bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symptomatic carotid web in a female patient
Authors: Krasteva Marina P , Diamantaras Andreas A , Siller Teresa , Mordasini Pasquale , Heldner Mirjam R 
Published: July 2020

We describe a 47-year-old female patient with a carotid web and ischemic stroke. A carotid web is a membrane-like shelf of tissue, predominantly affecting the intimal layer of the arterial wall, usually extending from the posterolateral wall of the carotid artery into the lumen, typically at the origin of the internal carotid artery just beyond the bifurcation. It is considered to be an under-recognized etiology of ischemic stroke in young and middle-aged patients. Typically, these patients do not show any coexistent or only few vascular risk factors. Digital subtraction angiography, computer tomography angiography, magnetic resonance angiography, and color-coded duplex sonography are able to identify carotid webs. Therapy strategies include conservative therapy with intake of antiplatelet agents and anticoagulants, or carotid endarterectomy or carotid artery stenting. Optimal therapy strategy remains open. A considerable rate of recurrent cerebrovascular ischemic events has been reported in patients with a symptomatic carotid web and conservative therapy. More data are needed on prevalence, diagnosis, prognosis and therapy of patients with an asymptomatic or a symptomatic carotid web. Subject Codes: [13] Cerebrovascular Disease/Stroke, [44] Acute Cerebral Infarction, [193] Clinical Studies
Influence of headache pain intensity and frequency on migraine-related disability in chronic migraine patients treated with OnabotulinumtoxinA
Authors: Torres-Ferrus Marta , Gallardo Victor José , Alpuente Alicia , Pozo-Rosich Patricia 
Published: July 2020

Abstract
Background
There is a need to establish which are the more relevant headache-related outcomes that have an impact on our patient’s lives to accurately evaluate treatment response in daily clinical practice.

Objective
The aim of this study was to evaluate the relevance of clinical trial endpoints in clinical real-life disability improvement in response to migraine preventive treatment with OnabotulinumtoxinA.

Methods
This is an observational prospective study. We included patients with chronic migraine fulfilling ICHD-3beta/3 criteria. We prospectively collected data of 8 headache-related and acute medication use endpoints recommended by the Guidelines of the International Headache Society for controlled trials of preventive treatment of chronic migraine. We evaluated their impact on disability improvement after 6 months of treatment with OnabotulinumtoxinA. We defined as a responder in disability, patients with ≥50% MIDAS score reduction after 2 cycles of treatment following PREEMPT protocol. We performed an analysis to measure the impact of improvement in the evaluated outcome measures according to perceived disability in clinical practice.

Results
We included 395 patients (85.1% women, mean age 46.7 ± 12.6 years). Mean headache frequency at baseline was 26.5 ± 5.2 headache days/month. After 6 months, 49.1% of patients were headache-related disability responders. From all outcome measures collected, variables independently associated to disability improvement were headache days reduction (p = 0.02) and ≥ 50% pain intensity reduction (p = 0.04). A ≥ 50% reduction in headache frequency or pain intensity showed similar influence on disability improvement after treatment.

Conclusions
Headache pain intensity is as important as frequency when evaluating the clinical response and impact on patient headache-related disability after migraine preventive treatment with OnabotulinumtoxinA.
Is there a reliable brain morphological signature for migraine?
Authors: Wang Hong Zhou , Wang Wan Hua , Shi Hai Cun , Yuan Cong Hu 
Published: July 2020

AbstractVoxel-based morphometry (VBM) is a popular non-invasive magnetic resonance imaging technique to investigate brain gray matter (GM) differences between groups. Recently, two VBM studies in migraine have been published in The Journal of Headache and Pain. Reviewing the two and those previous published VBM studies, we found considerable variations of the results. Spatially diverse brain regions with decreased and increased GM alterations and null findings have been reported. It is interesting to know whether there is a reliable brain morphological signature for migraine. Coordinate-based meta-analysis (CBMA) is increasingly used to quantitatively pool individual neuroimaging studies to identify consistent and reliable findings. Several CBMA have been conducted, however, their results were inconsistent. The algorithms for CBMA have evolved and more eligible VBM studies in migraine have been published. We therefore conducted an updated CBMA using the latest algorithms for CBMA, seed-based d mapping with permutation of subject images (SDM-PSI). The present CBMA of 32 VBM studies (41 datasets comprising 1252 patients and 1025 healthy controls) found no evidence of consistent GM alterations in migraine. Sensitivity analysis, subgroup meta-analyses, and meta-regression analyses revealed that the result was robust. This negative result indicates that there is no reliable brain morphological signature for migraine. VBM investigations in migraine remain a heterogeneous field. Many potential confounding factors, such as underpowered sample sizes, variations in demographic and clinical characteristics, and differences in MRI scanners, head coils, scanning parameters, preprocessing procedures, and statistical strategies may cause the inconsistences of the results. Future VBM studies are warranted to enroll well-characterized and homogeneous subtype samples with appropriate sample sizes, comprehensively assess comorbidities and medication status, and use well-validated and standardized imaging protocols and processing and analysis pipelines to produce robust and replicable results in migraine.
Lifestyle behaviors and home and school environment in association with sick building syndrome among elementary school children: a cross-sectional study
Authors: Ketema Rahel Mesfin , Araki Atsuko , Ait Bamai Yu , Saito Takeshi , Kishi Reiko 
Published: July 2020

Abstract
Background
Sick building syndrome (SBS) refers to the combination of symptoms experienced by occupants of specific building characteristics. This study investigated the associations of children’s lifestyle behaviors, allergies, home, and school environment with SBS symptoms.

Methods
A total of 4408 elementary school children living in Sapporo City, Japan participated in this study. SBS was determined on parental answers to MM080 standardized school questionnaires on symptoms that were weekly experienced by these children, and if the symptom is attributed to their home or school environment. The Japanese version of the International Study of Asthma and Allergies in Childhood questionnaire was used to assess wheeze, rhino-conjunctivitis, and eczema. A logistic regression analysis was conducted to evaluate the associations between SBS symptoms and variables by controlling the potential confounders (gender, grade, school, and parental history of allergies). A stepwise backward elimination was conducted to assess independent variables related to SBS.

Results
Participants revealed mucosal (6.9%), skin (2.0%), and general (0.8%) symptoms. The presence of one or more allergy was associated with increased mucosal and skin symptoms. Children who skipped breakfast, displayed faddiness (like/dislike of food), had constipation, have insufficient sleep, did not feel refreshed after sleep, and lacked deep sleep showed significantly high odds ratios with SBS symptoms. The stepwise analysis showed faddiness for mucosal symptoms and not feeling refreshed after sleep for mucosal and skin symptoms, whereas constipation and lacking deep sleep for general symptoms were independent variables in increasing the symptoms. We found no significant relationship between SBS in children and schools. Considering children’s home, old building, no ventilation, wall-to-wall carpet, and heavy nearby traffic were associated with elevated mucosal symptom, while living in a multifamily home increased general symptoms. Home dampness was an independent variable in increasing all SBS symptoms.

Conclusions
Allergies and lifestyle behaviors were associated with increased SBS in children, including skipping breakfast, displaying faddiness, constipation, insufficient sleep, not feeling refreshed after sleep, and the lack of deep sleep. Further, dampness at home was associated with increase in all SBS symptoms. Lifestyle (e.g., eating and sleeping habits) and home (i.e., dampness) improvements might alleviate SBS symptoms in children.
WSL9 Encodes an HNH Endonuclease Domain-Containing Protein that Is Essential for Early Chloroplast Development in Rice
Authors: Zhu Xingjie , Mou Changling , Zhang Fulin , Huang Yunshuai , Yang Chunyan , Ji Jingli , Liu Xi , Cao Penghui , Nguyen Thanhliem , Lan Jie , Zhou Chunlei , Liu Shijia , Jiang Ling , Wan Jianmin 
Published: July 2020

Abstract
Background
The plant chloroplast is essential for photosynthesis and other cellular processes, but an understanding of the biological mechanisms of plant chloroplast development are incomplete.

Results
A new temperature-sensitive white stripe leaf 9(wsl9) rice mutant is described. The mutant develops white stripes during early leaf development, but becomes green after the three-leaf stage under field conditions. The wsl9 mutant was albinic when grown at low temperature. Gene mapping of the WSL9 locus, together with complementation tests indicated that WSL9 encodes a novel protein with an HNH domain. WSL9 was expressed in various tissues. Under low temperature, the wsl9 mutation caused defects in splicing of rpl2, but increased the editing efficiency of rpoB. Expression levels of plastid genome-encoded genes, which are transcribed by plastid-coded RNA polymerase (PEP), chloroplast development genes and photosynthesis-related genes were altered in the wsl9 mutant.

Conclusion
WSL9 encodes an HNH endonuclease domain-containing protein that is essential for early chloroplast development. Our study provides opportunities for further research on regulatory mechanisms of chloroplast development in rice.
Keras R-CNN: library for cell detection in biological images using deep neural networks
Authors: Hung Jane , Goodman Allen , Ravel Deepali , Lopes Stefanie C. P. , Rangel Gabriel W. , Nery Odailton A. , Malleret Benoit , Nosten Francois , Lacerda Marcus V. G. , Ferreira Marcelo U. , Rénia Laurent , Duraisingh Manoj T. , Costa Fabio T. M. , Marti Matthias , Carpenter Anne E. 
Published: July 2020

AbstractBackgroundA common yet still manual task in basic biology research, high-throughput drug screening and digital pathology is identifying the number, location, and type of individual cells in images. Object detection methods can be useful for identifying individual cells as well as their phenotype in one step. State-of-the-art deep learning for object detection is poised to improve the accuracy and efficiency of biological image analysis.ResultsWe createdKeras R-CNNto bring leading computational research to the everyday practice of bioimage analysts.Keras R-CNNimplements deep learning object detection techniques using Keras and Tensorflow (https://github.com/broadinstitute/keras-rcnn). We demonstrate the command line tool’s simplified Application Programming Interface on two important biological problems, nucleus detection and malaria stage classification, and show its potential for identifying and classifying a large number of cells. For malaria stage classification, we compare results with expert human annotators and find comparable performance.ConclusionsKeras R-CNNis a Python package that performs automated cell identification for both brightfield and fluorescence images and can process large image sets. Both the package and image datasets are freely available on GitHub and the Broad Bioimage Benchmark Collection.
Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea
Authors: Garg Kritika M. , Chattopadhyay Balaji , Koane Bonny , Sam Katerina , Rheindt Frank E. 
Published: July 2020

Abstract
Background
Quaternary climate fluctuations are an engine of biotic diversification. Global cooling cycles, such as the Last Glacial Maximum (LGM), are known to have fragmented the ranges of higher-latitude fauna and flora into smaller refugia, dramatically reducing species ranges. However, relatively less is known about the effects of cooling cycles on tropical biota.

Results
We analyzed thousands of genome-wide DNA markers across an assemblage of three closely related understorey-inhabiting scrubwrens (Sericornis and Aethomyias; Aves) from montane forest along an elevational gradient on Mt. Wilhelm, the highest mountain of Papua New Guinea. Despite species-specific differences in elevational preference, we found limited differentiation within each scrubwren species, but detected a strong genomic signature of simultaneous population expansions at 27-29 ka, coinciding with the onset of the LGM.

Conclusion
The remarkable synchronous timing of population expansions of all three species demonstrates the importance of global cooling cycles in expanding highland habitat. Global cooling cycles have likely had strongly different impacts on tropical montane areas versus boreal and temperate latitudes, leading to population expansions in the former and serious fragmentation in the latter.
Detecting fitness epistasis in recently admixed populations with genome-wide data
Authors: Ni Xumin , Zhou Mengshi , Wang Heming , He Karen Y. , Broeckel Uli , Hanis Craig , Kardia Sharon , Redline Susan , Cooper Richard S. , Tang Hua , Zhu Xiaofeng 
Published: July 2020

Abstract
Background
Fitness epistasis, the interaction effect of genes at different loci on fitness, makes an important contribution to adaptive evolution. Although fitness interaction evidence has been observed in model organisms, it is more difficult to detect and remains poorly understood in human populations as a result of limited statistical power and experimental constraints. Fitness epistasis is inferred from non-independence between unlinked loci. We previously observed ancestral block correlation between chromosomes 4 and 6 in African Americans. The same approach fails when examining ancestral blocks on the same chromosome due to the strong confounding effect observed in a recently admixed population.

Results
We developed a novel approach to eliminate the bias caused by admixture linkage disequilibrium when searching for fitness epistasis on the same chromosome. We applied this approach in 16,252 unrelated African Americans and identified significant ancestral correlations in two pairs of genomic regions (P-value< 8.11 × 10− 7) on chromosomes 1 and 10. The ancestral correlations were not explained by population admixture. Historical African-European crossover events are reduced between pairs of epistatic regions. We observed multiple pairs of co-expressed genes shared by the two regions on each chromosome, including ADAR being co-expressed with IFI44 in almost all tissues and DARC being co-expressed with VCAM1, S1PR1 and ELTD1 in multiple tissues in the Genotype-Tissue Expression (GTEx) data. Moreover, the co-expressed gene pairs are associated with the same diseases/traits in the GWAS Catalog, such as white blood cell count, blood pressure, lung function, inflammatory bowel disease and educational attainment.

Conclusions
Our analyses revealed two instances of fitness epistasis on chromosomes 1 and 10, and the findings suggest a potential approach to improving our understanding of adaptive evolution.
Genome analyses provide insights into the evolution and adaptation of the eukaryotic Picophytoplankton Mychonastes homosphaera
Authors: Liu Changqing , Shi Xiaoli , Wu Fan , Ren Mingdong , Gao Guang , Wu Qinglong 
Published: July 2020

Abstract
Background
Picophytoplankton are abundant and can contribute greatly to primary production in eutrophic lakes. Mychonastes species are among the common eukaryotic picophytoplankton in eutrophic lakes. We used third-generation sequencing technology to sequence the whole genome of Mychonastes homosphaera isolated from Lake Chaohu, a eutrophic freshwater lake in China.

Result
The 24.23 Mbp nuclear genome of M.homosphaera, harboring 6649 protein-coding genes, is more compact than the genomes of the closely related Sphaeropleales species. This genome streamlining may be caused by a reduction in gene family number, intergenic size and introns. The genome sequence of M.homosphaera reveals the strategies adopted by this organism for environmental adaptation in the eutrophic lake. Analysis of cultures and the protein complement highlight the metabolic flexibility of M.homosphaera, the genome of which encodes genes involved in light harvesting, carbohydrate metabolism, and nitrogen and microelement metabolism, many of which form functional gene clusters. Reconstruction of the bioenergetic metabolic pathways of M.homosphaera, such as the lipid, starch and isoprenoid pathways, reveals characteristics that make this species suitable for biofuel production.

Conclusion
The analysis of the whole genome of M. homosphaera provides insights into the genome streamlining, the high lipid yield, the environmental adaptation and phytoplankton evolution.
Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites
Authors: Dougherty Michael W. , Kudin Oleksandr , Mühlbauer Marcus , Neu Josef , Gharaibeh Raad Z. , Jobin Christian 
Published: July 2020

Abstract
Background
The intestinal tract undergoes a period of cellular maturation during early life, primarily characterized by the organization of epithelial cells into specialized crypt and villus structures. These processes are in part mediated by the acquisition of microbes. Infants delivered at term typically harbor a stable, low diversity microbiota characterized by an overrepresentation of various Bacilli spp., while pre-term infants are colonized by an assortment of bacteria during the first several weeks after delivery. However, the functional effects of these changes on intestinal epithelium homeostasis and maturation remain unclear. To study these effects, human neonate feces were obtained from term and pre-term infants. Fecal 16S rDNA sequencing and global untargeted LC-MS were performed to characterize microbial composition and metabolites from each population. Murine enteral organoids (enteroids) were cultured with 0.22 μm filtered stool supernatant pooled from term or pre-term infants.

Results
Term and pre-term microbial communities differed significantly from each other by principle components analysis (PCoA, PERMANOVA p < 0.001), with the pre-term microbiome characterized by increased OTU diversity (Wilcox test p < 0.01). Term communities were less diverse and dominated by Bacilli (81.54%). Pre-term stools had an increased abundance of vitamins, amino acid derivatives and unconjugated bile acids. Pathway analysis revealed a significant increase in multiple metabolic pathways in pre-term samples mapped to E. coli using the KEGG database related to the fermentation of various amino acids and vitamin biosynthesis. Enteroids cultured with supernatant from pre-term stools proliferated at a higher rate than those cultured with supernatant from term stools (cell viability: 207% vs. 147.7%, p < 0.01), grew larger (area: 81,189μm2 vs. 41,777μm2, p < 0.001), and bud at a higher rate (6.5 vs. 4, p < 0.01). Additionally, genes involved in stem cell proliferation were upregulated in pre-term stool treated enteroid cultures (Lgr5, Ephb2, Ascl2 Sox9) but not term stool treated enteroids.

Conclusions
Our findings indicate that microbial metabolites from the more diverse gut microbiome associated with pre-term infants facilitate stem cell proliferation. Therefore, perturbations of the pre-term microbiota may impair intestinal homeostasis.
Tandem mass tag-based (TMT) quantitative proteomics analysis reveals the response of fine roots to drought stress in cotton (Gossypium hirsutum L.)
Authors: Xiao Shuang , Liu Liantao , Zhang Yongjiang , Sun Hongchun , Zhang Ke , Bai Zhiying , Dong Hezhong , Liu Yuchun , Li Cundong 
Published: July 2020

AbstractBackgroundCotton (Gossypium hirsutumL.) is one of the most important cash crops worldwide. Fine roots are the central part of the root system that contributes to plant water and nutrient uptake. However, the mechanisms underlying the response of cotton fine roots to soil drought remains unclear. To elucidate the proteomic changes in fine roots of cotton plants under drought stress, 70–75% and 40–45% soil relative water content treatments were imposed on control (CK) and drought stress (DS) groups, respectively. Then, tandem mass tags (TMT) technology was used to determine the proteome profiles of fine root tissue samples.ResultsDrought significantly decreased the value of average root diameter of cotton seedlings, whereas the total root length and the activities of antioxidases were increased. To study the molecular mechanisms underlying drought response further, the proteome differences between tissues under CK and DS treatments were compared pairwise at 0, 30, and 45 DAD (days after drought stress). In total, 118 differentially expressed proteins (DEPs) were up-regulated and 105 were down-regulated in the ‘DS30 versus CK30’ comparison; 662 DEPs were up-regulated, and 611 were down-regulated in the ‘DS45 versus CK45’ comparison. The functions of these DEPs were classified according to their pathways. Under early stage drought (30 DAD), some DEPs involved in the ‘Cutin, suberin, and wax synthesis’ pathway were up-regulated, while the down-regulated DEPs were mainly enriched within the ‘Monoterpenoid biosynthesis’ pathway. Forty-five days of soil drought had a greater impact on DEPs involved in metabolism. Many proteins involving ‘Carbohydrate metabolism,’ ‘Energy metabolism,’ ‘Fatty acid metabolism,’ ‘Amino acid metabolism,’ and ‘Secondary metabolite biosynthesis’ were identified as DEPs. Additionally, proteins related to ion transport, stress/defense, and phytohormones were also shown to play roles in determining the fine root growth of cotton plants under drought stress.ConclusionsOur study identified potential biological pathways and drought-responsive proteins related to stress/defense responses and plant hormone metabolism under drought stress. Collectively, our results provide new insights for further improving drought tolerance in cotton and other crops.