bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of primary headache disorder on quality of life among school students in Kuwait
Authors: Al-Hashel Jasem Y. , Alroughani R. , Shuaibi S. , AlAshqar A. , AlHamdan F. , AlThufairi H. , Owayed S. , Ahmed Samar F. 
Published: June 2020

AbstractBackgroundPrimary headache disorders have being increasingly reported in younger populations. They can have significant effects on their quality of life and academic achievement and may cause significant distress to their families.Aims and objectivesTo assess the burden of primary headache disorder and its impact on the quality of life on school student in Kuwait.MethodsAcross-sectional study was conducted among Kuwaiti primary and middle school students of both genders in randomly selected schools located in two governorates in 2018/2019 academic year. Headache-Attributed Restriction, Disability, Social Handicap and Impaired Participation (HARDSHIP) questionnaire for children and adolescents was used to assess the impact of primary headaches on the quality of life.ResultsOne thousand and ninety-one questionnaires were completed by primary and middle school students of both genders; of whom 466 students (girls 321 (68.88%) were diagnosed with primary headache disorders with mean age 11.98 ± 2.03 years. In the month prior to the survey, the effect of the headache was variable. The students lost a mean of 1.99 ± 2.015 days of school while they could not perform their usual activities for a mean of 2.84 ± 4.28 days. Their parents lost a mean of 2 ± 2.03 days of work because of headaches of their children and parents prohibited 5.7% of the students to engage in any activity due to their headaches. Difficulties in concentrations were reported as never sometimes (39.1%), often (24.8%), and always (26%). Majority of the students (51.5%) experienced a feeling of sadness ranging from sometimes to always. Most of the students (67.3%) struggled to cope with the headache and 22.4% were never able to cope. Additionally, 19.4% of students reported they did not want others noticing their headache.ConclusionPrimary headache disorder can have a significant impact on the quality of life in children. It can affect their engagement in activities and academic achievement. Implementing strategies to properly manage schoolchildren with primary headaches can have profound effects on their quality of life.
Migraine start, course and features over the cycle of combined hormonal contraceptive users with menstrual migraine – temporal relation to bleeding and hormone withdrawal: a prospective diary-based study
Authors: Merki-Feld Gabriele S. , Caveng Nina , Speiermann Gina , MacGregor E. Anne 
Published: June 2020

Abstract
Background
Many studies have described the features of menstrually-related migraines (MRM) in the natural cycle and the efficacy of prevention. MRM in combined hormonal contraceptive (CHC) users has scarcely been researched. Estrogen and progestin withdrawal in CHC users are both more abrupt and from higher hormone levels compared with the natural cycle. An advantage for prevention of MRM in CHC users is that the hormone withdrawal is predictable. It is unknown, whether the attacks during the hormone-free interval are associated with the hormone withdrawal or onset of bleeding. Improved understanding of this relation might contribute to better define and shorten the time interval for prevention.

Methods
For this prospective diary-based trial we collected migraine and bleeding data from CHC users with MRM in at least two of three cycles. We analyzed frequency of migraines over the whole CHC cycle. During the hormone-free phase the relation between onset of migraine and onset of bleeding was studied. We compared pain intensity and identified prolonged-migraine attacks during hormone use and the hormone-free phase.

Results
During the hormone-free interval the number of migraine days and the pain score/migraine day were significantly higher in comparison with the mean during hormone use. The prevalence of migraine attacks was fourfold on hormone-free days 3–6. Migraine typically started on days 1–4. Migraine in relation to bleeding mostly occurred on days − 1 to + 4. In 78% of the cycles the first migraine day occurred during bleeding days 1 ± 2 and 48% started on days − 1 and day 1. The predictability of the first bleeding day was very high.

Conclusion
The day of hormone-withdrawal migraine and the first bleeding day are highly predictable in CHC users. Migraine onset is mostly day − 1 and 1 of the bleeding and on days 1–4 of the hormone-free interval. Migraine attacks of CHC users in the hormone-free interval are severe and long lasting. Further trials are necessary to investigate if this knowledge can be used to optimise prevention.
Effects of a postnatal Atrx conditional knockout in neurons on autism-like behaviours in male and female mice
Authors: Martin-Kenny Nicole , Bérubé Nathalie G. 
Published: June 2020

Abstract
Background
Alpha-thalassemia/mental retardation, X-linked, or ATRX, is an autism susceptibility gene that encodes a chromatin remodeler. Mutations of ATRX result in the ATR-X intellectual disability syndrome and have been identified in autism spectrum disorder (ASD) patients. The mechanisms by which ATRX mutations lead to autism and autistic-like behaviours are not yet known. To address this question, we generated mice with postnatal Atrx inactivation in excitatory neurons of the forebrain and performed a battery of behavioural assays that assess autistic-like behaviours.

Methods
Male and female mice with a postnatal conditional ablation of ATRX were generated using the Cre/lox system under the control of the αCaMKII gene promoter. These mice were tested in a battery of behavioural tests that assess autistic-like features. We utilized paradigms that measure social behaviour, repetitive, and stereotyped behaviours, as well as sensory gating. Statistics were calculated by two-way repeated measures ANOVA with Sidak’s multiple comparison test or unpaired Student’s t tests as indicated.

Results
The behaviour tests revealed no significant differences between Atrx-cKO and control mice. We identified sexually dimorphic changes in odor habituation and discrimination; however, these changes did not correlate with social deficits.

Conclusion
The postnatal knockout of Atrx in forebrain excitatory neurons does not lead to autism-related behaviours in male or female mice.
The effect of natural materials used as sediment remediation on phosphorus and nitrogen control in a mesocosm
Authors: Tang Mengjuan , Deng Qinghui , Li Xiaowen , Cao Xiuyun , Zhang Zhimin , Zhou Yiyong , Sun Qingye , Song Chunlei 
Published: June 2020

Abstract
Background
Achieving nitrogen (N) and phosphorus (P) control in sediment remediation projects by adding natural materials is receiving increasing attention. In this study, different natural materials, including iron-rich clay minerals, calcite, kaoline, sugarcane bagasse and Phragmites detritus, were applied to test their effects on N and P in a mesocosm experiment.

Results
Iron-rich clay minerals and Phragmites detritus had obvious advantages for P control; they resulted in almost undetectable levels of soluble reactive phosphorus (SRP) in the water column throughout the experiment. This finding can be explained by their strong P adsorption ability. The high level of available organic carbon in the sediment and water column after sugarcane bagasse addition provided enough electron donors for denitrification and dissimilatory nitrate reduction to ammonium (DNRA), which caused nitrate (NO3−-N) deficiency and ammonium (NH4+-N) accumulation in the water column. Additionally, this resulted in anaerobic conditions, further fuelling the release of P from iron-bound P induced by anoxia. Thus, the amount of sugarcane bagasse applied should be considered carefully in order to balance denitrification and DNRA as well as P releases. Calcite and Phragmites detritus are recommended as remediation materials for N removal based on their significant promotion of denitrification and limitation of DNRA, which resulted in low NO3−-N and NH4+-N levels. These results can be explained by the shifts in the functional microbial community composition and abundance after the addition of natural materials.

Conclusions
Iron-rich clay minerals and Phragmites detritus are promising sediment remediation materials for P immobilization due to their strong P adsorption ability. Taken together, the selection of sediment remediation materials should consider the N and P coupling relationship, to prevent NO3−-N removal from causing P leaching or NH4+-N accumulation.
Mercury distribution in the surface soil of China is potentially driven by precipitation, vegetation cover and organic matter
Authors: Zhang Zhao-Yang , Li Gang , Yang Lei , Wang Xin-Jun , Sun Guo-Xin 
Published: June 2020

Abstract
Background
Understanding the mechanism of Hg accumulation in soil, which is a net Hg sink, at a national scale is important for protecting the environment and improving food safety. The mercury (Hg) distribution in surface soil in China is quite uneven, with relatively high concentrations in southeastern China and low concentrations in northwestern China. The reason for this distribution is inconclusive, especially at the continental scale. In this study, the relative contributions of the key impact factors, including dry and wet deposition, soil organic matter (SOM) and solar radiation to soil Hg, were evaluated.

Results
Wet and dry deposition associated with precipitation and vegetation cover and emissions influenced by SOM are key factors controlling Hg distribution in surface soil. In southeastern China, high levels of wet deposition associated with the South Asia monsoon and dry deposition, enhanced by vegetation canopies, together with low levels of emissions caused by highly vegetated surfaces and solar radiation, are responsible for the high Hg levels in soil (> 0.08 mg/kg). In northeastern China, moderate levels of wet Hg deposition, high levels of dry deposition via throughfall and litterfall, low emissions due to weak solar radiation and high levels of SOM are responsible for high Hg accumulation in soil. In northwestern China, low levels of wet deposition, together with high emissions levels, low vegetation cover (bare soil) and SOM and strong solar radiation, contributed to the low Hg level in the surface soil (< 0.03 mg/kg).

Conclusions
We suggest that wet deposition derived from the Asian monsoon, dry deposition linked to vegetated surfaces and Hg emissions associated with vegetation cover, SOM and solar radiation play key roles in the soil Hg level in China. In other terrestrial environments worldwide, especially in regions with significantly high levels of wet deposition and high amounts of vegetation cover and soil SOM, high Hg concentrations may exist in the surface soil.
FSBC: fast string-based clustering for HT-SELEX data
Authors: Kato Shintaro , Ono Takayoshi , Minagawa Hirotaka , Horii Katsunori , Shiratori Ikuo , Waga Iwao , Ito Koichi , Aoki Takafumi 
Published: June 2020

AbstractBackgroundThe combination of systematic evolution of ligands by exponential enrichment (SELEX) and deep sequencing is termed high-throughput (HT)-SELEX, which enables searching aptamer candidates from a massive amount of oligonucleotide sequences. A clustering method is an important procedure to identify sequence groups including aptamer candidates for evaluation with experimental analysis. In general, aptamer includes a specific target binding region, which is necessary for binding to the target molecules. The length of the target binding region varies depending on the target molecules and/or binding styles. Currently available clustering methods for HT-SELEX only estimate clusters based on the similarity of full-length sequences or limited length of motifs as target binding regions. Hence, a clustering method considering the target binding region with different lengths is required. Moreover, to handle such huge data and to save sequencing cost, a clustering method with fast calculation from a single round of HT-SELEX data, not multiple rounds, is also preferred.ResultsWe developed fast string-based clustering (FSBC) for HT-SELEX data. FSBC was designed to estimate clusters by searching various lengths of over-represented strings as target binding regions. FSBC was also designed for fast calculation with search space reduction from a single round, typically the final round, of HT-SELEX data considering imbalanced nucleobases of the aptamer selection process. The calculation time and clustering accuracy of FSBC were compared with those of four conventional clustering methods, FASTAptamer, AptaCluster, APTANI, and AptaTRACE, using HT-SELEX data (>15 million oligonucleotide sequences). FSBC, AptaCluster, and AptaTRACE could complete the clustering for all sequence data, and FSBC and AptaTRACE performed higher clustering accuracy. FSBC showed the highest clustering accuracy and had the second fastest calculation speed among all methods compared.ConclusionFSBC is applicable to a large HT-SELEX dataset, which can facilitate the accurate identification of groups including aptamer candidates.Availability of data and materialsFSBC is available athttp://www.aoki.ecei.tohoku.ac.jp/fsbc/.
CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination
Authors: Bobay Louis-Marie 
Published: June 2020

Abstract
Background
Prokaryotes are asexual, but these organisms frequently engage in homologous recombination, a process that differs from meiotic recombination in sexual organisms. Most tools developed to simulate genome evolution either assume sexual reproduction or the complete absence of DNA flux in the population. As a result, very few simulators are adapted to model prokaryotic genome evolution while accounting for recombination. Moreover, many simulators are based on the coalescent, which assumes a neutral model of genomic evolution, and those are best suited for organisms evolving under weak selective pressures, such as animals and plants. In contrast, prokaryotes are thought to be evolving under much stronger selective pressures, suggesting that forward-in-time simulators are better suited for these organisms.

Results
Here, I present CoreSimul, a forward-in-time simulator of core genome evolution for prokaryotes modeling homologous recombination. Simulations are guided by a phylogenetic tree and incorporate different substitution models, including models of codon selection.

Conclusions
CoreSimul is a flexible forward-in-time simulator that constitutes a significant addition to the limited list of available simulators applicable to prokaryote genome evolution.
Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites
Authors: Cheng Jin-Tao , Cao Fei , Chen Xin-Ai , Li Yong-Quan , Mao Xu-Ming 
Published: June 2020

Abstract
Background
Secondary metabolites as natural products from endophytic fungi are important sources of pharmaceuticals. However, there is currently little understanding of endophytic fungi at the omics levels about their potential in secondary metabolites. Calcarisporium arbuscula, an endophytic fungus from the fruit bodies of Russulaceae, produces a variety of secondary metabolites with anti-cancer, anti-nematode and antibiotic activities. A comprehensive survey of the genome and transcriptome of this endophytic fungus will help to understand its capacity to biosynthesize secondary metabolites and will lay the foundation for the development of this precious resource.

Results
In this study, we reported the high-quality genome sequence of C. arbuscula NRRL 3705 based on Single Molecule Real-Time sequencing technology. The genome of this fungus is over 45 Mb in size, larger than other typical filamentous fungi, and comprises 10,001 predicted genes, encoding at least 762 secretory-proteins, 386 carbohydrate-active enzymes and 177 P450 enzymes. 398 virulence factors and 228 genes related to pathogen-host interactions were also predicted in this fungus. Moreover, 65 secondary metabolite biosynthetic gene clusters were revealed, including the gene cluster for the mycotoxin aurovertins. In addition, several gene clusters were predicted to produce mycotoxins, including aflatoxin, alternariol, destruxin, citrinin and isoflavipucine. Notably, two independent gene clusters were shown that are potentially involved in the biosynthesis of alternariol. Furthermore, RNA-Seq assays showed that only expression of the aurovertin gene cluster is much stronger than expression of the housekeeping genes under laboratory conditions, consistent with the observation that aurovertins are the predominant metabolites. Gene expression of the remaining 64 gene clusters for compound backbone biosynthesis was all lower than expression of the housekeeping genes, which partially explained poor production of other secondary metabolites in this fungus.

Conclusions
Our omics data, along with bioinformatics analysis, indicated that C. arbuscula NRRL 3705 contains a large number of biosynthetic gene clusters and has a huge potential to produce a profound number of secondary metabolites. This work also provides the basis for development of endophytic fungi as a new resource of natural products with promising biological activities.
Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis
Authors: Dasgupta Pratiti , Das Abhishek , Datta Sambit , Banerjee Ishani , Tripathy Sucheta , Chaudhuri Shubho 
Published: June 2020

AbstractBackgroundCellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to other plant species originating in tropical and sub-tropical areas,indicarice is highly sensitive to low temperature that adversely affects its growth and grain productivity. Substantial work has been done to understand cold induced changes in gene expression in rice plants. However, adequate information is not available for early gene expression, especially inindicavariety. Therefore, a transcriptome profile was generated for cold shock treated seedlings of IR64 variety to identify early responsive genes.ResultsThe functional annotation of early DEGs shows enrichment of genes involved in altered membrane rigidity and electrolytic leakage, the onset of calcium signaling, ROS generation and activation of stress responsive transcription factors in IR64. Gene regulatory network suggests that cold shock induced Ca2+ signaling activates DREB/CBF pathway and other groups of transcription factors such as MYB, NAC and ZFP; for activating various cold-responsive genes. The analysis also indicates that cold induced signaling proteins like RLKs, RLCKs, CDPKs and MAPKK and ROS signaling proteins. Further, several late-embryogenesis-abundant (LEA), dehydrins and low temperature-induced-genes were upregulated under early cold shock condition, indicating the onset of water-deficit conditions. Expression profiling in different high yielding cultivars shows high expression of cold-responsive genes in Heera and CB1indicavarieties. These varieties show low levels of cold induced ROS production, electrolytic leakage and high germination rate post-cold stress, compared to IR36 and IR64. Collectively, these results suggest that these varieties may have improved adaptability to cold stress.ConclusionsThe results of this study provide insights about early responsive events inOryza sativa l.ssp. indicacv IR64 in response to cold stress. Our data shows the onset of cold response is associated with upregulation of stress responsive TFs, hydrophilic proteins and signaling molecules, whereas, the genes coding for cellular biosynthetic enzymes, cell cycle control and growth-related TFs are downregulated. This study reports that the generation of ROS is integral to the early response to trigger the ROS mediated signaling events during later stages.
Transcriptome profiling of venom gland from wasp species: de novo assembly, functional annotation, and discovery of molecular markers
Authors: Tan Junjie , Wang Wenbo , Wu Fan , Li Yunming , Fan Quanshui 
Published: June 2020

Abstract
Background
Vespa velutina, one of the most aggressive and fearful wasps in China, can cause grievous allergies and toxic reactions, leading to organ failure and even death. However, there is little evidence on molecular data regarding wasps. Therefore, we aimed to provide an insight into the transcripts expressed in the venom gland of wasps.

Results
In our study, high-throughput RNA sequencing was performed using the venom glands of four wasp species. First, the mitochondrial cytochrome C oxidase submit I (COI) barcoding and the neighbor joining (NJ) tree were used to validate the unique identity and lineage of each individual species. After sequencing, a total of 127,630 contigs were generated and 98,716 coding domain sequences (CDS) were predicted from the four species. The Gene ontology (GO) enrichment analysis of unigenes revealed their functional role in important biological processes (BP), molecular functions (MF) and cellular components (CC). In addition, c-type, p1 type, p2 type and p3 type were the most commonly found simple sequence repeat (SSR) types in the four species of wasp transcriptome. There were differences in the distribution of SSRs and single nucleotide polymorphisms (SNPs) among the four wasp species.

Conclusions
The transcriptome data generated in this study will improve our understanding on bioactive proteins and venom-related genes in wasp venom gland and provide a basis for pests control and other applications. To our knowledge, this is the first study on the identification of large-scale genomic data and the discovery of microsatellite markers from V. tropica ducalis and V. analis fabricius.
NeuroConstruct-based implementation of structured-light stimulated retinal circuitry
Authors: Elbaz Miriam , Buterman Rachel , Ezra Tsur Elishai 
Published: June 2020

Abstract
Background
Retinal circuitry provides a fundamental window to neural networks, featuring widely investigated visual phenomena ranging from direction selectivity to fast detection of approaching motion. As the divide between experimental and theoretical visual neuroscience is fading, neuronal modeling has proven to be important for retinal research. In neuronal modeling a delicate balance is maintained between bio-plausibility and model tractability, giving rise to myriad modeling frameworks. One biologically detailed framework for neuro modeling is NeuroConstruct, which facilitates the creation, visualization and analysis of neural networks in 3D.

Results
Here, we extended NeuroConstruct to support the generation of structured visual stimuli, to feature different synaptic dynamics, to allow for heterogeneous synapse distribution and to enable rule-based synaptic connectivity between cell populations. We utilized this framework to demonstrate a simulation of a dense plexus of biologically realistic and morphologically detailed starburst amacrine cells. The amacrine cells were connected to a ganglion cell and stimulated with expanding and collapsing rings of light.

Conclusions
This framework provides a powerful toolset for the investigation of the yet elusive underlying mechanisms of retinal computations such as direction selectivity. Particularly, we showcased the way NeuroConstruct can be extended to support advanced field-specific neuro-modeling.