bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design
Authors: Chong Li Chuin , Khan Asif M. 
Published: December 2019

AbstractBackgroundThe sequence diversity of dengue virus (DENV) is one of the challenges in developing an effective vaccine against the virus. Highly conserved, serotype-specific (HCSS), immune-relevant DENV sequences are attractive candidates for vaccine design, and represent an alternative to the approach of selecting pan-DENV conserved sequences. The former aims to limit the number of possible cross-reactive epitope variants in the population, while the latter aims to limit the cross-reactivity between the serotypes to favour a serotype-specific response. Herein, we performed a large-scale systematic study to map and characterise HCSS sequences in the DENV proteome.MethodsAll reported DENV protein sequence data for each serotype was retrieved from the NCBI Entrez Protein (nr) Database (txid: 12637). The downloaded sequences were then separated according to the individual serotype proteins by use of BLASTp search, and subsequently removed for duplicates and co-aligned across the serotypes. Shannon’s entropy and mutual information (MI) analyses, by use of AVANA, were performed to measure the diversity within and between the serotype proteins to identify HCSS nonamers. The sequences were evaluated for the presence of promiscuous T-cell epitopes by use of NetCTLpan 1.1 and NetMHCIIpan 3.2 server for human leukocyte antigen (HLA) class I and class II supertypes, respectively. The predicted epitopes were matched to reported epitopes in the Immune Epitope Database.ResultsA total of 2321 nonamers met the HCSS selection criteria of entropy < 0.25 and MI > 0.8. Concatenating these resulted in a total of 337 HCSS sequences. DENV4 had the most number of HCSS nonamers; NS5, NS3 and E proteins had among the highest, with none in the C and only one in prM. The HCSS sequences were immune-relevant; 87 HCSS sequences were both reported T-cell epitopes/ligands in human and predicted epitopes, supporting the accuracy of the predictions. A number of the HCSS clustered as immunological hotspots and exhibited putative promiscuity beyond a single HLA supertype. The HCSS sequences represented, on average, ~ 40% of the proteome length for each serotype; more than double of pan-DENV sequences (conserved across the four serotypes), and thus offer a larger choice of sequences for vaccine target selection. HCSS sequences of a given serotype showed significant amino acid difference to all the variants of the other serotypes, supporting the notion of serotype-specificity.ConclusionThis work provides a catalogue of HCSS sequences in the DENV proteome, as candidates for vaccine target selection. The methodology described herein provides a framework for similar application to other pathogens.
Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae
Authors: Li Jing , Gao Xiaoyang , Sang Shiye , Liu Changning 
Published: December 2019

Abstract
Background
Euphorbiaceae is one of the largest families of flowering plants. Due to its exceptional growth form diversity and near-cosmopolitan distribution, it has attracted much interest since ancient times. SBP-box (SBP) genes encode plant-specific transcription factors that play critical roles in numerous biological processes, especially flower development. We performed genome-wide identification and characterization of SBP genes from four economically important Euphorbiaceae species.

Results
In total, 77 SBP genes were identified in four Euphorbiaceae genomes. The SBP proteins were divided into three length ranges and 10 groups. Group-6 was absent in Arabidopsis thaliana but conserved in Euphorbiaceae. Segmental duplication played the most important role in the expansion processes of Euphorbiaceae SBP genes, and all the duplicated genes were subjected to purify selection. In addition, about two-thirds of the Euphorbiaceae SBP genes are potential targets of miR156, and some miR-regulated SBP genes exhibited high intensity expression and differential expression in different tissues. The expression profiles related to different stress treatments demonstrated broad involvement of Euphorbiaceae SBP genes in response to various abiotic factors and hormonal treatments.

Conclusions
In this study, 77 SBP genes were identified in four Euphorbiaceae species, and their phylogenetic relationships, protein physicochemical characteristics, duplication, tissue and stress response expression, and potential roles in Euphorbiaceae development were studied. This study lays a foundation for further studies of Euphorbiaceae SBP genes, providing valuable information for future functional exploration of Euphorbiaceae SBP genes.
The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers
Authors: Ou Xiaohong , Li Shipeng , Liao Peiran , Cui Xiuming , Zheng Binglian , Yang Ye , Liu Dahui , Zheng Yun 
Published: December 2019

AbstractBackgroundThe sensitivity of plants to ammonia is a worldwide problem that limits crop production. Excessive use of ammonium as the sole nitrogen source results in morphological and physiological disorders, and retarded plant growth.ResultsIn this study we found that the root growth ofPanax notoginsengwas inhibited when only adding ammonium nitrogen fertilizer, but the supplement of nitrate fertilizer recovered the integrity, activity and growth of root. Twelve RNA-seq profiles in four sample groups were produced and analyzed to identify deregulated genes in samples with different treatments. In comparisons to NH${~}_{4}^{+}$4+treated samples,ACLA-3gene is up-regulated in samples treated with NO${~}_{3}^{-}$3−and with both NH$_{4}^{+}$4+and NO${~}_{3}^{-}$3−, which is further validated by qRT-PCR in another set of samples. Subsequently, we show that the some key metabolites in the TCA cycle are also significantly enhanced when introducing NO${~}_{3}^{-}$3−. These potentially enhance the integrity and recover the growth ofPanax notoginsengroots.ConclusionThese results suggest that the activated TCA cycle, as demonstrated by up-regulation ofACLA-3and several key metabolites in this cycle, contributes to the increasedPanax notoginsengroot yield when applying both ammonium and nitrate fertilizer.
Diet and irradiation effects on the bacterial community composition and structure in the gut of domesticated teneral and mature Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)
Authors: Woruba Deane N. , Morrow Jennifer L. , Reynolds Olivia L. , Chapman Toni A. , Collins Damian P. , Riegler Markus 
Published: December 2019

AbstractBackgroundMass-rearing, domestication and gamma irradiation of tephritid fruit flies used in sterile insect technique (SIT) programmes can negatively impact fly quality and performance. Symbiotic bacteria supplied as probiotics to mass-reared fruit flies may help to overcome some of these issues. However, the effects of tephritid ontogeny, sex, diet and irradiation on their microbiota are not well known.ResultsWe have used next-generation sequencing to characterise the bacterial community composition and structure within Queensland fruit fly,Bactrocera tryoni(Froggatt),by generating 16S rRNA gene amplicon libraries derived from the guts of 58 individual teneral and mature, female and male, sterile and fertile adult flies reared on artificial larval diets in a laboratory or mass-rearing environment, and fed either a full adult diet (i.e. sugar and yeast hydrolysate) or a sugar only adult diet. Overall, the amplicon sequence read volume in tenerals was low and smaller than in mature adult flies. Operational taxonomic units (OTUs), belonging to the families Enterobacteriaceae (8 OTUs) and Acetobacteraceae (1 OTU) were most prevalent. Enterobacteriaceae dominated laboratory-reared tenerals from a colony fed a carrot-based larval diet, while Acetobacteraceae dominated mass-reared tenerals from a production facility colony fed a lucerne chaff based larval diet. As adult flies matured, Enterobacteriaceae became dominant irrespective of larval origin. The inclusion of yeast in the adult diet strengthened this shift away from Acetobacteraceae towards Enterobacteriaceae. Interestingly, irradiation increased 16S rRNA gene sequence read volume.ConclusionsOur findings suggest that bacterial populations in fruit flies experience significant bottlenecks during metamorphosis. Gut bacteria in teneral flies were less abundant and less diverse, and impacted by colony origin. In contrast, mature adult flies had selectively increased abundances for some gut bacteria, or acquired these bacteria from the adult diet and environment. Furthermore, irradiation augmented bacterial abundance in mature flies. This implies that either some gut bacteria were compensating for damage caused by irradiation or irradiated flies had lost their ability to regulate bacterial load. Our findings suggest that the adult stage prior to sexual maturity may be ideal to target for probiotic manipulation of fly microbiota to increase fly performance in SIT programmes.
Neuropsychiatric decompensation in adolescents and adults with Phelan-McDermid syndrome: a systematic review of the literature
Authors: Kolevzon Alexander , Delaby Elsa , Berry-Kravis Elizabeth , Buxbaum Joseph D. , Betancur Catalina 
Published: December 2019

AbstractPhelan-McDermid syndrome (PMS) is caused by haploinsufficiency of theSHANK3gene on chromosome 22q13.33 and is characterized by intellectual disability, hypotonia, severe speech impairments, and autism spectrum disorder. Emerging evidence indicates that there are changes over time in the phenotype observed in individuals with PMS, including severe neuropsychiatric symptoms and loss of skills occurring in adolescence and adulthood. To gain further insight into these phenomena and to better understand the long-term course of the disorder, we conducted a systematic literature review and identified 56 PMS cases showing signs of behavioral and neurologic decompensation in adolescence or adulthood (30 females, 25 males, 1 gender unknown). Clinical presentations included features of bipolar disorder, catatonia, psychosis, and loss of skills, occurring at a mean age of 20 years. There were no apparent sex differences in the rates of these disorders except for catatonia, which appeared to be more frequent in females (13 females, 3 males). Reports of individuals with point mutations inSHANK3exhibiting neuropsychiatric decompensation and loss of skills demonstrate that loss of one copy ofSHANK3is sufficient to cause these manifestations. In the majority of cases, no apparent cause could be identified; in others, symptoms appeared after acute events, such as infections, prolonged or particularly intense seizures, or changes in the individual’s environment. Several individuals had a progressive neurological deterioration, including one with juvenile onset metachromatic leukodystrophy, a severe demyelinating disorder caused by recessive mutations in theARSAgene in 22q13.33. These reports provide insights into treatment options that have proven helpful in some cases, and are reviewed herein. Our survey highlights how little is currently known about neuropsychiatric presentations and loss of skills in PMS and underscores the importance of studying the natural history in individuals with PMS, including both cross-sectional and long-term longitudinal analyses. Clearer delineation of these neuropsychiatric symptoms will contribute to their recognition and prompt management and will also help uncover the underlying biological mechanisms, potentially leading to improved interventions.
Determinants and Measurement of Neonatal Vitamin D: Overestimation of 25(OH)D in Cord Blood Using CLIA Assay Technology
Authors: Lu Mengdi , Hollis Bruce W , Carey Vincent J , Laranjo Nancy , Singh Ravinder J , Weiss Scott T , Litonjua Augusto A 
Published: December 2019

Abstract

Context
Vitamin D (VD) deficiency in pregnancy and the neonatal period has impacts on childhood outcomes. Maternal VD sufficiency is crucial for sufficiency in the neonate, though the effect of early versus late pregnancy 25-hydroxy-vitamin D (25(OH)D) levels on neonatal levels is unknown. Furthermore, chemiluminescence immunoassays (CLIAs) are widely used, though their validity in measuring 25(OH)D specifically in cord blood specimens has not been established.

Objective
To assess the validity of a CLIA in the measurement of cord blood 25(OH)D and to evaluate maternal determinants of neonatal 25(OH)D, including early versus late pregnancy 25(OH)D levels.

Design
This is an ancillary analysis from the Vitamin D Antenatal Asthma Reduction Trial (VDAART), a randomized, double-blinded, placebo-controlled study.

Participants and Intervention
A total of 881 pregnant women at high risk of having offspring asthma were randomized to receive VD supplementation or placebo. Serum samples were collected from mothers in early and late pregnancy and from offspring cord blood at birth. 25(OH)D levels were assayed by CLIA in all maternal and offspring samples and by LC-MS/MS in all offspring samples and a subset of 200 maternal third trimester samples.

Results
Cord blood 25(OH)D levels were higher as measured by CLIA (mean 37.13 ng/mL [SD 18.30]) than by LC-MS/MS (mean 23.54 ng/mL [SD 11.99]), with a mean positive bias of 13.54 ng/mL (SD 12.92) by Bland-Altman analysis. This positive bias in measurement by CLIA was not observed in maternal samples. Third trimester 25(OH)D was a positive determinant of neonatal 25(OH)D levels.

Conclusion
Chemiluminescence immunoassays overestimate 25(OH)D levels in human cord blood samples, an effect not observed in maternal blood samples. The quantification of 25(OH)D by CLIA should therefore not be considered valid when assayed in cord blood samples. Third trimester, but not first trimester, maternal 25(OH)D is one of several determinants of neonatal 25(OH)D status.
Circulating miR-181c-5p and miR-497-5p Are Potential Biomarkers for Prognosis and Diagnosis of Osteoporosis
Authors: Ma Jianhua , Lin Xiao , Chen Chu , Li Siyu , Zhang Shasha , Chen Zhihao , Li Dijie , Zhao Fan , Yang Chaofei , Yin Chong , Qiu Wuxia , Xiao Yunyun , Zhang Kewen , Miao Zhiping , Yang Tuanmin , Qian Airong 
Published: December 2019

Abstract

Context
Osteoporosis is a degenerative bone disease in aging men and women. MiRNAs associated with progressive bone loss in osteoporosis had not been clearly demonstrated.

Objective
The evaluation of the differentially expressed miRNAs in the bone tissue and serum of osteoporotic women with aging.

Methods
MiRNAs GeneChip and real-time PCR were used to screen differently expressed miRNAs in bone tissues of 21 osteoporotic women ages 60–69 years and 80–89 years. Identified miRNAs were detected in the serum of the validation cohort, which consisted of 14 healthy premenopausal women and 86 postmenopausal women with osteopenia or osteoporosis. MiR-181c-5p and miR-497-5p expression were validated in aging and OVX mice models, and osteoblasts. Their role in osteogenesis was validated in vitro.

Results
Twenty-four miRNAs showed the highest differential expression in bone tissues of osteoporotic women in initial screening. Among them, four miRNAs were identified both in the bone tissue and serum in the validation cohort. The levels of miR-181c-5p and miR-497-5p were decreased in the serum of postmenopausal women with osteopenia or osteoporosis, but increased in subjects treated with bisphosphonate plus calcitriol. MiR-181c-5p and miR-497-5p were significantly downregulated in the bone tissue of aging and OVX mice models, and upregulated during the osteogenic differentiation of hFOB1.19 and MC3T3-E1 cells. Overexpression of miR-181c-5p and miR-497-5p promoted the differentiation and mineralization of osteoblasts.

Conclusions
MiR-181c-5p and miR-497-5p are involved in bone metabolism and associated with progressive bone loss of due to osteoporosis, suggesting that circulating miR-181c-5p and miR-497-5p might act as potential biomarkers for monitoring the effects of antiosteoporotic therapies or the diagnostic approach.
In Situ Preparation and Unique Electrical Behaviors of Gold@Hollow Polyaniline Nanospheres through Recovery of Gold from Simulated e-Waste
Authors: Tian Xiangyu , Zhang Bin , Hou Jie , Gu Minchao , Chen Yu 
Published: December 2019

Abstract
One of the most effective ways to solve the dilemma between resources shortages and increasing demand is to develop a cost-effective approach for recovery and reuse of the precious metals (especially Au and Ag) derived from e-wastes (electronic devices and the components thereof), which will most likely be driven by breakthroughs in environmentally friendly methodologies that combine the economy of scale with function. Here a facile and novel approach is described for the recovery of gold from simulated e-wastes by using hollow polyaniline nanospheres (P(VAn-g-PANI)) in which PANI and its derivatives can not only be used to reduce Au3+ to Au0 from the metal salts, but also be used to stabilize the achieved polymer nanosphere-supported Au nanoparticles (Au@P(VAn-g-PANI)). The Au@P(VAn-g-PANI) was directly used to fabricate electronic devices with a configuration of Al/Au@P(VAn-g-PANI) + PVA]/ITO, in which Au@P(VAn-g-PANI) was uniformly integrated into poly(vinyl alcohol) (PVA) as electrically insulating matrix. When the Au/N molar ratio in P(VAn-g-PANI) reached 1:10, the device could be electrically erased and reprogrammed showing typical nonvolatile rewritable memory effect, with an ON/OFF current ratio exceeding 105, a turn-on voltage of −1.85 V and a turn-off voltage of 2.90 V. In the case of Au/N molar ratio of 1:1, the corresponding device exhibited conductor behaviour. This work opens a way that can both recycle gold in situ from e-wastes and fabricate electronic devices by using polymer nanosphere-supported Au nanoparticles.
The Cascade Analysis Tool: software to analyze and optimize care cascades
Authors: Kedziora David J , Abeysuriya Romesh , Kerr Cliff C , Chadderdon George L , Harbuz Vlad-Ștefan , Metzger Sarah , Wilson David P , Stuart Robyn M 
Published: December 2019

Introduction: Cascades, which track the progressive stages of engagement on the path towards a successful outcome, are increasingly being employed to quantitatively assess progress towards targets associated with health and development responses. Maximizing the proportion of people with successful outcomes within a budget-constrained context requires identifying and implementing interventions that are not only effective, but also cost-effective. Methods: We developed a software application called the Cascade Analysis Tool that implements advanced analysis and optimization methods for understanding cascades, combined with the flexibility to enable application across a wide range of areas in health and development. The tool allows users to design the cascade, collate and enter data, and then use the built-in analysis methods in order to answer key policy questions, such as: understanding where the biggest drop-offs along the cascade are; visualizing how the cascade varies by population; investigating the impact of introducing a new intervention or scaling up/down existing interventions; and estimating how available funding should be optimally allocated among available interventions in order to achieve a variety of different objectives selectable by the user (such as optimizing cascade outcomes in target years). The Cascade Analysis Tool is available via a user-friendly web-based application, and comes with a user guide, a library of pre-made examples, and training materials. Discussion: Whilst the Cascade Analysis Tool is still in the early stages of existence, it has already shown promise in preliminary applications, and we believe there is potential for it to help make sense of the increasing quantities of data on cascades.
A Rent-Seeking View of the Ageing Problem in Developed Countries
Authors: Colombatto Enrico 
Published: December 2019

I Paesi industrialmente avanzati stanno sperimentando un notevole incremento nel loro tasso di dipendenza dagli anziani ed una caduta nella quota dei giovani.
Questo scritto si concentra sul problema delle pensioni, suggerendo che il peso di questi fattori dovrebbe essere correlato al modo in cui essi influiscono sul sottostante contratto tra contribuenti e altre coalizioni, ivi incluse la burocrazia e i politici.
Dal punto di vista della logica economica, non vi sarebbero ragioni per riconoscere alio Stato un potere decisionale nella redistribuzione di risorse tra eenerazioni. Il fatto che, invece, lo Stato svolga questo ruolo richiede una spiegazione delle ragioni per cui lo Stato trovi necessaria la redistribuzione.
L’esclusione dei giovani dal processo decisionale permette agli elettori ed ai politici di accordarsi su soluzioni che sono svantaggiose per le giovani generazioni.
Il sistema di pagamento delle pensioni sulla base delle entrate correnti garantisce i beneficiari che in ciascun momento le pensioni siano pagate da qualcun altro, cioè da chi in quel momento lavora.
Due tipi di soluzioni possono essere perseguiti: 1) riduzione del welfare state, con aumento delle risorse destinate alle pensioni; 2) se, però il potere della burocrazia e delle classi che usufruiscono di rendite parassitarie è molto forte, è più probabile che la spesa si stabilizzi, aumentando le imposte o riducendo le pensioni, o spostando in avanti l’età della pensione.
L’aspetto che qui viene evidenziato è che un problema può emergere se gli individui non adattano sistematicamente i loro profili di risparmio e consumo per tener conto dei futuri sviluppi demografici. Tale incapacità degli individui potrebbe richiedere l’intervento pubblico, peraltro limitato all’informazione, che sarebbe certamente di qualità migliore di quella disponibile a livello privato.
The Economics of Election Campaign Spending Limits
Authors: Palda Filip 
Published: December 2019

I limiti alia spesa sono una regola importante nel «gioco» elettorale. I critici dei limiti affermano che i candidati già in carica (gli «uscenti») elaborano queste norme per tenere lontani i possibili sfidanti.
Questi ragionamenti sono interessanti, ma non poggiano su di una base empirica solida. I dati potrebbero sostenere o respingere l’opinione critica, dopo opportuno trattamento.
La tesi di quest’articolo è che se i candidati già in carica traggono vantaggio dai limiti alia spesa, tale vantaggio viene ottenuto in un modo che non è in alcun modo evidenziato dai dati.
Il vantaggio non emerge in forma di maggiori voti per i candidati in carica, ma in termini di maggiori benefici per i loro più stretti sostenitori.
Questa spiegazione va al di là di quella tradizionale sul modo in cui le limitazioni alle spese elettorali aiutano i candidati in carica. Essa può anche contribuire alia comprensione dei motivi per cui non è possibile dare una risposta definitiva alia controversia su chi trae vantaggio dai limiti alle spese elettorali.
The Regional Policy of the European Communities and the Subsidiarity Principle
Authors: van Meerhaeghe Marcel A.G. 
Published: December 2019

Il principio di «sussidiarietà» è stato utilizzato nell’ambito europeo per indicare che le decisioni non devono essere prese al livello più alto (Comunità), quando è possibile prenderle a livelli minori (Stati membri).
Dopo essersi soffermato sul principio di sussidiarietà, evidenziandone il carattere dinamico, questo scritto approfondisce la politica regionale della Comunità Europea, dapprima delineando le principali norme del Trattato di Roma che riguardano la politica regionale e poi considerando la corrispondente politica.
Vengono particolarmente approfonditi i problemi delle regioni prioritarie e i principali strumenti della politica in loro sostegno, i cosiddetti «fondi strutturali», giungendo alia conclusione che sino ad oggi tali strumenti non hanno dato luogo a risultati conformi alle aspettative.