bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species
Authors: Maughan Peter J. , Lee Rebekah , Walstead Rachel , Vickerstaff Robert J. , Fogarty Melissa C. , Brouwer Cory R. , Reid Robert R. , Jay Jeremy J. , Bekele Wubishet A. , Jackson Eric W. , Tinker Nicholas A. , Langdon Tim , Schlueter Jessica A. , Jellen Eric N. 
Published: November 2019

AbstractBackgroundCultivated hexaploid oat (Common oat;Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes,Avena atlanticaandAvena eriantharespectively. The diploidAvenaspecies serve as important genetic resources for improving common oat’s adaptive and food quality characteristics.ResultsTheA. atlanticaandA. erianthagenome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species—including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genomeAvenaspecies.ConclusionsThe genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.
Midbrain microglia mediate a specific immunosuppressive response under inflammatory conditions
Authors: Abellanas Miguel Angel , Zamarbide Marta , Basurco Leyre , Luquin Esther , Garcia-Granero Marta , Clavero Pedro , San Martin-Uriz Patxi , Vilas Amaia , Mengual Elisa , Hervas-Stubbs Sandra , Aymerich Maria S. 
Published: November 2019

Abstract
Background
Inflammation is a critical process for the progression of neuronal death in neurodegenerative disorders. Microglia play a central role in neuroinflammation and may affect neuron vulnerability. Next generation sequencing has shown the molecular heterogeneity of microglial cells; however, the variability in their response to pathological inputs remains unknown.

Methods
To determine the effect of an inflammatory stimulus on microglial cells, lipopolysaccharide (LPS) was administered peripherally to mice and the inflammatory status of the cortex, hippocampus, midbrain, and striatum was assessed. Microglial activation and interaction with the immune system were analyzed in single cell suspensions obtained from the different brain regions by fluorescence-activated cell sorting, next generation RNA sequencing, real-time PCR, and immunohistochemical techniques. Antigen-presenting properties of microglia were evaluated by the ability of isolated cells to induce a clonal expansion of CD4+ T cells purified from OT-II transgenic mice.

Results
Under steady-state conditions, the midbrain presented a high immune-alert state characterized by the presence of two unique microglial subpopulations, one expressing the major histocompatibility complex class II (MHC-II) and acting as antigen-presenting cells and another expressing the toll-like receptor 4 (TLR4), and by the presence of a higher proportion of infiltrating CD4+ T cells. This state was not detected in the cortex, hippocampus, or striatum. Systemic LPS administration induced a general increase in classic pro-inflammatory cytokines, in co-inhibitory programmed death ligand 1 (PD-L1), and in cytotoxic T lymphocyte antigen 4 (CTLA-4) receptors, as well as a decrease in infiltrating effector T cells in all brain regions. Interestingly, a specific immune-suppressive response was observed in the midbrain which was characterized by the downregulation of MHC-II microglial expression, the upregulation of the anti-inflammatory cytokines IL10 and TGFβ, and the increase in infiltrating regulatory T cells.

Conclusions
These data show that the midbrain presents a high immune-alert state under steady-state conditions that elicits a specific immune-suppressive response when exposed to an inflammatory stimulus. This specific inflammatory tone and response may have an impact in neuronal viability.
The interplay between m6A RNA methylation and noncoding RNA in cancer
Authors: Ma Shuai , Chen Chen , Ji Xiang , Liu Jinbo , Zhou Quanbo , Wang Guixian , Yuan Weitang , Kan Quancheng , Sun Zhenqiang 
Published: November 2019

AbstractN6-methyladenosine (m6A) methylation, one of the most common RNA modifications, has been reported to execute important functions that affect normal life activities and diseases. Most studies have suggested that m6A modification can affect the complexity of cancer progression by regulating biological functions related to cancer. M6A modification of noncoding RNAs regulates the cleavage, transport, stability, and degradation of noncoding RNAs themselves. It also regulates cell proliferation and metastasis, stem cell differentiation, and homeostasis in cancer by affecting the biological function of cells. Interestingly, noncoding RNAs also play significant roles in regulating these m6A modifications. Additionally, it is becoming increasingly clear that m6A and noncoding RNAs potentially contribute to the clinical application of cancer treatment. In this review, we summarize the effect of the interactions between m6A modifications and noncoding RNAs on the biological functions involved in cancer progression. In particular, we discuss the role of m6A and noncoding RNAs as possible potential biomarkers and therapeutic targets in the treatment of cancers.
Kagami–Ogata syndrome in a fetus presenting with polyhydramnios, malformations, and preterm delivery: a case report
Authors: Huang Haipeng , Mikami Yukiko , Shigematsu Kosuke , Uemura Nozomi , Shinsaka Mamiko , Iwatani Ayaka , Miyake Fumihito , Kabe Kazuhiko , Takai Yasushi , Saitoh Masahiro , Baba Kazunori , Seki Hiroyuki 
Published: November 2019

Abstract
Background
Kagami–Ogata syndrome is also known as paternal uniparental disomy 14 and related disorders and is caused by abnormal genomic imprinting in the long arm of the chromosome 14q32.2 region. Its clinical manifestations include polyhydramnios in the fetal stage, respiratory insufficiency because of a small thorax, abdominal wall abnormalities, and peculiar facial features after birth.

Case presentation
A 38-year-old Japanese primigravida woman was referred to our hospital in the 19th week of pregnancy for suspected omphalocele. She had a history of hypothyroidism but was prescribed orally administered levothyroxine (50 μg/day) prior to conception and was euthyroid. Her ultrasound scan prior to visiting our hospital revealed fetal omphalocele, heavy for date, and polyhydramnios. The mother was advised to be admitted for observation from 28 weeks of gestation for threatened premature delivery. She required amniodrainage at 29 and 32 weeks of gestation. At 35 weeks of gestation, the fetal membrane prematurely ruptured and she gave birth after an emergency Cesarean section. The infant was a male child with a birth weight of 3188 g, and was suspected to have Kagami–Ogata syndrome after birth based on thoracic hypoplasia, swallowing function abnormalities, and peculiar facial features. A definitive diagnosis was established by performing genetic testing of the infant after obtaining informed written consent from both the parents; the results of the genetic testing revealed hypermethylated intergenic-differentially methylated region and maternally expressed gene 3-differentially methylated region in the corresponding chromosome 14 region. Both the parents were genetically tested after adequate genetic counseling, which revealed a de novo microdeletion in a differentially methylated region.

Conclusion
Kagami–Ogata syndrome should have been suspected because of the presence of polyhydramnios and omphalocele during pregnancy. Respiratory insufficiency soon after birth, because of a small thorax, is expected in this disease and a diagnosis during pregnancy may have enabled appropriate care after birth.
Association of IKZF1 SNPs in cold medicine-related Stevens–Johnson syndrome in Thailand
Authors: Chantaren Patchima , Jongkhajornpong Passara , Ueta Mayumi , Puangsricharern Vilavun , Lekhanont Kaevalin , Pisuchpen Phattrawan , Prabhasawat Pinnita , Suphapeetiporn Kanya , Kinoshita Shigeru 
Published: November 2019

Abstract
Purpose
Our meta-analysis of several ethnic groups (Japanese, Korean, Indian, Brazilian) revealed a significant genome-wide association between cold medicine-related SJS/TEN (CM-SJS/TEN) with severe ocular complications (SOC) and IKZF1 SNPs, suggesting that IKZF1 might be a potential marker for susceptibility to CM-SJS/TEN with SOC. In this study, we examined the association between CM-SJS/TEN with SOC and the IKZF1 SNPs in the Thai population.

Methods
57 CM-SJS/TEN with SOC and 171 control samples were collected at Chulalongkorn University and Mahidol University. Genomic DNA samples were genotyped for the IKZF1 SNPs at Kyoto Prefectural University of Medicine in Japan using the TaqMan SNP genotyping assay.

Results
The four SNPs previously reported to be associated with CM-SJS/TEN with SOC in the Japanese were examined in the Thai samples. Although the number of Thai cases (n = 57) was small, a significant association between CM-SJS/TEN with SOC and IKZF1 SNPs which included rs4917014 (T vs G, OR = 2.9, p = 0.0012, Pc = 0.0049), rs4917129 (T vs C, OR = 2.8, p = 0.0026, Pc = 0.010) and rs10276619 (G vs A, OR = 1.8, p = 0.012, Pc = 0.048) was identified.

Conclusion
In addition to the Japanese, Korean and Indian populations, Thai cases with CM-SJS/TEN and SOC were significantly associated with IKZF1 SNPs. With our previous report of the critical role of IKZF1 in mucocutaneous inflammation, these results suggest that IKZF1 is important in the pathogenesis of CM-SJS/TEN with SOC.
Adrenocortical adenoma in a Sudanese girl with Beckwith-Wiedemann syndrome
Authors: Elnaw Eman Abdalla Ali , Abdalla Awad Rhmattalla , Abdullah Mohamed Ahmed 
Published: November 2019

Abstract
Background
We report a case of right adrenocortical adenoma in a girl with features suggestive of Beckwith Wiedemann syndrome to show the importance of tumor surveillance in patients with Beckwith Wiedemann syndrome.

Case presentation
A 4-years-old female with features suggestive of Beckwith-Wiedemann syndrome presented with 9 months history of virilization. Hormonal investigations results showed high levels of testosterone (2.3 ng/ml, normal values 0.1–0.4 ng/ml), and DHEAS (73 ng/ml normal values 1-6 ng/ml) with normal cortisol level. Computed tomography revealed a right adrenal mass. She underwent right adrenalectomy. Histopathological examination of the resected adrenal gland showed adrenocortical adenoma. Her postoperative evaluation showed a normal testosterone level.

Conclusion
Adrenocortical neoplasms though rare in children are well documented in Beckwith-Wiedemann syndrome patients. So tumor surveillance protocol should be employed, even in a resource-limited setting for early tumor detection and a better outcome.
A retrospective analysis of risk factors of oromaxillofacial infection in patients presenting to a hospital emergency ward
Authors: Park Jinyoung , Lee Jae-Yeol , Hwang Dae-Seok , Kim Yong-Deok , Shin Sang-Hun , Kim Uk-Kyu , Song Jae-Min 
Published: November 2019

Abstract
Background
The purpose of this study was to review the clinical features of oromaxillofacial infections in patients presenting to a hospital emergency ward, to identify the key factors affecting the requirement for hospitalization, and the potential risk factors predisposing to a prolonged length of hospital stay.

Methods
A retrospective medical record review of the 598 patients treated for oromaxillofacial infection from 2013 to 2017 at the oral and maxillofacial surgery department, Yangsan Pusan National University Hospital, was conducted. The following information was collected from each patient: sex, age, past medical history, site of infection, etiology, admission or outpatient care, level of C-reactive protein (mg/dL), fascial spaces involved, treatment method, and duration of hospitalization. Chi-squared tests were used to identify risk factors, which were further analyzed using multivariable logistic regression.

Results
A total of 606 patients were eligible for inclusion in the study, of which eight were excluded due to having incomplete charts; thus, 598 patients were included: 55% were male, mean patient age was 47.1 ± 19.9 years, and 12.9% of patients were diabetic. Furthermore, 71.2% of patients had infection originating in the mandible; the most common tooth of origin was lower posterior, and 29.8% of patients were hospitalized. Risk factors for hospital admission were elderly patients with concurrent disease, elevated C-reactive protein level, and multiple-space infection in the oromaxillofacial area. The duration of hospitalization was correlated with both diabetes and age.

Conclusions
The requirement for hospital admission is determined by the severity of the infection; even severe infections, once treated with appropriate surgery, have no relation to the length of hospital stay. The important risk factors for increased duration of hospitalization are diabetes mellitus and older age. The understanding of risk factors associated with a prolonged hospital stay during the treatment of oromaxillofacial infection will aid in treatment planning as well as highlight the importance of adequate diabetes control in patients at risk of such infection.
Understanding disasters: managing and accommodating different worldviews in humanitarian response
Authors: Clarke Matthew , Parris Brett W. 
Published: November 2019

AbstractOver the past decade, humanitarian events affected on average 120 million people annually. Whilst many of these events are human-induced, a large number of the 400 or so complex humanitarian emergencies that require international response each year are natural. Such events result in loss of life, injure and maim survivors, destroy infrastructure and give rise to psycho-social trauma. Aid agencies working alongside affected communities must address all these consequences as part of their responses. What is also required though is an appreciation that worldviews will inform how affected communities both understand the cause of the event, their role in the event and how they will subsequently participate in rebuilding or reconstruction programs. Disasters can be affected by religious beliefs. With more than 85% of the global population self-professing religious belief, these worldviews are often shaped in whole or in part by sacred texts, religious teachings and sectarian practices. In this regard, it is not uncommon for those affected by disasters (particularly natural disasters) to genuinely describe these events as ‘acts of God’. Effective responses require the local context to be central in assessing needs and determining capacities. This must include an understanding of and authentic engagement with religious beliefs and how this may affect how the humanitarian event interacts with these beliefs. There is though little evidence as to how professional humanitarian workers accommodate the religious beliefs of local populations in their planning, implementation and evaluation of humanitarian responses. This paper draws on the experiences of humanitarian workers based in the USA and Australia from both faith-based and secular international non-governmental organizations to consider both how these workers themselves accommodate the religious views of affected communities in their responses and also their experience as to how such views affect the effectiveness of responses. This paper will consider why aid agencies must incorporate (and appreciate) different worldviews around disasters in order to more effectively respond to the needs of communities affected by humanitarian events. It will also identify difficulties and opportunities experienced by individual humanitarian practitioners as well as agencies when working in such environments.
Systematic review and meta-analysis of fire regime research in ponderosa pine (Pinus ponderosa) ecosystems, Colorado, USA
Authors: McKinney Shawn T. 
Published: November 2019

Abstract
Background
Forest management, especially restoration, is informed by understanding the dominant natural disturbance regime. In many western North American forests, the keystone disturbance is fire, and a plethora of research exists characterizing various fire regime parameters, although often only one or two parameters are addressed in individual studies. I performed a systematic review of the literature and meta-analysis of the derived data from 26 publications to characterize five parameters of the historical fire regime of ponderosa pine (Pinus ponderosa Lawson & C. Lawson) ecosystems in Colorado, USA: fire frequency, severity, extent, seasonality, and climate.

Results
The collection of evidence indicates a fire regime predominantly characterized by moderate to high frequency, low- and mixed-severity fires that occurred in late summer to fall, with fires occurring in drier than average years that were often preceded by two to three years of wetter than average conditions. The overall average mean fire return interval (MFI) was 21 years (SD = 1.4 years, n = 78 sites) and increased with site elevation (r = 0.33, P < 0.05). Low- and mixed-severity fires accounted for 83% of all observations, and 69% of fires occurred in late summer to fall with no relationship found between latitude and seasonality. Geographic region (Front Range and southwestern Colorado) was associated with variability in fire regime parameter values, with southwestern Colorado sites having a stronger association with wetter than average conditions in the three years preceding fire years and a shorter mean MFI (18 years) relative to Front Range sites (23 years). Data were insufficient to evaluate changes in fire severity and extent due to a lack of historical information, as well as differences in sampling methods and reporting.

Conclusion
This meta-analytic approach identified variation within and among fire regime parameter values that occurred along elevational and geographic axes, and this information should be useful to managers engaging in forest restoration aimed at enhancing resilience of fire-adapted forests to disturbance and climate change.
Sex-Dependent Mechanisms of Glucocorticoid Regulation of the Mouse Hypothalamic Corticotropin-Releasing Hormone Gene
Authors: Heck Ashley L , Thompson Maranda K , Uht Rosalie M , Handa Robert J 
Published: November 2019

Abstract
To limit excessive glucocorticoid secretion following hypothalamic-pituitary-adrenal (HPA) axis stimulation, circulating glucocorticoids inhibit corticotropin-releasing hormone (CRH) expression in paraventricular nucleus (PVN) neurons. As HPA function differs between sexes and depends on circulating estradiol (E2) levels in females, we investigated sex/estrous stage-dependent glucocorticoid regulation of PVN Crh. Using NanoString nCounter technology, we first demonstrated that adrenalectomized (ADX’d) diestrous female (low E2), but not male or proestrous female (high E2), mice exhibited a robust decrease in PVN CRH mRNA following 2-day treatment with the glucocorticoid receptor (GR) agonist RU28362. Immunohistochemical analysis of PVN CRH neurons in Crh-IRES-Cre;Ai14 mice, where TdTomato fluorescence permanently tags CRH-expressing neurons, showed similarly abundant co-expression of GR-immunoreactivity in males, diestrous females, and proestrous females. However, we identified sex/estrous stage-related glucocorticoid regulation or expression of GR transcriptional coregulators. Out of 17 coregulator genes examined using nCounter multiplex analysis, mRNAs that were decreased by RU28362 in ADX’d mice in a sex/estrous stage-dependent fashion included: GR (males = diestrous females &gt; proestrous females), signal transducer and activator of transcription 3 (STAT3) (males &lt; diestrous = proestrous), and HDAC1 (males &lt; diestrous &gt; proestrous). Steroid receptor coactivator 3 (SRC-3), nuclear corepressor 1 (NCoR1), heterogeneous nuclear ribonucleoprotein U (hnrnpu), CREB binding protein (CBP) and CREB-regulated transcription coactivator 2 (CRTC2) mRNAs were lower in ADX’d diestrous and proestrous females versus males. Additionally, most PVN CRH neurons co-expressed methylated CpG binding protein 2 (MeCP2)-immunoreactivity in diestrous female and male Crh-IRES-Cre;Ai14 mice. Our findings collectively suggest that GR’s sex-dependent regulation of PVN Crh may depend upon differences in the GR transcriptional machinery and an underlying influence of E2 levels in females.