bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo assembly of the zucchini genome reveals a whole‐genome duplication associated with the origin of the Cucurbita genus
Authors: Montero‐Pau Javier , Blanca José , Bombarely Aureliano , Ziarsolo Peio , Esteras Cristina , Martí‐Gómez Carlos , Ferriol María , Gómez Pedro , Jamilena Manuel , Mueller Lukas , Picó Belén , Cañizares Joaquín 
Published: November 2017

SummaryThe Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high‐quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole‐genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have occurred 30 ± 4 Mya in the ancestral species that gave rise to the genus.
MEF2C mRNA expression and cognitive function in Japanese patients with Alzheimer's disease
Authors: Sao Tomoko , Yoshino Yuta , Yamazaki Kiyohiro , Ozaki Yuki , Mori Yoko , Ochi Shinichiro , Yoshida Taku , Mori Takaaki , Iga Jun‐ichi , Ueno Shu‐ichi 
Published: November 2017

AimDespite continuing research into Alzheimer's disease (AD), its pathological mechanisms and modulating factors remain unknown. Several genes influence AD pathogenesis by affecting inflammatory pathways. Myocyte‐enhancer factor 2C (MEF2C) is one such candidate gene for AD.MethodsWe examined MEF2C mRNA expression levels and methylation rates of CpG on its promoter region in peripheral leukocytes from Japanese AD patients compared with age‐ and sex‐matched control subjects.ResultsIn peripheral leukocytes, MEF2C mRNA expression levels in AD subjects were significantly lower than those in control subjects (0.86 ± 0.25 vs 0.99 ± 0.27, respectively, P = 0.007) and were correlated with the Alzheimer's Disease Assessment Scale (r = −0.345, P = 0.049) and the Mini Mental State Examination (r = 0.324, P = 0.02). No significant differences were found in methylation rates between AD and control subjects.ConclusionMEF2C mRNA expression in leukocytes may be a biological marker for cognitive decline in AD.
Renal glucosuria in schoolchildren: Clinical characteristics
Authors: Urakami Tatsuhiko , Yoda Midori , Yoshida Kei , Mine Yusuke , Aoki Masako , Suzuki Junichi 
Published: November 2017

AbstractBackgroundWe conducted an annual urine glucose screening program at schools, and diagnosed schoolchildren with diabetes at an early stage of the disease. We also identified some cases of renal glucosuria (RG), based on positive urine glucose with normal glucose tolerance.MethodsDuring 2000–2015, 3 309 631 schoolchildren participated in the screening program. The positive rate for glucosuria in the first test was approximately 0.1%, whereas on repeat urine test it was approximately 0.05%. In total 350 schoolchildren were positive for glucosuria on detailed examination. Oral glucose tolerance test (OGTT) was also used to evaluate glucose intolerance.ResultsOne hundred and two schoolchildren (29.7%) were diagnosed with diabetes, whereas RG was identified in 246 (70.3%) with normal glucose metabolism. In regard to the characteristics of RG, the percentage of boys was 50.3%, and the mean age at diagnosis was 11.2 ± 2.4 years. Twenty‐eight children (11.4%) were overweight (body mass index standard deviation score [BMI‐SDS] > +2.0 SD), whereas five (2.0%) were underweight (BMI‐SDS < −2.0 SD). First‐degree family history was suspected in 176 cases (71.5%). All RG subjects had normal glucose tolerance in the absence of insulin resistance and decreased insulin secretion (homeostasis model assessment for β‐cell function, 78.8 ± 59.5%) on OGTT.ConclusionsRG is not rare in Japanese schoolchildren with glucosuria. This disorder seems to have a strong genetic background, and to involve less growth retardation and weight loss than expected despite continuous excretion of glucose in urine.
Long‐term Genoprotection Effect of Sechium edule Fruit Extract Against UVA Irradiation in Keratinocytes
Authors: Metral Elodie , Rachidi Walid , Damour Odile , Demarne Frédéric , Bechetoille Nicolas 
Published: November 2017

AbstractPhotoprotection is essential to prevent the long‐term deleterious effects of ultraviolet (UV), including skin cancer and photoaging. So far, there has been an increase in the use of natural bioactive phytochemicals for the development of more effective skin photoprotective agents. However, the molecular mechanisms underlying the photochemoprotection activity of such compounds remain largely unknown. The objective of this study was to investigate the effects of a Sechium edule fruit extract (SEE) in terms of photoprotection against UVA in primary human keratinocytes. We found that SEE protected keratinocytes against UVA‐induced cytotoxicity, decreased the intracellular amounts of reactive oxygen species, and reduced oxidatively induced DNA lesions after UVA exposure. Furthermore, SEE decreased the induction of CPD lesions in UVA‐irradiated keratinocytes and exhibited increased DNA repair of such photoproducts at 24 h postexposure. Finally, using DNA repair biochips, we demonstrated that SEE‐treated keratinocytes had DNA enzymatic repair activities more efficient for abasic sites, CPD and thymine glycols. Therefore, the benefits of SEE against UVA could be explained by a combination of antioxidant activity, the reduction in DNA damage, and the enhancement of DNA repair capacities.
Wellington Playgrounds Uncovered: An Examination of Solar Ultraviolet Radiation and Shade Protection in New Zealand
Authors: Gage Ryan , O'Toole Chris , Robinson Andrew , Reeder Anthony , Signal Louise , Mackay Christina 
Published: November 2017

AbstractProviding effective shade in summer recreation spaces can reduce children's risk of skin cancer. This study explored the quantity and protective quality of shade in Wellington, New Zealand playgrounds. Two researchers visited 50 randomly selected playgrounds during peak ultraviolet radiation (UVR) hours in summer and recorded the mean shade cover of playground equipment, seats, tables and open areas. A solar meter was used to calculate the proportion of UVR blocked by each built structure and tree. The results found that 95% of playground equipment and 64% of sitting and eating areas had no shade protection. Trees blocked a mean of 80.1% (95% CI: 66.0–94.1) of direct solar UVR, but mostly covered open areas, not playground equipment, seats and tables. The findings demonstrate that Wellington playgrounds have insufficient shade available. Increased shade in Wellington playgrounds is urgently needed to protect children from harmful UVR exposure, particularly through planting trees with heavy foliage and building structures with large, protective roofing. This may well be the case for other regions of NZ and for other countries where UVR exposure is dangerous. The method used in this study provides a reliable means to evaluate shade.
Evaporative cooling in late gestation heat‐stressed Murrah buffaloes increases efficiency of next reproductive cycle
Authors: Aarif O , Aggarwal A , Sheikh AA 
Published: November 2017

ContentsEvaporative cooling during late gestation period improves post‐partum reproductive performance in Murrah buffaloes. To prove this hypothesis, sixteen pregnant dry Murrah buffaloes at sixty days pre‐partum were selected and divided into two groups of eight animals each. Group 1 of buffaloes (Cooled/CL) was managed under fan and mist cooling during dry period, whereas second group of buffaloes (non‐cooled/NCL) remained without the provision of cooling. After parturition, all the animals were managed under evaporative cooling till the end of experimental period. Reproductive performance in cooled (CL) and non‐cooled (NCL) groups, respectively, viz. 1st and 2nd ovulation from calving (48.63 ± 2.41, 69.25 ± 2.34 days and 57.75 ± 3.35, 93.63 ± 2.84 days); calving to conception interval (117.88 ± 4.21 days and 117.88± 4.21 days); conception rate (87.5% ± 2.16% and 57% ± 2.26%); and follicular diameter at the time of 1st and 2nd ovulation (14.84 ± 0.16, 15.75 ± 0.13 mm and 12.65 ± 0.13, 13.35 ± 0.11 mm) varied significantly (p < .05). Total peak oestrogen concentration was significantly (p < .05) higher in cooled (26.7 ± 1.32 pg/ml) relative to non‐cooled (20.7 ± 1.22 pg/ml) buffaloes. Time from onset of oestrus to ovulation varied significantly (p < .05) in cooled (32 ± 2.22 hr) and non‐cooled (40 ± 2.86 hr) buffaloes. The peak progesterone concentration reached to (4.25 ng/ml) in cooled group and (4.16 ng/ml) in non‐cooled group after first ovulation.
Morphological variation, genetic differentiation and phylogeography of the East Asia cicada Hyalessa maculaticollis (Hemiptera: Cicadidae)
Authors: LIU YUNXIANG , QIU YUE , WANG XU , YANG HUAN , HAYASHI MASAMI , WEI CONG 
Published: November 2017

AbstractThe cicada Hyalessa maculaticollis is widely distributed in East Asia, and is noted for its great morphological variability. The variation in this species and its allies has been a long‐standing controversy. The population differentiation, genetic structure and phylogeography of this species are explored based on morphological observations, mitochondrial and nuclear DNA analyses, and comparison of the calling song structure of males. Our results reveal that the abundant intraspecific morphological variations are consistent with high levels of genetic divergence in this species, but incongruence between the morphological variations and genetic divergence is found in a few lineages. Phylogenetic and network analyses indicate that H. maculaticollis is composed of two major lineages – China and Japan. The East China Sea (ECS) land bridge acted as a dispersal corridor for H. maculaticollis during the glacial period. The climatic oscillations in the Pleistocene and the terrain structure of East Asia influenced population differentiation. The divergence time between the two sides of the East China Sea is estimated to be ∼1.05 (95% CI = 0.80–1.30) Ma, which was about the same period during which the sea level increased rapidly during the ‘Ryukyu Coral Sea Stage’ (0.2–1.3 Ma). Populations of H. maculaticollis are structured phylogeographically, with the China populations differentiated into a greater number of highly structured haplogroups. Qinling Mountains and the mountainous regions around the Sichuan Basin are presumed to have been major refugia for H. maculaticollis in glacial periods, and a recent population expansion has been detected for populations distributed in the area to the north of Qinling Mountains. The high degree of haplotype and nucleotide diversity shown in East China populations suggests that the flat terrain with low‐altitude hills are suitable for the survival of H. maculaticollis. The species H. fuscata, treated as an independent species from H. maculaticollis by some researchers based on acoustic analyses of the calling song structure, is confirmed to be a junior synonym of H. maculaticollis based on the results of our analyses of morphological variation, calling song structure and acoustic playback experiments.
The influence of immunosuppressants on direct‐acting antiviral therapy is dependent on the hepatitis C virus genotype
Authors: Frey Alexandra , Piras‐Straub Katja , Walker Andreas , Timm Jörg , Gerken Guido , Herzer Kerstin 
Published: November 2017

AbstractBackgroundDirect‐acting antivirals (DAAs) have substantially increased sustained virological response rates after liver transplantation, with improved tolerance compared to interferon‐based therapy. The influence of immunosuppressive agents on the efficacy of DAAs has not been clarified.MethodsSubgenomic hepatitis C virus (HCV) replicons for genotype (GT) 1b, 2b, 3a, and 4a were treated with the mammalian target of rapamycin (mTOR) inhibitors everolimus and sirolimus or with the calcineurin inhibitors (CNIs) cyclosporine or tacrolimus, either alone or in combination with selected DAAs. Cell proliferation‐related effects were excluded with MTT assays. HCV replication activity was quantified by quantitative real‐time polymerase chain reaction or luciferase assay.ResultsAddition of either mTOR inhibitor to the DAA daclatasvir (DAC) resulted in a 30% increase in antiviral activity compared to DAC alone for HCV GT2a, GT3a, and GT4a (all P ≤ .01). Similar results were obtained using sofosbuvir and ledipasvir. In contrast, addition of either mTOR inhibitor to DAC induced a 30% reduction in antiviral activity in GT1b cells (P ≤ .01 vs DAC alone). Neither CNI affects the antiviral activity of the DAAs in any HCV GT.ConclusionFor patients with HCV GT2a, GT3a, or GT4a infection, mTOR‐based immunosuppressive therapy may be beneficial. CNI‐based therapy may be more efficacious in GT1b patients, as mTOR inhibitors seem to impair antiviral efficacy of DAAs in HCV GT1b infection.
Compliance between clinical and genetic diagnosis of choroidal hypoplasia in 103 Norwegian Border Collie puppies
Authors: Grosås Siv , Lingaas Frode , Prestrud Kristin Wear , Ropstad Ernst‐Otto 
Published: November 2017

AbstractObjectiveTo describe the frequency of the nonhomologous end‐joining factor 1 (NHEJ1) mutation and the compliance between clinical and genetic diagnosis of choroidal hypoplasia (CH) in a group of Norwegian Border Collies.Animals studiedBorder collie puppies in the age from 5 to 8 weeks.Material and methodsPuppies included in the study had a complete ophthalmological examination. All findings were recorded, and an ECVO scheme form was issued for each puppy. DNA samples were achieved from buccal swabs. Genetic typing was performed for the 7.8‐kb deletion in the gene encoding NHEJ1. Dogs with none, one, or two copies of the mutated allele were classified as free, carriers, and affected, respectively.Results103 Border Collie puppies from 16 litters, 52 females and 51 males, were included in the study. Ages ranged from 5.1 to 8.9 weeks. One puppy had clinical findings consistent with CH and optic nerve coloboma compatible with the diagnosis Collie Eye Anomaly (CEA). Findings on ophthalmological examination of the remaining puppies were within normal limits. On genetic testing, 85 puppies were clear of the mutation in the NHEJ1 gene, 17 puppies were carriers, and one puppy was genetically affected.ConclusionsA good compliance between the clinical diagnosis and the genetic test results was found in all of the puppies examined. The allele frequency of the mutation was 6.3%.
Human case of bubonic plague resulting from the bite of a wild Gunnison's prairie dog during translocation from a plague‐endemic area
Authors: Melman S. D. , Ettestad P. E. , VinHatton E. S. , Ragsdale J. M. , Takacs N. , Onischuk L. M. , Leonard P. M. , Master S. S. , Lucero V. S. , Kingry L. C. , Petersen J. M. 
Published: November 2017

SummaryPlague is a zoonotic disease (transmitted mainly by fleas and maintained in nature by rodents) that causes severe acute illness in humans. We present a human plague case who became infected by the bite of a wild Gunnison's prairie dog, and a good practical example of the One Health approach that resulted in a rapid public health response. The exposure occurred while the animal was being transported for relocation to a wildlife refuge after being trapped in a plague enzootic area. This is the first report of a human plague case resulting from the bite of a Gunnison's prairie dog. Additionally, we present an observation of a longer incubation period for plague in captive prairie dogs, leading to a recommendation for a longer quarantine period for prairie dogs during translocation efforts.
Dissociation of intramyocellular lipid storage and insulin resistance in trained athletes and type 2 diabetes patients; involvement of perilipin 5?
Authors: Gemmink Anne , Daemen Sabine , Brouwers Bram , Huntjens Peter R. , Schaart Gert , Moonen‐Kornips Esther , Jörgensen Johanna , Hoeks Joris , Schrauwen Patrick , Hesselink Matthijs K. C. 
Published: November 2017

Key points
Intramyocellular lipid storage is negatively associated with insulin sensitivity. However, endurance trained athletes and type 2 diabetes mellitus (T2DM) patients store similar amounts of lipids in their muscle; the so‐called athlete's paradox.
Compared to T2DM, trained athletes possess higher levels of perilipin 5 (PLIN5), a lipid droplet (LD) coating protein. We examined whether coating LD with PLIN5 affects the pattern of muscle lipid (LD size and number) in relation to the athlete's paradox.
Despite differences in PLIN5 protein content, we observed that coating the LD with PLIN5 could not explain the observed differences in LD size and number between athletes and T2DM. PLIN5‐coated LDs were positively associated with oxidative capacity but not with insulin sensitivity.
We conclude that coating of LDs with PLIN5 cannot causally explain the athlete's paradox.
AbstractIntramyocellular lipid (IMCL) hampers insulin sensitivity, albeit not in endurance‐trained athletes (Trained). Compared to type 2 diabetes mellitus (T2DM) patients, Trained subjects have high levels of perilipin 5 (PLIN5). In the present study, we tested whether the fraction of PLIN5‐coated lipid droplets (LDs) is a determinant of skeletal muscle insulin sensitivity and contributes to the athlete's paradox. Muscle biopsies were taken from eight Trained, Lean sedentary, Obese and T2DM subjects. Trained, Obese and T2DM subjects were matched for total IMCL content. Confocal images were analysed for lipid area fraction, LD size and number and PLIN5+ and PLIN5– LDs were measured. A stepwise linear regression was performed to identify factors explaining observed variance in glucose infusion rate (GIR). Trained and T2DM subjects stored IMCL differently; Trained subjects had a higher number of LDs compared to T2DM subjects (0.037 ± 0.004 μm−2 vs. 0.023 ± 0.003 μm−2, P = 0.024) that were non‐significantly smaller (0.27 ± 0.01 μm2 vs. 0.32 ± 0.02 μm2, P = 0.197, Trained vs. T2DM). Even though total PLIN5 protein content was almost double in Trained vs. T2DM subjects (1.65 ± 0.21 AU vs. 0.89 ± 0.09 AU, P = 0.004), PLIN5 coating did not affect LD number or size significantly. Of the observed variance in GIR, the largest fraction by far (70.2%) was explained by maximal oxygen uptake. Adding PLIN5 protein content or PLIN5+ LDs increased the explained variance in GIR (74.7% and 80.7% for PLIN5 protein content and PLIN5+ LDs, respectively). Thus, the putative relationship between PLIN5 and insulin sensitivity is at best indirect and is apparent only in conjunction with maximal oxygen uptake. Hence, PLIN5 abundance cannot be causally linked to the athlete's paradox.
Development of a Single-Degree-of-Freedom Mechanical Model for Predicting Strain-Based Brain Injury Responses
Authors: Gabler Lee F. , Joodaki Hamed , Crandall Jeff R. , Panzer Matthew B. 
Published: November 2017

Linking head kinematics to injury risk has been the focus of numerous brain injury criteria. Although many early forms were developed using mechanics principles, recent criteria have been developed using empirical methods based on subsets of head impact data. In this study, a single-degree-of-freedom (sDOF) mechanical analog was developed to parametrically investigate the link between rotational head kinematics and brain deformation. Model efficacy was assessed by comparing the maximum magnitude of displacement to strain-based brain injury predictors from finite element (FE) human head models. A series of idealized rotational pulses covering a broad range of acceleration and velocity magnitudes (0.1–15 krad/s2 and 1–100 rad/s) with durations between 1 and 3000 ms were applied to the mechanical models about each axis of the head. Results show that brain deformation magnitude is governed by three categories of rotational head motion each distinguished by the duration of the pulse relative to the brain's natural period: for short-duration pulses, maximum brain deformation depended primarily on angular velocity magnitude; for long-duration pulses, brain deformation depended primarily on angular acceleration magnitude; and for pulses relatively close to the natural period, brain deformation depended on both velocity and acceleration magnitudes. These results suggest that brain deformation mechanics can be adequately explained by simple mechanical systems, since FE model responses and experimental brain injury tolerances exhibited similar patterns to the sDOF model. Finally, the sDOF model was the best correlate to strain-based responses and highlighted fundamental limitations with existing rotational-based brain injury metrics.
Evaluation of Serum Nidogen-2 as a Screening and Diagnostic Tool for Ovarian Cancer
Authors: Torky Haitham A. , Sherif Ahmed , Abo-Louz Ashraf , Ali Mohamed , Ahmed Ali , Ali Ahmad 
Published: November 2017

<b><i>Introduction:</i></b> Ovarian cancer is a relatively common occurrence with the formation of a tumour in the ovaries and is the leading cause of death in the gynecological field. Despite enormous efforts, there are no successful screening methods developed until now to decrease mortality in this regard. <b><i>Aim:</i></b> To evaluate nidogen-2 as a new tumour marker combined with higher sensitivity, specificity and accuracy than carbohydrate antigen (CA-125) and Doppler ultrasound to improve early diagnosis of ovarian cancer. <b><i>Patients and Methods:</i></b> One hundred and forty-four qualified women with a preliminary diagnosis of adnexal mass were subjected to history, examination, transvaginal Doppler ultrasound and Quantitative assessment of serum level of CA-125 and nidogen-2 followed by the resection of the masses, which were sent for histopathological examination. <b><i>Results:</i></b> One-hundred and sixteen cases were benign and 28 cases were malignant. The surgical procedures ranged from limited resection to radical hysterectomy. There was a highly significant correlation between both serum nidogen-2 and CA-125 and the results of histopathological examination (<i>p</i> = 0.0001). Serum nidogen-2 had 91.6% sensitivity, 62% specificity, 37.1% positive predictive value, 97.9% negative predictive value and 68% accuracy (<i>p &#x3c;</i> 0.05). <b><i>Conclusion:</i></b> Nidogen-2 is a new promising ovarian malignancy biomarker that correlates closely with ultrasound and CA125. It did improve the accuracy of diagnosis, but further studies are needed.