bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptome analyses define genes and gene modules differing between two Populus genotypes with contrasting stem growth rates
Authors: Han Xiao , An Yi , Zhou Yangyan , Liu Chao , Yin Weilun , Xia Xinli 
Published: August 2020

Abstract
Background
Wood provides an important biomass resource for biofuel production around the world. The radial growth of tree stems is central to biomass production for forestry and biofuels, but it is challenging to dissect genetically because it is a complex trait influenced by many genes. In this study, we adopted methods of physiology, transcriptomics and genetics to investigate the regulatory mechanisms of tree radial growth and wood development.

Results
Physiological comparison showed that two Populus genotypes presented different rates of radial growth of stems and accumulation of woody biomass. A comparative transcriptional network approach was used to define and characterize functional differences between two Populus genotypes. Analyses of transcript profiles from wood-forming tissue of the two genotypes showed that 1542, 2295 and 2110 genes were differentially expressed in the pre-growth, fast-growth and post-growth stages, respectively. The co-expression analyses identified modules of co-expressed genes that displayed distinct expression profiles. Modules were further characterized by correlating transcript levels with genotypes and physiological traits. The results showed enrichment of genes that participated in cell cycle and division, whose expression change was consistent with the variation of radial growth rates. Genes related to secondary vascular development were up-regulated in the faster-growing genotype in the pre-growth stage. We characterized a BEL1-like (BELL) transcription factor, PeuBELL15, which was up-regulated in the faster-growing genotype. Analyses of transgenic Populus overexpressing as well as CRISPR/Cas9-induced mutants for BELL15 showed that PeuBELL15 improved accumulation of glucan and lignin, and it promoted secondary vascular growth by regulating the expression of genes relevant for cellulose synthases and lignin biosynthesis.

Conclusions
This study illustrated that active division and expansion of vascular cambium cells and secondary cell wall deposition of xylem cells contribute to stem radial increment and biomass accumulation, and it identified relevant genes for these complex growth traits, including a BELL transcription factor gene PeuBELL15. This provides genetic resources for improving and breeding elite genotypes with fast growth and high wood biomass.
Associations of childhood exposure to malaria with cognition and behavior outcomes: a systematic review protocol
Authors: Ssemata Andrew Sentoogo , Nakitende Jacquelline Ann , Kizito Simon , Whipple Elizabeth C. , Bangirana Paul , Nakasujja Noeline , John Chandy C. , McHenry Megan S. 
Published: August 2020

Abstract
Background
Malaria is one of the major contributing risk factors for poor development of children living in low- and middle-income countries (LMICs). However, little is known about the specific domains of cognition and behavior that are impacted by malaria, the extent of these deficits, and the different types of the malaria spectrum that are associated with these deficits. The objective of this systematic review is to determine the association of the different types of malaria infection on cognition and behavioral outcomes among children living in LMICs.

Methods and analysis
We will systematically search online bibliographic databases including MEDLINE (via PubMed), CINAHL (via EBSCO), PsycINFO (via EBSCO), Embase, and The Cochrane Central Register of Controlled Trials (CENTRAL) as well as Google Scholar and bibliographies of pertinent articles. We will include studies with a comparison group (e.g., clinical trials, cohort, observational, cross-sectional case–control, and controlled before and after or interrupted–time–series studies) involving children under 18 years of age living in LMICs, as determined by the World Bank criteria, with either an active malaria infection or history of malaria. Included articles must also measure cognitive and/or behavior outcomes determined by standardized psychological assessments (questionnaire-based scales and or neurocognitive assessments). Studies will be excluded if they are not in English, lack a control group, take place in a high-income country, or if a standardized instrument was not used. Two reviewers will independently review all articles to determine if they meet eligibility criteria. Any conflicts will be resolved after discussion with a third reviewer. When a list of included articles is finalized, two reviewers will extract data to populate and then cross check within an electronic table. Risk of bias and the strength of evidence and recommendations will be assessed independently using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) criteria, and a final score will be given upon consensus. For sufficiently homogeneous data on measured outcomes in multiple studies, we will investigate the possibility of pooling data to perform a meta-analysis.

Discussion
This systematic review will evaluate the evidence of the association of malaria on the cognitive and behavioral outcomes. Findings from this planned review will generate insight on the domains affected by the different forms of malaria infection and may inform subsequent malaria interventions and future research in pediatric care.

Systematic review registration
PROSPERO CRD42020154777
Don’t click: towards an effective anti-phishing training. A comparative literature review
Authors: Jampen Daniel , Gür Gürkan , Sutter Thomas , Tellenbach Bernhard 
Published: August 2020

AbstractEmail is of critical importance as a communication channel for both business and personal matters. Unfortunately, it is also often exploited for phishing attacks. To defend against such threats, many organizations have begun to provide anti-phishing training programs to their employees. A central question in the development of such programs is how they can be designed sustainably and effectively to minimize the vulnerability of employees to phishing attacks. In this paper, we survey and categorize works that consider different elements of such programs via a clearly laid-out methodology, and identify key findings in the technical literature. Overall, we find that researchers agree on the answers to many relevant questions regarding the utility and effectiveness of anti-phishing training. However, we identified influencing factors, such as the impact of age on the success of anti-phishing training programs, for which mixed findings are available. Finally, based on our comprehensive analysis, we describe how a well-founded anti-phishing training program should be designed and parameterized with a set of proposed research directions.
Cloud spot instance price prediction using kNN regression
Authors: Liu Wenqiang , Wang Pengwei , Meng Ying , Zhao Caihui , Zhang Zhaohui 
Published: August 2020

AbstractCloud computing can provide users with basic hardware resources, and there are three instance types: reserved instances, on-demand instances and spot instances. The price of spot instance is lower than others on average, but it fluctuates according to market demand and supply. When a user requests a spot instance, he/she needs to give a bid. Only if the bid is not lower than the spot price, user can obtain the right to use this instance. Thus, it is very important and challenging to predict the price of spot instance. To this end, we take the most popular and representative Amazon EC2 as a testbed, and use the price history of its spot instance to predict future price by building a k-Nearest Neighbors (kNN) regression model, which is based on our mathematical description of spot instance price prediction problem. We compare our model with Linear Regression (LR), Support Vector Machine Regression (SVR), Random Forest (RF), Multi-layer Perception Regression (MLPR), gcForest, and the experiments show that our model outperforms the others.
Bioleaching of Zn from sphalerite using Leptospirillum ferriphilum isolate: effect of temperature and kinetic aspects
Authors: Sundramurthy Venkatesa Prabhu , Rajoo Baskar , Srinivasan Natesan Rajendran , Kavitha Rajan 
Published: August 2020

AbstractBiological methods for leaching of nonferrous and noble metals from its sulfide ores are widely applied at industrial enterprises of different countries. This process is based on the use of the oxidative activity of acidophilic microorganisms. Since all bio systems are quite sensitive to the temperature, bacterial leaching process also significantly effects. In the present study, the impact of temperature on bacterial leaching of Zn from its sulphide ore, sphalerite, was investigated using ore adapted iron oxidizing bacteria. The bacteria were isolated from mine drainage samples and subjected to gene sequencing. The acquired nucleotide sequence revealed that the isolate was Leptospirillum ferriphilum. The nucleotide sequence of L. ferriphilum isolate was submitted to National Center for Biotechnology Information (NCBI) and accession number KF743135 was assigned. Using the isolate, the Zn leaching data were collected in the 298–318 K temperature range. The results showed that leaching of Zn increases with temperature until optimum temperature of 313 K and achieves highest leaching efficiency of 96.96% within 20 days. Since bioleaching of minerals have become increasingly applied in different mining industries, there is immense important to analyze mechanistically-based kinetics for the design, optimization, operation, and control of biochemical processes. The kinetic study showed that the rate of Zn leaching was maximized at the optimum temperature. Further, the leaching data were analyzed using shrinking core model which revealed that the rate of leaching was inhibited by diffusion through product layer. Reaction kinetics is also to be contrasted with thermodynamics. Using Arrhenius law of thermodynamics, it was found that activation energy for Zn bioleaching reaction was 39.557 kJ mol−1. Such investigations will be necessitated for designing and implanting the ideal bioleaching system for metal bio-mining industries.
Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community
Authors: Panwar Pratibha , Allen Michelle A. , Williams Timothy J. , Hancock Alyce M. , Brazendale Sarah , Bevington James , Roux Simon , Páez-Espino David , Nayfach Stephen , Berg Maureen , Schulz Frederik , Chen I-Min A. , Huntemann Marcel , Shapiro Nicole , Kyrpides Nikos C. , Woyke Tanja , Eloe-Fadrosh Emiley A. , Cavicchioli Ricardo 
Published: August 2020

Abstract
Background
Cold environments dominate the Earth’s biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000–7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles.

Results
The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts.

Conclusion
Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems.
Identification of predation events in wild fish using novel acoustic transmitters
Authors: Weinz Amy A. , Matley Jordan K. , Klinard Natalie V. , Fisk Aaron T. , Colborne Scott F. 
Published: August 2020

Abstract
Background
Acoustic telemetry is a commonly used tool to gain knowledge about aquatic animal ecology through the study of their movements. In telemetry studies researchers must make inferences regarding the movements and the fates of tagged animals. Until recently, predation has been inferred in telemetry data using a variety of methods including abrupt changes in movement patterns or habitat use. An acoustic telemetry transmitter has been developed to detect predation events of tagged animals, and while they have performed well in controlled laboratory trials, literature regarding the application of these novel transmitters in field settings is limited. The objective of this research was to describe the detection data obtained from field studies using predation tags and propose methods to incorporate this information in decision-making about the fate of tagged animals. We implanted 60 yellow perch (Perca flavescens) with predation transmitters and evaluated their spatial use in a receiver array (34 ha) using a combination of centres of activity, roaming indices, and step length measures to examine detection data.

Results
Over 5 months, 19 apparent predation events were identified by the transmitters. Roaming indices and centres of activity revealed a variety of detection patterns, including instances of altered behaviour before and after predation that matched tag-indentified predation events, dropped tags post-predation, and detections that ceased post-predation indicating the predator might have left the array. Based on the observed patterns, probable predation was inferred for 15 of 19 triggered tags, with unclear fates for four fish.

Conclusions
Our study provided a framework to assess the fate of animals tagged with predation transmitters and demonstrate how these tags can contribute to telemetry studies. We showed how detections can be categorized using tag status to compare movement metrics among individuals, provided tools to explore space use surrounding predation events, and synthesized this information to inform uncertainty surrounding tag-identified predation events. Predation tags do not remove all uncertainty about the fate of tagged individuals, but combined with other metrics they increase the likelihood of identifying abnormal movements that could otherwise introduce biased detection histories into studies of small-sized fishes.
Improving access to and effectiveness of mental health care for personality disorders: the guideline-informed treatment for personality disorders (GIT-PD) initiative in the Netherlands
Authors: Hutsebaut Joost , Willemsen Ellen , Bachrach Nathan , Van Rien 
Published: August 2020

AbstractEvidence-based treatment for patients suffering from personality disorders (PDs) is only available to a limited extend in the Netherlands. Consequently, most patients receive non-manualized, unspecialized care.This manuscript describes the background, rationale and design of the Guideline-Informed Treatment for Personality Disorders (GIT-PD) initiative. GIT-PD aims to provide a simple, principle-driven, ‘common-factors’ framework for the treatment of PDs. The GIT-PD framework integrates scientific knowledge, professional expertise and patient experience to design a good-enough practice, based on common factors. It offers a basic framework including general principles, a structured clinical pathway, a basic professional stance, interventions focused on common factors, and team and organizational strategies, based on common features of evidence-based treatments and generic competences of professionals.The GIT-PD initiative has had a large impact on the organization of treatment for PDs in the Netherlands. For countries with an interest in improving their health care system for PDs, it could serve as a template that requires only limited resources.
Management of medical emergencies in orthodontic practice
Authors: Amiri Bavandpour M. , Livas C. , Jonkman R. E. G. 
Published: August 2020

Abstract
Background
The aims of this study were to survey the occurrence of acute medical situations in Dutch orthodontic practice and to examine the self-perceived competence of orthodontists in managing acute medical emergencies.

Methods
A self-designed questionnaire was distributed among all 149 Dutch orthodontists attending the spring meeting of the Dutch Society for Orthodontists. The questionnaire was divided into three parts, addressing background information of the orthodontist, precautions against and experiences in acute medical situations, and self-perceived competence of nine common medical emergencies. The statistical analysis was performed using the chi-square test and a multiple logistic regression analysis.

Results
The response rate was 74.5% (105 out of 149). The male to female ratio in this population was 55:50. Mean age of all participants was 46.9 years (SD 10.4 years) with on average 16.7 years of working experience (SD 10.6 years). The most common medical emergency reported by Dutch orthodontists was vasovagal collapse (n = 219), followed by acute allergic reaction (n = 163) and hyperventilation (n = 83). On average, 75% (n = 79) of the orthodontists felt competent to handle any acute medical situation with an average occurrence of 0.36 acute medical emergencies per orthodontist per year. Male participants were more likely to send patients towards the emergency department (p = 0.049). Moreover, a statistically significant negative correlation was observed between self-perceived competence handling hypoglycemia and years of clinical experience. The longer orthodontists were clinically active, the less competent they felt when encountered with a hypoglycemia (p = 0.031).

Conclusions
Medical emergencies may be rare but challenging occurrences in the orthodontic practice. It is strongly recommended for all orthodontists and supporting staff to be trained regularly in the management of medical emergencies and to possess up-to-date evidence-based knowledge. Familiarity with and availability of appropriate drugs and equipment are deemed essential to the management of acute medical emergencies that may arise in the orthodontic practice.
The p48 MW flow modulation device for treatment of unruptured, saccular intracranial aneurysms: a single center experience from 77 consecutive aneurysms
Authors: AlMatter Muhammad , Henkes Elina , Sirakov Alexander , Aguilar Pérez Marta , Hellstern Victoria , Serna Candel Carmen , Ganslandt Oliver , Henkes Hans 
Published: August 2020

Abstract
Background
The p48 MW Flow Modulation Device (phenox, Bochum Germany) is a low profile flow diverter stent (FDS), designed for implantation into intracranial arteries with a diameter of less than 3.5 mm.

Objective
To evaluate the safety and efficacy of the p48 MW FDS in the treatment of unruptured aneurysms located at intracranial arteries with less than 3.5 mm diameter based on a retrospective analysis from a single tertiary neurovascular center.

Methods
A prospectively maintained database was retrospectively reviewed to identify all cases of intracranial saccular aneurysms treated electively with the p48 MW device. Records were made of basic demographics, aneurysmal characteristics, interventional procedures, adverse events, clinical outcomes and occlusion rates on angiographic follow-ups.

Results
A total of 77 aneurysms and 74 patients were included. The mean size of the treated aneurysms was 3.5 ± 2.4 mm and the mean aspect ratio was 1.3 ± 0.4. A total of 80 endovascular procedures were performed with a total of 12 (15%) adverse events leading to two (2.5%) permanent morbidities/mortalities. Technical issues were encountered in 3 (3.9%) cases. Adequate occlusion of the treated aneurysm was recorded in 55.6% and 63.9% on the first and latest available DSA follow-ups, respectively. There were no cases of side-branch occlusion.

Conclusions
The p48 MW is an easy-to-use implant with very good safety margins. Side branch occlusion and significant in-stent stenosis are infrequently encountered. The time from implantation to sufficient aneurysm occlusion takes longer than with FDS with lower porosity.
Sexually Dimorphic Crosstalk at the Maternal-Fetal Interface
Authors: Sun Tianyanxin , Gonzalez Tania L , Deng Nan , DiPentino Rosemarie , Clark Ekaterina L , Lee Bora , Tang Jie , Wang Yizhou , Stripp Barry R , Yao Changfu , Tseng Hsian-Rong , Karumanchi S Ananth , Koeppel Alexander F , Turner Stephen D , Farber Charles R , Rich Stephen S , Wang Erica T , Williams John , Pisarska Margareta D 
Published: August 2020

AbstractContextCrosstalk through receptor ligand interactions at the maternal-fetal interface is impacted by fetal sex. This affects placentation in the first trimester and differences in outcomes. Sexually dimorphic signaling at early stages of placentation are not defined.ObjectiveInvestigate the impact of fetal sex on maternal-fetal crosstalk.DesignReceptors/ligands at the maternal-fetal surface were identified from sexually dimorphic genes between fetal sexes in the first trimester placenta and defined in each cell type using single-cell RNA-Sequencing (scRNA-Seq).SettingAcademic institution.SamplesLate first trimester (~10-13 weeks) placenta (fetal) and decidua (maternal) from uncomplicated ongoing pregnancies.Main outcome measuresTranscriptomic profiling at tissue and single-cell level; immunohistochemistry of select proteins.ResultsWe identified 91 sexually dimorphic receptor-ligand pairs across the maternal-fetal interface. We examined fetal sex differences in 5 major cell types (trophoblasts, stromal cells, Hofbauer cells, antigen-presenting cells, and endothelial cells). Ligands from the CC family chemokine ligand (CCL) family were most highly representative in females, with their receptors present on the maternal surface. Sexually dimorphic trophoblast transcripts, Mucin-15 (MUC15) and notum, palmitoleoyl-protein carboxylesterase (NOTUM) were also most highly expressed in syncytiotrophoblasts and extra-villous trophoblasts respectively. Gene Ontology (GO) analysis using sexually dimorphic genes in individual cell types identified cytokine mediated signaling pathways to be most representative in female trophoblasts. Upstream analysis demonstrated TGFB1 and estradiol to affect all cell types, but dihydrotestosterone, produced by the male fetus, was an upstream regulator most significant for the trophoblast population.ConclusionsMaternal-fetal crosstalk exhibits sexual dimorphism during placentation early in gestation.