bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ensemble Postprocessing Using Quantile Function Regression Based on Neural Networks and Bernstein Polynomials
Authors: Bremnes John Bjørnar 
Published: October 2019

Abstract
The value of ensemble forecasts is well documented. However, postprocessing by statistical methods is usually required to make forecasts reliable in a probabilistic sense. In this work a flexible statistical method for making probabilistic forecasts in terms of quantile functions is proposed. The quantile functions are specified by linear combinations of Bernstein basis polynomials, and their coefficients are assumed to be related to ensemble forecasts by means of a highly adaptable neural network. This leads to many parameters to estimate, but a recent learning algorithm often applied to deep-learning problems makes this feasible and provides robust estimates. The method is applied to ~2 yr of ensemble wind speed forecasting data at 125 Norwegian stations for lead time +60 h. An intercomparison with two quantile regression methods shows improvements in quantile skill score of nearly 1%. The most appealing feature of the method is arguably its versatility.
Validity, functional impairment and complications related to Internet gaming disorder in the DSM-5 and gaming disorder in the ICD-11
Authors: Ko Chih-Hung , Lin Huang-Chi , Lin Pai-Cheng , Yen Ju-Yu 
Published: October 2019

Background: Many concerns have been raised regarding the Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5) criteria for Internet gaming disorder and International Classification of Diseases, 11th Revision (ICD-11) criteria for gaming disorder. Aims: In this study, we demonstrated the diagnostic validity of each criterion for Internet gaming disorder in the DSM-5 in terms of their intensity and frequency thresholds and evaluated functional impairments, unhealthy behaviors and complications among adults with Internet gaming disorder and gaming disorder. Methods: We recruited 69 subjects with Internet gaming disorder, 69 regular gamers and 69 controls without regular gaming based on diagnostic interviewing conducted by a psychiatrist according to the DSM-5 Internet gaming disorder criteria. Results: Except for the ‘deceiving’ and ‘escapism’ criteria, all criteria for Internet gaming disorder had a diagnostic accuracy ranging from 84.7% to 93.5% in differentiating between adults with Internet gaming disorder and regular gamers. A total of 44 participants with Internet gaming disorder (63.8%) fulfilled the gaming disorder criteria. In addition, 89% and 100% of the Internet gaming disorder and gaming disorder groups, respectively, had academic, occupational or social functional impairment. Both the Internet gaming disorder and gaming disorder groups had higher rates of delayed sleep phase syndrome and insomnia. The gaming disorder group also had a higher obesity proportion. Conclusion: The ‘deceiving’ and ‘escapism’ criteria had relatively lower diagnostic accuracy. Both the Internet gaming disorder and gaming disorder groups demonstrated functional impairments and unhealthy behaviors. They also exhibited complications, such as obesity and sleep disorders. These results support the utility of the DSM-5 Internet gaming disorder and ICD-11 gaming disorder criteria in identifying individuals who need treatment for both gaming addiction symptoms and complications resulting from the addiction.
Silencing PSME3 induces colorectal cancer radiosensitivity by downregulating the expression of cyclin B1 and CKD1
Authors: Song Wen , Guo Cuiping , Chen Jianxiong , Duan Shiyu , Hu Yukun , Zou Ying , Chi Honggang , Geng Jian , Zhou Jun 
Published: October 2019

Resistance to radiotherapy remains a severe obstacle in the treatment of high-risk colorectal cancer patients. Recent studies have indicated that proteasome activator complex subunit 3 (PSME3) participates in the development and progression of various human malignancies and is proposed to play a role in tumor radioresistance. However, the impact of PSME3 on radioresistance of colorectal cancer has been largely unknown. In the present study, the enhanced expression of PSME3 was observed in colorectal cancer cells and tissue. Upregulation of PSME3 was significantly implicated in lymph node state, lymphovascular invasion, and Dukes' stage. Furthermore, high PSME3 expression was closely linked to poorer overall and progression-free survival in patients with colorectal cancer. The study further demonstrated that the proliferative, invasive and migratory potential of colorectal cancer cells was effectively inhibited in vitro after silencing PSME3. Our results verified that knockdown of PSME3 probably triggered cell cycle arrest at the G2/M phase by downregulation of cyclinB1 and CDK1, thereby enhancing the radiosensitivity of colorectal cancer cells. These data illustrated that PSME3 is a promising biomarker predictive of colorectal cancer prognosis and silencing of PSME3 may provide with a new approach for sensitizing the radiotherapy in colorectal cancer. Impact statement It is reported that colorectal cancer (CRC) is the third most common cancer worldwide and the fourth leading cause of cancer-related death. At present, the main treatment method of colorectal cancer is surgery, supplemented by radiotherapy and chemotherapy. Among them, radiotherapy plays an important role in the treatment of locally advanced colorectal cancer, surgery, and chemotherapy. Our study found that down-regulation of PSME3 may enhance the radiosensitivity of CRC cells by triggering cell cycle arrest, which suggests that silence PSME3 may provide a new method for improving the radiosensitivity of CRC. What’more, our research also demonstrated that PSME3 may promote proliferation, invasive and migratory potential of CRC cells, which implies that PSME3 might be a biomarker of CRC for early diagnosis and treatment.
The efficacy of herbal medicines on anxiety and depression in peri- and postmenopausal women: A systematic review and meta-analysis
Authors: Shahmohammadi Afshar , Ramezanpour Negar , Mahdavi Siuki Mahsa , Dizavandi Fathemeh , Ghazanfarpour Masumeh , Rahmani Yousef , Tahajjodi Rezvan , Babakhanian Masoudeh 
Published: October 2019

Objective The main objective in this systematic review was to analyse herbal medicine interventions for anxiety and depression to detect possible benefits of herbal medicines in peri- and postmenopausal women. Material and method The trials published since inception to August 2017 were searched on the databases of MEDLINE, ISI Web of Science, Scopus and Cochran central register of controlled trials Results Twenty-one trials were included into systematic review. The anxiety score (standardized mean difference = −1.19; p = 0.04; six trials) and depression (standardized mean difference = −0.952; p = 0.023; five trials) was lower in the phytoestrogen group compared to the placebo. However, the heterogeneity was notably high among trials that assessed anxiety outcome (p < 0.0001; I2 = 97.12%) and depression (p < 0.0001; I2 = 94.51%), and we were unable to reduce the heterogeneity to below 90% after one with one exclusion of the studies; 1000 mg of fenugreek extract on depression and anxiety, 600 mg of Trigonella foenum‐graecum de‐husked seed extract on psychosocial symptoms, 0.4 mg/ml Maca extract on anxiety, 500 mg of Hop plant on depression and anxiety, 80 mg or more than 80 mg of red clover-derived isoflavones on psychological symptoms had significant effect. Non-significant effect was observed in black cohosh on anxiety. However, significant effect of black cohosh was seen on psychological symptoms. Fennel had a positive effect in both patients with anxiety or depression and healthy women. Flaxseed group showed a non-significant effect on psychological symptoms. Conclusion The present systematic review found that some of the herbal medicines may have good effect in the relief of the anxiety and the depression.
The Weaklaw Vent, SE Scotland: Metasomatism of eruptive products by carbo-hydro-fluids of probable mantle origin
Authors: Upton Brian G. J. , Odling Nic , Kirstein Linda A. , Underhill John R. , Puziewicz Jacek , Ntaflos Theodore , Bagiński Bogusław , Hillier Steve , Andersen Jens C. , Rollinson Gavin K. , Perrillat Jean-Philippe 
Published: October 2019

AbstractThe Weaklaw vent in SE Scotland (East Lothian coast), inferred to be Namurian, produced lava spatter and volcanic bombs. The latter commonly contained ultramafic xenoliths. All were metasomatised by carbonic fluids rich in incompatible elements. The lavas and xenoliths are inferred to have been basanites and lherzolites prior to metasomatism. The abundance and size of (carbonated) peridotite xenoliths at Weaklaw denotes unusual rapidity of magma ascent and high-energy eruption making Weaklaw exceptional in the British Isles. The lavas and xenoliths were altered subsequently by low-temperature (<200°C) carbo-hydrous fluids to carbonate, clay and quartz assemblages. A small irregular tuffisite ‘dyke’ that transects the ejecta is also composed dominantly of carbonates and clays. The peridotitic xenoliths are typically foliated, interpreted as originating as pre-entrainment mantle shear-planes.Analyses of the relic spinels shows them to be compositionally similar to spinels in local unaltered lherzolites from near-by basanitic occurrences. Chromium showed neither significant loss nor gain but was concentrated in a di-octahedral smectite allied to volkonskoite. It is in the complex association of smectite with other clays, chlorite and possibly fuchsite that the diverse incompatible elements are concentrated.We conclude that late Palaeozoic trans-tensional fault movement caused mantle shearing. Rapid ascent of basanite magma entrained large quantities of sheared lithospheric mantle. This was followed by ascent of an aggressive carbonate-/ hydroxyl-rich fluid causing pervasive metasomatism. The vent is unique in several ways: in its remarkable clay mineralogy and in displaying such high Cr-clays in a continental intra-plate setting; in being more productive in terms of its ‘cargo’ of peridotite xenoliths; in presenting an essentially un-eroded sequence of Namurian extrusives; and, not least, for giving evidence for post-eruptive, surface release of small-melt, deep-source fluids.
Using imputation-based whole-genome sequencing data to improve the accuracy of genomic prediction for combined populations in pigs
Authors: Song Hailiang , Ye Shaopan , Jiang Yifan , Zhang Zhe , Zhang Qin , Ding Xiangdong 
Published: October 2019

AbstractBackgroundFor genomic selection in populations with a small reference population, combining populations of the same breed or populations of related breeds is an effective way to increase the size of the reference population. However, genomic predictions based on single nucleotide polymorphism (SNP)-chip genotype data using combined populations with different genetic backgrounds or from different breeds have not shown a clear advantage over using within-population or within-breed predictions. The increasing availability of whole-genome sequencing (WGS) data provides new opportunities for combined population genomic prediction. Our objective was to investigate the accuracy of genomic prediction using imputation-based WGS data from combined populations in pigs. Using 80K SNP panel genotypes, WGS genotypes, or genotypes on WGS variants that were pruned based on linkage disequilibrium (LD), three methods [genomic best linear unbiased prediction (GBLUP), single-step (ss)GBLUP, and genomic feature (GF)BLUP] were implemented with different prior information to identify the best method to improve the accuracy of genomic prediction for combined populations in pigs.ResultsIn total, 2089 and 2043 individuals with production and reproduction phenotypes, respectively, from three Yorkshire populations with different genetic backgrounds were genotyped with the PorcineSNP80 panel. Imputation accuracy from 80K to WGS variants reached 92%. The results showed that use of the WGS data compared to the 80K SNP panel did not increase the accuracy of genomic prediction in a single population, but using WGS data with LD pruning and GFBLUP with prior information did yield higher accuracy than the 80K SNP panel. For the 80K SNP panel genotypes, using the combined population resulted in a slight improvement, no change, or even a slight decrease in accuracy in comparison with the single population for GBLUP and ssGBLUP, while accuracy increased by 1 to 2.4% when using WGS data. Notably, the GFBLUP method did not perform well for both the combined population and the single populations.ConclusionsThe use of WGS data was beneficial for combined population genomic prediction. Simply increasing the number of SNPs to the WGS level did not increase accuracy for a single population, while using pruned WGS data based on LD and GFBLUP with prior information could yield higher accuracy than the 80K SNP panel.
Asian elephants exhibit post-reproductive lifespans
Authors: Chapman Simon N. , Jackson John , Htut Win , Lummaa Virpi , Lahdenperä Mirkka 
Published: October 2019

AbstractBackgroundThe existence of extended post-reproductive lifespan is an evolutionary puzzle, and its taxonomic prevalence is debated. One way of measuring post-reproductive life is with post-reproductive representation, the proportion of adult years lived by females after cessation of reproduction. Analyses of post-reproductive representation in mammals have claimed that only humans and some toothed whale species exhibit extended post-reproductive life, but there are suggestions of a post-reproductive stage for false killer whales and Asian elephants. Here, we investigate the presence of post-reproductive lifespan in Asian elephants using an extended demographic dataset collected from semi-captive timber elephants in Myanmar. Furthermore, we investigate the sensitivity of post-reproductive representation values to availability of long-term data over 50 years.ResultsWe find support for the presence of an extended post-reproductive stage in Asian elephants, and that post-reproductive representation and its underlying demographic rates depend on the length of study period in a long-lived animal.ConclusionsThe extended post-reproductive lifespan is unlikely due to physiological reproductive cessation, and may instead be driven by mating preferences or condition-dependent fertility. Our results also show that it is crucial to revisit such population measures in long-lived species as more data is collected, and if the typical lifespan of the species exceeds the initial study period.
Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae)
Authors: Yao Xin , Tan Yun-hong , Yang Jun-bo , Wang Yan , Corlett Richard T. , Manen Jean-François 
Published: October 2019

Abstract

Background
The genus Ilex (Aquifoliaceae) has a near-cosmopolitan distribution in mesic habitats from tropical to temperate lowlands and in alpine forests. It has a high rate of hybridization and plastid capture, and comprises four geographically structured plastid groups. A previous study showed that the plastid rbcL gene, coding for the large subunit of Rubisco, has a particularly high rate of non-synonymous substitutions in Ilex, when compared with other plant lineages. This suggests a strong positive selection on rbcL, involved in yet unknown adaptations. We therefore investigated positive selection on rbcL in 240 Ilex sequences from across the global range.

Results
The rbcL gene shows a much higher rate of positive selection in Ilex than in any other plant lineage studied so far (> 3000 species) by tests in both PAML and SLR. Most positively selected residues are on the surface of the folded large subunit, suggesting interaction with other subunits and associated chaperones, and coevolution between positively selected residues is prevalent, indicating compensatory mutations to recover molecular stability. Coevolution between positively selected sites to restore global stability is common.

Conclusions
This study has confirmed the predicted high incidence of positively selected residues in rbcL in Ilex, and shown that this is higher than in any other plant lineage studied so far. The causes and consequences of this high incidence are unclear, but it is probably associated with the similarly high incidence of hybridization and introgression in Ilex, even between distantly related lineages, resulting in large cytonuclear discordance in the phylogenies.
Modeling honey yield, defensive and swarming behaviors of Italian honey bees (Apis mellifera ligustica) using linear-threshold approaches
Authors: Andonov Sreten , Costa Cecilia , Uzunov Aleksandar , Bergomi Patrizia , Lourenco Daniela , Misztal Ignacy 
Published: October 2019

Abstract

Background
Genetic improvement of honey bees is more difficult compared to other livestock, due to the very different reproductive behavior. Estimation of breeding values requires specific adjustment and the use of sires in the pedigree is only possible when mating of queens and drones is strictly controlled. In the breeding program of the National Registry for Italian Queen Breeders and Bee Producers the paternal contribution is mostly unknown. As stronger modeling may compensate for the lack of pedigree information, we tested two models that differed in the way the direct and maternal effects were considered. The two models were tested using 4003 records for honey yield, defensive and swarming behaviors of Italian honey bee queens produced between 2002 and 2014. The first model accounted for the direct genetic effect of worker bees and the genetic maternal effect of the queen, whereas model 2 considered the direct genetic effect of the queen without maternal effect. The analyses were performed by linear (honey production) and threshold (defensive and swarming behavior) single-trait models; estimated genetic correlations among traits were obtained by a three-trait linear-threshold model.

Results
For all traits, the highest predictability (correlation between breeding values estimated with and without performance records) was obtained with model 2, where direct genetic effect of queens was considered. With this model, heritability estimates were 0.26 for honey yield, 0.36 for defensive behavior, and 0.34 for swarming behavior. Multi-trait estimation resulted in similar or higher heritability estimates for all traits. A low, positive genetic correlation (0.19) was found between honey yield and defensive behavior, whereas the genetic correlation between honey yield and swarming behavior was moderate (0.41). A strong, positive genetic correlation was found between defensive and swarming behaviors (0.62). Predictability for multi-trait evaluations was higher for honey yield (0.46) and defensive behavior (0.30) but almost identical for swarming behavior (0.45) compared to corresponding single-trait predictability.

Conclusions
Multi-trait evaluation using a model that accounts for the direct genetic effect of queen was the best approach for breeding value estimation of Italian honey bees. The results suggest a new direction for selection of linear and categorical traits in breeding programs where drone origin is unknown.
A high-resolution genomic composition-based method with the ability to distinguish similar bacterial organisms
Authors: Zhou Yizhuang , Zhang Wenting , Wu Huixian , Huang Kai , Jin Junfei 
Published: October 2019

AbstractBackgroundGenomic composition has been found to be species specific and is used to differentiate bacterial species. To date, almost no published composition-based approaches are able to distinguish between most closely related organisms, including intra-genus species and intra-species strains. Thus, it is necessary to develop a novel approach to address this problem.ResultsHere, we initially determine that the “tetranucleotide-derived z-value Pearson correlation coefficient” (TETRA) approach is representative of other published statistical methods. Then, we devise a novel method called “Tetranucleotide-derivedZ-valueManhattanDistance” (TZMD) and compare it with the TETRA approach. Our results show that TZMD reflects the maximal genome difference, while TETRA does not in most conditions, demonstrating in theory that TZMD provides improved resolution. Additionally, our analysis of real data shows that TZMD improves species differentiation and clearly differentiates similar organisms, including similar species belonging to the same genospecies, subspecies and intraspecific strains, most of which cannot be distinguished by TETRA. Furthermore, TZMD is able to determine clonal strains with the TZMD = 0 criterion, which intrinsically encompasses identical composition, high average nucleotide identity and high percentage of shared genomes.ConclusionsOur extensive assessment demonstrates that TZMD has high resolution. This study is the first to propose a composition-based method for differentiating bacteria at the strain level and to demonstrate that composition is also strain specific. TZMD is a powerful tool and the first easy-to-use approach for differentiating clonal and non-clonal strains. Therefore, as the first composition-based algorithm for strain typing, TZMD will facilitate bacterial studies in the future.
The interplay between miR156/SPL13 and DFR/WD40–1 regulate drought tolerance in alfalfa
Authors: Feyissa Biruk A. , Arshad Muhammad , Gruber Margaret Y. , Kohalmi Susanne E. , Hannoufa Abdelali 
Published: October 2019

AbstractBackgroundDevelopingMedicago sativaL. (alfalfa) cultivars tolerant to drought is critical for the crop’s sustainable production. miR156 regulates various plant biological functions by silencing SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors.ResultsTo understand the mechanism of miR156-modulated drought stress tolerance in alfalfa we used genotypes with altered expression levels of miR156, miR156-regulatedSPL13, andDIHYDROFLAVONOL-4-REDUCTASE(DFR) regulatingWD40–1. Previously we reported the involvement of miR156 in drought tolerance, but the mechanism and downstream genes involved in this process were not fully studied. Here we illustrate the interplay between miR156/SPL13 and WD40–1/DFR to regulate drought stress by coordinating gene expression with metabolite and physiological strategies. Low to moderate levels of miR156 overexpression suppressedSPL13and increasedWD40–1to fine-tuneDFRexpression for enhanced anthocyanin biosynthesis. This, in combination with other accumulated stress mitigating metabolites and physiological responses, improved drought tolerance. We also demonstrated that SPL13 binds in vivo to theDFRpromoter to regulate its expression.ConclusionsTaken together, our results reveal that moderate relative miR156 transcript levels are sufficient to enhance drought resilience in alfalfa by silencingSPL13and increasingWD40–1expression, whereas higher miR156 overexpression results in drought susceptibility.