authors sought to ascertain the efficacy and safety of intralesional electrosurgery utilizing a monopolar radiofrequency device with a single insulated microneedle for the treatment of periorbital syringomas.

Methods

A retrospective analysis was performed employing data from medical records, routine questionnaires, and clinical photographs of 55 patients with periorbital syringoma who underwent intralesional electrosurgery.

Results

Approximately one-half of the patients (50.9%) experienced marked resolution after 1 treatment. The lesion clearance rate increased and lesion severity decreased each time the treatment was repeated. No persistent therapy-related adverse event was found except transient erythema or crusting.

Conclusions

Intralesional electrosurgery with insulated microneedle is an effective and safe treatment option for periorbital syringomas.

Level of Evidence: 4
Disrupted glycosylation of lipids and proteins is a cause of neurodegeneration
Authors: Moll Tobias , Shaw Pamela J , Cooper-Knock Johnathan
Published: October 2019

Glycosyltransferases represent a large family of enzymes that catalyse the biosynthesis of oligosaccharides, polysaccharides, and glycoconjugates. A number of studies have implicated glycosyltransferases in the pathogenesis of neurodegenerative diseases but differentiating cause from effect has been difficult. We have recently discovered that mutations proximal to the substrate binding site of glycosyltransferase 8 domain containing 1 (GLT8D1) are associated with familial amyotrophic lateral sclerosis (ALS). We demonstrated that ALS-associated mutations reduce activity of the enzyme suggesting a loss-of-function mechanism that is an attractive therapeutic target. Our work is the first evidence that isolated dysfunction of a glycosyltransferase is sufficient to cause a neurodegenerative disease, but connection between neurodegeneration and genetic variation within glycosyltransferases is not new. Previous studies have identified associations between mutations in UGT8 and sporadic ALS, and between ST6GAL1 mutations and conversion of mild cognitive impairment into clinical Alzheimer’s disease. In this review we consider potential mechanisms connecting glycosyltransferase dysfunction to neurodegeneration. The most prominent candidates are ganglioside synthesis and impaired addition of O-linked β-N-acetylglucosamine (O-GlcNAc) groups to proteins important for axonal and synaptic function. Special consideration is given to examples where genetic mutations within glycosyltransferases are associated with neurodegeneration in recognition of the fact that these changes are likely to be upstream causes present from birth.
Loss of ARID1A induces a stemness gene ALDH1A1 expression with histone acetylation in the malignant subtype of cholangiocarcinoma
Authors: Yoshino Jun , Akiyama Yoshimitsu , Shimada Shu , Ogura Toshiro , Ogawa Kosuke , Ono Hiroaki , Mitsunori Yusuke , Ban Daisuke , Kudo Atsushi , Yamaoka Shoji , Tanabe Minoru , Tanaka Shinji
Published: October 2019

Genomic analyses have recently discovered the malignant subtype of human intrahepatic cholangiocarcinoma (ICC) characterized by frequent mutations of chromatin remodeling gene ARID1A; however, the biological and molecular functions still remain obscure. We here examined the clinical and biological significances of ARID1A deficiency in human ICC. Immunohistochemical analysis demonstrated that the loss of ARID1A was an independent prognostic factor for overall survival of ICC patients (P = 0.023). We established ARID1A-knockout (KO) cells by using the CRISPR/Cas9 system from two human cholangiocarcinoma cell lines. ARID1A-KO cells exhibited significantly enhanced migration, invasion, and sphere formation activity. Microarray analysis revealed that ALDH1A1, a stemness gene, was the most significantly elevated genes in ARID1A-KO cells. In addition, ALDH enzymatic activity as a hallmark of cancer stem cells was markedly high in the KO cells. ARID1A and histone deacetylase 1 were directly recruited to the ALDH1A1 promoter region in cholangiocarcinoma cells with undetectable ALDH1A1 expression by chromatin immunoprecipitation assay. The histone H3K27 acetylation level at the ALDH1A1 promoter region was increased in cells when ARID1A was disrupted (P < 0.01). Clinically, inverse correlation between ARID1A and ALDH1A1 expression was also identified in primary ICC (P = 0.018), and ARID1A-negative and ALDH1A1-positve ICCs showed worse prognosis than only ARID1A-negative cases (P = 0.002). In conclusion, ARID1A may function as a tumor suppressor in ICC through transcriptional downregulation of ALDH1A1 expression with decreasing histone H3K27 acetylation. Our studies provide the basis for the development of new epigenetic approaches to ARID1A-negative ICC.

Immunohistochemical loss of ARID1A is an independent prognostic factor in intrahepatic cholangiocarcinoma patients. ARID1A recruits HDAC1 to the promoter region of ALDH1A1, a stemness gene, and epigenetically suppresses ALDH1A1 expression with decreasing histone H3K27 acetylation in cholangiocarcinoma cells.
Cefazolin and Ertapenem Salvage Therapy Rapidly Clears Persistent Methicillin-Susceptible Staphylococcus aureus Bacteremia
Authors: Ulloa Erlinda R , Singh Kavindra V , Geriak Matthew , Haddad Fadi , Murray Barbara E , Nizet Victor , Sakoulas George
Published: October 2019

Cefazolin and ertapenem combination therapy was used successfully to salvage 11 cases (6 endocarditis) of persistent methicillin-susceptible Staphylococcus aureus (MSSA) bacteremia, including immediate clearance (≤24 hours) in 8 cases. While in vitro synergy was modest, cefazolin plus ertapenem exhibited synergistic action in a rat model of MSSA endocarditis. The combination of cefazolin and ertapenem provides potent in vivo activity against MSSA beyond what is predicted in vitro and warrants further clinical study in the treatment of refractory MSSA bacteremia and endocarditis.
‘But the Last Word Is Ours’: The Monopoly of Jurisdiction of the Court of Justice of the European Union in Light of the Investment Court System
Authors: de Abreu Duarte Francisco
Published: October 2019

This article develops the concept of the monopoly of jurisdiction of the Court of Justice of the European Union (CJEU) through the analysis of the case study of the Investment Court System (ICS). By providing a general framework over the criteria that have been developed by the Court, the work sheds light on the controversial principle of autonomy of the European Union (EU) and its implications to the EU’s external action. The work intends to be both pragmatic and analytical. On the one hand, the criteria are extracted as operative tools from the jurisprudence of the CJEU and then used in the context of the validity of the ICS. This provides the reader with some definitive standards that can then be applied to future cases whenever a question concerning autonomy arises. On the other hand, the article questions the reasons behind the idea of the monopoly of jurisdiction of the CJEU, advancing a concept of autonomy of the EU as a claim for power and critiquing the legitimacy and coherence of its foundations. Both dimensions will hopefully help to provide some clarity over the meaning of autonomy and the monopoly of jurisdiction, while, at the same time, promoting a larger discussion on its impact on the external action of the EU.
A comparison of prokaryote communities inhabiting sponges, bacterial mats, sediment and seawater in Southeast Asian coral reefs
Authors: Cleary DFR , Polónia ARM , Huang YM , Putchakarn S , Gomes NCM , de Voogd NJ
Published: October 2019

In the present study, we used Illumina sequencing to explore the prokaryote communities of 17 demosponge species and how they compare with bacterial mat, sediment and seawater samples (all sampled from coral reef habitat in Taiwan and Thailand). The studied sponge species formed three clusters. OTU richness and evenness were by far highest in the sediment and bacterial mat biotopes. There were pronounced differences in OTU richness and evenness among clusters and also considerable variation among certain host species within clusters. Additionally, the relative abundance of some prokaryotic taxa also differed among clusters with Poribacteria, for example, being recorded in all sponge species, but with very low relative abundances in species of two of the three clusters. This sponge-associated phylum was, however, recorded at relatively high mean abundance in bacterial mat samples, which also housed relatively high abundances of actinobacterial and Chloroflexi members. Our results support the HMA status of the species Aaptos lobata, Hyrtios erectus, Pseudoceratina purpurea and Xestospongia testudinaria, which clustered together and LMA status of the species Acanthella cavernosa, Echinodictyum asperum, Jaspis splendens, Ptilocaulis spiculifer, Stylissa carteri and Suberites diversicolor, which also clustered together. Other species (Agelas cavernosa, Agelas nemoechinata, Acanthostylotella cornuta, Paratetilla sp., Hymeniacidon sp. and Haliclona cymaeformis) deviated somewhat from the typical HMA/LMA dichotomy and formed a strongly supported cluster.
GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals
Authors: Cerbin Stefan , Wai Ching Man , VanBuren Robert , Jiang Ning
Published: October 2019

Transposable elements represent the largest components of many eukaryotic genomes and different genomes harbor different combinations of elements. Here, we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla. Further searching for related sequences to the conserved DDE region uncovered the presence of this superfamily of elements in fish, coral, sea anemone, and other animal species. However, this element appears restricted to Bryophytes and Lycophytes in plants. This transposon, named GingerRoot, is associated with a 6 bp (base pair) target site duplication, and 100–150 bp terminal inverted repeats. Analysis of transposase sequences identified the DDE motif, a catalytic domain, which shows similarity to the integrase of Gypsy-like long terminal repeat retrotransposons, the most abundant component in plant genomes. A total of 77 intact and several hundred truncated copies of GingerRoot elements were identified in S. lepidophylla. Like Gypsy retrotransposons, GingerRoots show a lack of insertion preference near genes, which contrasts to the compact genome size of about 100 Mb. Nevertheless, a considerable portion of GingerRoot elements was found to carry gene fragments, suggesting the capacity of duplicating gene sequences is unlikely attributed to the proximity to genes. Elements carrying gene fragments appear to be less methylated, more diverged, and more distal to genes than those without gene fragments, indicating they are preferentially retained in gene-poor regions. This study has identified a broadly dispersed, novel DNA transposon, and the first plant DNA transposon with an integrase-related transposase, suggesting the possibility of de novo formation of Gypsy-like elements in plants.
DNA methylation age and physical and cognitive ageing
Authors: Maddock Jane , Castillo-Fernandez Juan , Wong Andrew , Cooper Rachel , Richards Marcus , Ong Ken K , Ploubidis George B , Goodman Alissa , Kuh Diana , Bell Jordana T , Hardy Rebecca
Published: October 2019

Background

DNA methylation (DNAm) age acceleration (AgeAccel) has been shown to be predictive of all-cause mortality but it is unclear what functional aspect/s of ageing it captures. We examine associations between four measures of AgeAccel in adults aged 45-87 years and physical and cognitive performance and their age-related decline.

Methods

AgeAccelHannum, AgeAccelHorvath, AgeAccelPheno and AgeAccelGrim were calculated in the Medical Research Council National Survey of Health and Development (NSHD), National Child Development Study (NCDS) and TwinsUK. Three measures of physical (grip strength, chair rise speed and forced expiratory volume in one second[FEV1]) and two measures of cognitive (episodic memory and mental speed) performance were assessed.

Results

AgeAccelPheno and AgeAccelGrim, but not AgeAccelHannum and AgeAccelHorvath were related to performance in random effects meta-analyses (n=1388-1685). For example, a one year increase in AgeAccelPheno/AgeAccelGrim was associated with a 0.01ml[95%CI:0.01,0.02]/0.03ml[95%CI:0.01,0.05] lower mean FEV1. In NSHD, AgeAccelPheno and AgeAccelGrim at 53 years were associated with age-related decline in performance between 53 and 69 years as tested by linear mixed models (p<0.05). In a subset of NSHD participants(n=482), there was little evidence that change in any AgeAccel measure was associated with change in performance conditional on baseline performance.

Conclusions

We found little evidence to support associations between the first generation of DNAm-based biomarkers of ageing and age-related physical or cognitive performance in mid-life to early old age. However, there was evidence that the second generation biomarkers, AgeAccelPheno and AgeAccelGrim, could act as makers of an individual’s health-span as proposed.
Rare palaeomagnetic evidence of long-term mantle control of the geodynamo and possible role of the NAD field in the reversal process
Authors: Hoffman Kenneth A , Camps Pierre , Carlton Matt
Published: October 2019

The degree to which the lowermost mantle influences behaviour of the geodynamo has been debated over the past quarter century. Our analysis of a comprehensive set of 17 Cenozoic palaeomagnetic transitional field records obtained from lavas in the Southern Hemisphere provides robust evidence of stable mantle control since the Pliocene. The records come from a region where—given a significantly weakened axial dipole—the magnetic field today would be largely controlled by the non-axial dipole (NAD) flux patch currently emanating from Earth's outer core beneath western Australia. The palaeomagnetic recording sites from west to east include the south Indian Ocean, eastern Australia, New Zealand and French Polynesia. The analysed records contain from 2 to 26 sequential transitional virtual geomagnetic poles (VGPs). 10 of the 17 records supply at least one VGP within a narrow longitudinal band 10°-wide between 60°S and the equator, centred along 102.4°E. That is, transitional data from 59 per cent of the Cenozoic recordings are found to reside in a region that encompasses a mere 2.8 per cent of the VGP transitional area on Earth's surface. A robust Monte Carlo approach applied to this data set, one that takes into account the number of transitional VGPs contained in each record, finds this result highly improbable (p-value = 0.0006). The present-day pattern of vertical flux at the core–mantle boundary shows an anomalously strong, thin Southern Hemisphere longitudinal band off the west coast of Australia that strikingly coincides with this unusual palaeomagnetic finding. We conclude with a high degree of confidence that this band of flux has remained virtually unmoved for at least the past 3 Myr. Seemingly independent of the behaviour of the axial dipole, our findings indicate that it has dominated the magnetic field over an area of considerable size during attempts by the geodynamo to reverse polarity.
Sources of uncertainties and artifacts in back-projection results
Authors: Hongyu Zeng , Shengji Wei , Wenbo Wu
Published: October 2019

Back-projecting high-frequency (HF) waves is a common procedure for imaging rupture processes of large earthquakes (i.e. Mw > 7.0). However, obtained back-projection (BP) results could suffer from large uncertainties since high-frequency seismic waveforms are strongly affected by factors like source depth, focal mechanisms, and the Earth's 3D velocity structures. So far, these uncertainties have not been thoroughly investigated. Here, we use synthetic tests to investigate the influencing factors for which scenarios with various source and/or velocity set-ups are designed, using either Tohoku-Oki (Japan), Kaikoura (New Zealand), Java/Wharton Basin (Indonesia) as test areas. For the scenarios, we generate either 1D or 3D teleseismic synthetic data, which are then back-projected using a representative BP method, MUltiple SIgnal Classification (MUSIC). We also analyze corresponding real cases to verify the synthetic test results. The Tohoku-Oki scenario shows that depth phases of a point source can be back-projected as artifacts at their bounce points on the earth's surface, with these artifacts located far away from the epicenter if earthquakes occur at large depths, which could significantly contaminate BP images of large intermediate-depth earthquakes. The Kaikoura scenario shows that for complicated earthquakes, composed of multiple sub-events with varying focal mechanisms, BP tends to image sub-events emanating large amplitude coherent waveforms, while missing sub-events whose P nodal directions point to the arrays, leading to discrepancies either between BP images from different arrays, or between BP images and other source models. Using the Java event, we investigate the impact of 3D source-side velocity structures. The 3D bathymetry together with a water layer can generate strong and long-lasting coda waves, which are mirrored as artifacts far from the true source location. Finally, we use a Wharton Basin outer-rise event to show that the wavefields generated by 3D near trench structures contain frequency-dependent coda waves, leading to frequency-dependent BP results. In summary, our analyses indicate that depth phases, focal mechanism variations, and 3D source-side structures can affect various aspects of BP results. Thus, we suggest that target-oriented synthetic tests, for example, synthetic tests for subduction earthquakes using more realistic 3D source-side velocity structures, should be conducted to understand the uncertainties and artifacts before we interpret detailed BP images to infer earthquake rupture kinematics and dynamics.
Genome-wide heritability analysis of severe malaria resistance reveals evidence of polygenic inheritance
Authors: Damena Delesa , Chimusa Emile R
Published: October 2019

Background: Estimating single nucleotide polymorphism (SNP)-heritability (h2g) of severe malaria resistance and its distribution across the genome might shed new light in to the underlying biology. Method: We investigated h2g of severe malaria resistance from a genome-wide association study (GWAS) dataset (sample size = 11 657). We estimated the h2g and partitioned in to chromosomes, allele frequencies and annotations using the genetic relationship-matrix restricted maximum likelihood approach. We further examined non-cell type-specific and cell type-specific enrichments from GWAS-summary statistics. Results: The h2g of severe malaria resistance was estimated at 0.21 (se = 0.05, P = 2.7 × 10−5), 0.20 (se = 0.05, P = 7.5 × 10−5) and 0.17 (se = 0.05, P = 7.2 × 10−4) in Gambian, Kenyan and Malawi populations, respectively. A comparable range of h2g [0.21 (se = 0.02, P < 1 × 10−5)] was estimated from GWAS-summary statistics meta-analysed across the three populations. Partitioning analysis from raw genotype data showed significant enrichment of h2g in genic SNPs while summary statistics analysis suggests evidences of enrichment in multiple categories. Supporting the polygenic inheritance, the h2g of severe malaria resistance is distributed across the chromosomes and allelic frequency spectrum. However, the h2g is disproportionately concentrated on three chromosomes (chr 5, 11 and 20), suggesting cost-effectiveness of targeting these chromosomes in future malaria genomic sequencing studies. Conclusion: We report for the first time that the heritability of malaria resistance is largely ascribed by common SNPs and the causal variants are overrepresented in protein coding regions of the genome. Further studies with larger sample sizes are needed to better understand the underpinning genetics of severe malaria resistance.
Rational or Irrational Decision? Examination on Gamers’ Intention to Purchase Probability-Type Items
Authors: Seo Young-nam , Jung Younbo , Sng Jeremy , Park Jongmin
Published: October 2019

Expanding the theory of planned behavior (TPB) model with non-volitional factors, this study investigated determinants of purchase intention (PI) for probability-type items (PTI) in a popular mobile game. An online survey was conducted with 534 players of Summoners War. The overall results show that the PI of PTI is associated with both rational and impulsive factors. Specifically, the results of hierarchical regression analysis demonstrate that along with two TPB elements (attitude and perceived control), individual factors of self-control and general stress, as well as game-related factors of advancement, competition, purchase frequency and spending amount were all significant predictors of PTI PI. These non-volitional factors account for additional 18% of variance out of 48% total variance (R2 = .48) in PI.
Tandem amplification of the vanM gene cluster drives vancomycin resistance in vancomycin-variable enterococci
Authors: Sun Lingyan , Chen Yan , Hua Xiaoting , Chen Yiyi , Hong Jinjing , Wu Xueqing , Jiang Yan , van Schaik Willem , Qu Tingting , Yu Yunsong
Published: October 2019

Background

Vancomycin-variable enterococci (VVE) are a potential risk factor for vancomycin resistance gene dissemination and clinical treatment failure. vanM has emerged as a new prevalent resistance determinant among clinical enterococci in China. A total of 54 vancomycin-susceptible enterococci (VSE) isolates carrying incomplete vanM gene clusters were isolated in our previous study.

Objectives

To determine the potential of vanM-carrying VSE to develop vancomycin resistance and investigate the mechanism of alteration of the resistance phenotype.

Methods

Fifty-four vanM-positive VSE strains were induced in vitro by culturing in increasing concentrations of vancomycin. Genetic changes between three parent VVE strains and their resistant variants were analysed using Illumina and long-read sequencing technologies, quantitative PCR and Southern blot hybridization. Changes in expression level were determined by quantitative RT–PCR.

Results

Twenty-five of the 54 VSE strains carrying vanM became resistant upon vancomycin exposure. A significant increase in vanM copy number was observed ranging from 5.28 to 127.64 copies per cell in induced resistant VVE strains. The vanM transposon was identified as tandem repeats with IS1216E between them, and occurred in either the plasmid or the chromosome of resistant VVE cells. In addition, an increase in vanM expression was observed after resistance conversion in VVE.

Conclusions

This study identified tandem amplification of the vanM gene cluster as a new mechanism for vancomycin resistance in VVE strains, offering a competitive advantage for VVE under antibiotic pressure.
Regrafting of the Split-Thickness Skin Graft Donor-Site: Is It Beneficial?
Authors: Legemate Catherine M , Lucas Ymke , Oen Irma M M H , Van Der Vlies Cornelis H
Published: October 2019

Split-thickness skin grafting remains a fundamental treatment for patients with deep burns and other traumatic injuries. Unfortunately, the donor site wound that remains after split skin graft (SSG) harvesting may also cause problems for the patient; they can lead to discomfort and scars with a poor cosmetic outcome. Regrafting of the donor site is one of the methods described to improve donor site healing and scarring. In this report, we describe a case of a 26-year-old woman with a self-inflicted chemical burn (0.5% TBSA) who underwent split skin grafting. During surgery, only part of the donor site was regrafted with split skin graft remnants. This part healed faster and had a better scar quality at 3 months postsurgery. Nevertheless, the appearance and patients’ opinion on the regrafted part deteriorated after 12 months. With this case report, we aim to create awareness of the long-term consequences of regrafting, which may differ from short-time results. Patients expected to have poor reepithelialization potential may benefit from regrafting of the SSG on the donor site. But in healthy young individuals, timewise there would be no benefit since it can lead to an aesthetically displeasing result.
Biology and Management of the New Zealand Endemic Wheat Bug, Nysius huttoni (Hemiptera: Lygaeidae)
Authors: Tiwari Sundar , Wratten Steve D
Published: October 2019

The wheat bug, Nysius huttoni White, mainly reported as a pest of wheat and forage brassicas, is native to New Zealand. This pest has been accidentally introduced into The Netherland and Belgium during apple exports from New Zealand. The bug population is abundant in open sparse vegetations and hot-dry habitats, and feeds on dropping seeds. It damages wheat grains during milk-ripe stage by piercing through the glumes into the developing grains that can reduce gluten protein and reduce baking quality. Bugs also suck phloem fluid from seedlings, which can reduce plant establishment in forage brassicas. Early scouting and field monitoring are suggested before making pest management decisions. Seed treatment with neonicotinoids, permethrin, and chlorpyrifos spray in the standing crops are chemical methods of management in New Zealand. These conventional synthetic pesticides have nontarget effects on human health, the environment, and biodiversity. However, preventive measures such as the use of less-susceptible cultivars, and using potential trap crops is other important pest management options. Alyssum (Lobularia maritima L. Desv. Brassicales: Brassicaceae) and wheat (Triticum aestivum L. Poales: Poaceae) are two potential trap crops of wheat bug. Kale (Brassica oleracea L.) cultivars, such as Corka and Regal, and wheat (Triticum aestivum) cultivars, such as Batten, Domino, and Oroua, are less-susceptible cultivars. Understanding the biology and ecology of the pest, and utilizing preventative pest management measures such as the use of trap crops and less-susceptible cultivars, and integrating these with ‘soft’ chemicals make a suitable integrated pest management strategy for this pest.
Comparative Analysis of Transcriptome Responses to Cold Stress in Galeruca daurica (Coleoptera: Chrysomelidae)
Authors: Zhou Xiao-Rong , Shan Yan-Min , Tan Yao , Zhang Zhuo-Ran , Pang Bao-Ping
Published: October 2019

Galeruca daurica (Joannis) has become a new insect pest in the Inner Mongolia grasslands since 2009, and its larvae and eggs have strong cold tolerance. To get a deeper insight into its molecular mechanisms of cold stress responses, we performed de novo transcriptome assembly for G. daurica by RNA-Seq and compared the transcriptomes of its larvae exposed to five different temperature treatments (−10, −5, 0, 5, and 25°C for 1 h and then recovered at 25°C for 1 h), respectively. Compared with the control (25°C), the numbers of differentially expressed genes (DEGs) decreased from 1,821 to 882, with the temperature declining from 5 to −10°C. Moreover, we obtained 323 coregulated DEGs under different low temperatures. Under four low temperatures (−10, −5, 0, and 5°C), a large number of genes were commonly upregulated during recovery from cold stresses, including those related to cuticle protein, followed by cytochrome P450, clock protein, fatty acid synthase, and fatty acyl-CoA reductase; meanwhile, lots of genes encoding cuticle protein, RNA replication protein, RNA-directed DNA polymerase, and glucose dehydrogenase were commonly downregulated. Our findings provide important clues for further investigations of key genes and molecular mechanisms involved in the adaptation of G. daurica to harsh environments.