bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of miRNA-mediated Regulation of Flowering Induction in Lilium × formolongi
Authors: Zhang Qian , Zhao Yu-Qian , Gao Xue , Jia Guixia 
Published: December 2020

Abstract
Background: MicroRNAs play pivotal roles in plant vegetative phase change and flowering induction via integrating into multiple flowering pathways. Lilium × formolongi is an important ornamental lily cultivar that can flower within one year after sowing. However, it remains unresolved how miRNA-mediated regulation networks contribute to the L. × formolongi characteristics of a short vegetative growth period and rapid flowering.Results: In this study, five small RNA libraries and one degradome library were constructed for L. × formolongi during vegetative growth and flowering initiation, and 366 conserved miRNAs and 32 novel miRNAs were identified. Additionally, 84 miRNAs were significantly differentially expressed during development. A total of 396 targets of 185 miRNAs were identified and validated through degradome sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that functions of the targets were top enriched in the cold and cadmium ion responses, pentose phosphate pathway and carbon fixation in photosynthetic organisms pathway. Furthermore, among 23 differentially expressed miRNA-target pairs, the miR156s-LfSPL2, miR172a-LfAP2 and miR164a-LfNAC pairs as well as miR159a-LfSPL2 were found to be relevant to flowering based on the correlation analysis of expression profiles in the miRNA libraries, degradome and transcriptome. A coexpression regulatory network focused on differentially expressed pairs was also constructed by WGCNA, and 14 miRNAs were considered putative key miRNAs during vegetative development and flowering induction. miR156a/ d/ e showed particularly strong relationships with other miRNAs in the coexpression network. Conclusions: This study provides cues for the further exploration of the regulatory mechanisms of short vegetative development and flowering in L. × formolongi.
Swarm-based Counter UAV Defense System
Authors: Brust Matthias , Danoy Grégoire , Stolfi Daniel , Bouvry Pascal 
Published: December 2020

Abstract
Unmanned Aerial Vehicles (UAVs) have quickly become one of the promising Internet-of-Things (IoT) devices for smart cities thanks to their mobility, agility, and onboard sensors' customizability. UAVs are used in many applications expanding beyond the military to more commercial ones, ranging from monitoring, surveillance, mapping to parcel delivery. As governments plan using UAVs to build fresh economic potential for innovation, urban planners are moving forward to incorporate so-called UAV flight zones and UAV highways in their smart city design. However, the high-speed and dynamic flow of UAVs needs to be monitored to detect and, subsequently, to deal with intruders, rough drones, and UAVs with a malicious intent. Autonomous defense systems consisting of collaboratively working UAVs as a swarm will gain increasing importance, since a manually conducted defense is bound to fail due to the high dynamics involved in UAV maneuvering. This paper proposes a UAV defense system for intercepting and escorting intruders. The proposed UAV defense system consists of a defense UAV swarm, which is capable to self-organize their defense formation in the event of intruder detection, and chase the malicious UAV. Our fully localized approach follows a modular design regarding the defense phases and it uses a newly developed balanced clustering to realize the intercept- and capture-formation. The resulting networked defense UAV swarm is resilient against communication losses. Finally, a prototype UAV simulator has been implemented. Through extensive simulations, we demonstrate the feasibility and performance of our approach.
Adaptation of Central Metabolite Pools to Variations in Growth Rate and Cultivation Conditions in Saccharomyces Cerevisiae
Authors: Kumar Kanhaiya , Venkatraman Vishwesh , Bruheim Per 
Published: December 2020

Abstract
Background: Saccharomyces cerevisiae is a well-known popular model system for basic biological studies and to serve as host organism for heterologous production of commercially interesting small molecules and proteins. The central metabolism is at the core to provide building blocks and energy to support growth and survival in normal situations as well as during exogeneous stresses and forced heterologous protein production. Here, we present a comprehensive study of intracellular central metabolite pool profiling when growing S. cerevisiae on different carbon sources in batch cultivations and at different growth rates in nutrient limited glucose chemostats. Latest versions of absolute quantitative mass spectrometry-based metabolite profiling methodology were applied to cover glycolytic and pentose phosphate pathway metabolites, TCA, complete amino acid and deoxy-/nucleoside phosphate pools. We have attempted to correlate the total metabolite pool composition with growth rates and nutrient limitation in both batch and chemostat cultivations. We have also tried to dissect the Crabtree-effect, i.e. ethanol-producing cultivation conditions, based on metabolite pool composition. Results: Glutamate, glutamine, alanine and citrate were the four most abundant metabolites for most conditions tested. Amino acid is the dominant metabolite class even though a marked relative reduction compared to the other metabolite classes was observed for nitrogen and phosphate limited chemostats. Interestingly, glycolytic and PPP metabolites display largest variation among the cultivation conditions while the nucleoside phosphate pools are more stable and vary within a closer concentration window. The overall trends for glucose and nitrogen limited chemostats were increased metabolite pools with increasing growth rate. Next, comparing the chosen chemostat reference growth rate (0.12 h -1 , approximate one-fourth of maximal unlimited growth rate) illuminates an interesting pattern: almost all pools are lower in nitrogen and phosphate limited conditions compared to glucose limitation, except for the TCA metabolites citrate, isocitrate and a-ketoglutarate. Conclusions: This study provides new knowledge how the central metabolism is adapting to various cultivations conditions and growth rates which is essential for expanding our understanding of cellular metabolism and development of improved phenotypes in metabolic engineering.
Genetic Diversity and Natural Selection on the Thrombospondin-Related Adhesive Protein (TRAP) Gene of Plasmodium Falciparum on Bioko Island, Equatorial Guinea and Global Comparative Analysis
Authors: Lin Li-Yun , Huang Hui-Ying , Liang Xue-Yan , Xie Dong-De , Chen Jiang-Tao , Wei Hua-Gui , Huang Wei-Yi , Ehapo Carlos Salas , Eyi Urbano Monsuy , Li Jian , Wang Jun-Li , Zheng Yu-Zhong , Zha Guang-Cai , Wang Yu-Ling , Chen Wei-Zhong , Liu Xiang-Zhi , Mo Huan-Tong , Chen Xin-Yao , Lin Min 
Published: December 2020

Abstract
Background: Thrombospondin-related adhesive protein (TRAP) is a transmembrane protein that plays a crucial role during the invasion of Plasmodium falciparum into liver cells. As the potential malaria vaccine candidate, the genetic diversity and natural selection of PfTRAP was assessed and the global PfTRAP polymorphism pattern was painted. Methods: 153 blood spot samples from Bioko malaria patients were collected during 2016-2018 and the target TRAP gene was amplified. Together with the sequences from database, nucleotide diversity and natural selection analysis, and the structural prediction were preformed using bioinformatical tools.Results: A total of 119 monoclonal Bioko PfTRAP sequences were amplified successfully. On Bioko Island, PfTRAP shows its high degree of genetic diversity and heterogeneity, with π value for 0.01046 and Hd for 0.99. The value of dN-dS (6.2231, p<0.05) and the nagetive Tajima's D (-0.41438) hinted at natural selection of PfTRAP on Bioko Island. Globally, the African PfTRAPs showed more diverse than the Asian ones, and significant genetic differentiation was discovered by the fixation index between African and Asian countries (Fst>0.15, p<0.05). 667 Asian isolates clustered in 136 haplotypes and 739 African isolates clustered in 528 haplotypes by network analysis. The mutations I116T, L221I, Y128F, G228V and P299S were predicted as probably damaging by PolyPhen online service, while mutations L49V, R285G, R285S, P299S and K421N would lead to a significant increase of free energy difference (ΔΔG>1) indicated a destabilization of protein structure. Conclusions: Evidences in the present investigation supported that PfTRAP gene from Bioko Island and other malaria endemic countries is highly polymorphic (especially at T cell epitopes) and the global PfTRAP gene is under natural selection, which provided the genetic information background for developing an PfTRAP-based universal effective vaccine. Moreover, some mutations showed destructive to the protein structure or function and deserve further study and continuous monitoring.
Population Structure of 93 Varieties of Rice ( Oryza Sativa&nbsp;L. subsp. Hsien Ting) in Qinba, China
Authors: Zhang Yu , Wang Ye wen , Wang Yue xing , Zheng Shi mao , Zhou Wan ying , Liu Hong 
Published: December 2020

Abstract
BackgroundThe Qinba region is the transition region between indica and japonica varieties with a long history of indica varieties planting. 72,824 SNPs data based on GBS method, 48 pairs core primers of SSRs, and 15 agronomic traits were employed to explore the population structure of 93 rice varieties. The Mantel test was used to analyze the distance matrix generated using NlaIII-GBS only, MseI-GBS only, by combining NlaIII-GBS and MseI-GBS data and SSR.ResultIn this study, a total of 379 alleles were obtained using 48 pairs core primer of SSR, encompassing an average of 8.0 alleles per primer. The PPB and PIC was 88.65% and 0.77, respectively. Among these, RM278 possess the highest TNB and NPB, and the PPB in 29 pairs of SSR markers was 100%. RM176 showed the highest PIC. MAF was set to 0.05, and 39,872, 35,547 and 67,621 SNPs were obtained via NlaIII-GBS only, MseI-GBS only, and merged NlaIII-GBS and MseI-GBS data, respectively. The IBS genetic similarity coefficient average was 0.74. The results showed that the correlation between the genetic distance matrix based on NlaIII-GBS and MseI-GBS was the largest (R2=0.88), followed by NlaIII-GBS and SSR (R2=0.35), then by merged NlaIII-GBS and MseI-GBS data and SSR (R2=0.33), and the smallest by MseI-GBS and SSR (R2=0.27). The results showed that the 93 rice varieties could be clustered into two subgroups. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations. Tajima’s D value was 1.66, and the FST between the two populations was 0.61, and the Nm was 0.16.ConclusionThe population genetic variation explained by SNP was larger than that explained by SSR. Through cluster analysis, the 93 samples were divided into 2 subgroups, with more than 97% of the samples clustered into one subgroup. The gene flow of 93 samples used in this study is larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of indica varieties in the Qinba region. However, the genetic structure of the rice population is simple and lacked rare alleles.
Do Patients with a Poor Karnofsky Performance Status Scale Profit from Tumour Volume Reduction?
Authors: Barz Melanie , Gerhardt Julia , Bette Stefanie , Aftahy A. Kaywan , Huber Thomas , Combs Stephanie E. , Ryang Yu-Mi , Wiestler Benedikt , Skardelly Marco , Gepfner-Tuma Irina , Behling Felix , Schmidt-Graf Friederike , Meyer Bernhard , Gempt Jens 
Published: December 2020

Abstract
Purpose: Median overall survival (OS) after diagnosis of glioblastoma (GBM) remains 15 months amongst patients receiving aggressive surgical resection, chemotherapy and irradiation. Treatment of patients with a poor preoperative Karnofsky Performance Status Scale (KPSS) is still controversial. Therefore, we retrospectively assessed the outcome after surgical treatment in patients with a KPSS of ≤ 60%.Methods: We retrospectively included patients with a de-novo glioblastoma WHO °IV and preoperative KPSS ≤ 60%, who underwent surgery at two neurosurgical centres between September 2006 and March 2016. We recorded pre- and postoperative tumour volume, pre- and postoperative KPSS, OS, age and MGMT promoter status.Results: 123 patients (58 females/65 males, mean age 67.4 ± 13.4 years) met the inclusion criteria. 75 of the 123 patients (61%) underwent surgical resection. 48/123 patients (39%) received a biopsy. The median preoperative and postoperative tumour volume of all patients was 33.0 ± 31.3 cm3 (IR 15.0–56.5cm3) and 3.1 ± 23.8 cm3 (IR 0.2–15.0 cm3), respectively. The median KPSS was 60% (range 20–60%) preoperatively and 50% (range 0–80%) postoperatively. The median OS was 123 ± 220 days (IR 52–395 days). Age (p<0.001, HR: 1.045 [95% CI 1.022–1.068]), postoperative tumour volume (p=0.02, HR: 1.016 [95% CI 1.002–1.029]) and MGMT promotor status (p=0.016, HR: 0.473 [95% CI 0.257–0.871]) were statistically significant in multivariate analysis.Conclusion: Patients with a preoperative KPSS of ≤ 60% benefit from low postoperative residual tumour volumes. Age and MGMT-methylation status were also significant prognostic parameters in this patient cohort.
Outcomes of Assisted Reproductive Technology in Women Infected with the Hepatitis B Virus
Authors: Zhu Yimin , Hu Xiaoling , Wan Shan , Chen Yunwen , Meng Xia , Tang Minyue , Fu Yanling , Yan Huanmiao , Liu Aixia , Chen Xijing , Lu Yongchao 
Published: December 2020

Abstract
Objectives: To investigate whether women infected with the hepatitis B virus affects the outcomes of assisted reproductive technology (ART). Methods：A total of 1542 HBV infected women, and the same number of non-infected age-matched women undergoing fresh ART treatments. All male partners were without any history of HBV infection. Three groups were defined: HBV-positive, HBeAg/preS1-positive, and HBV-negative. Pregnancy outcomes were evaluated and compared using multivariate logistic regression analysis to control for confounding factors.Results: No difference was observed in the live birth rate among couples according to HBV status; that is, women were HBsAg- or HBeAg/preS1-seropositive, or both partners were HBsAg-seronegative (35.29%, 32.79%, and 34.27%, respectively; P < 0.05). After multivariate modeling to adjust for the possible confounding variables, the live birth rate still did not differ significantly between the HBV-positive group or the HBeAg/preS1-positive group and the HBV-negative group (adjusted OR 1.11, 95% CI 0.93−1.32 and adjusted OR 1.02, 95% CI 0.83−1.25, respectively). Furthermore, no differences were found in clinical pregnancy rate, miscarriage rate, birth weight, low birth weight rate, preterm rate or ovarian responses among the three groups. The incidence of secondary infertility and tubal factor infertility in women who were HBsAg- or HBeAg/preS1-seropositive was significantly higher than that in women without HBV infection. Conclusions: HBV infection in women was associated with a higher risk of secondary infertility and tubal factor infertility, but has no significant impact on pregnancy outcomes and ovarian responses in HBsAg-seropositive women as compared with HBsAg-seronegative women, irrespective of their serum HBeAg and preS1 status.
Construction of an ultrahigh-density linkage map and graphical representation of the arrangement of transcriptome-based unigene markers on the chromosomes of Allium cepa L.
Authors: Fujito Satoshi , Akyol Turgut Yigit , Mukae Takuya , Wako Tadayuki , Yamashita Ken-ichiro , Tsukazaki Hikaru , Hirakawa Hideki , Tanaka Keisuke , Mine Yoko , Sato Shusei , Shigyo Masayoshi 
Published: December 2020

Abstract
BackgroundGenomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an A. cepa mapping population for transcriptome-based SNP genotyping.ResultsWe mapped the transcriptome sequence reads from a series of A. fistulosum-A. cepa MALs onto the unigene sequence of the doubled haploid shallot A. cepa Aggregatum group (DHA) and compared the MAL genotype call for parental bunching onion and shallot transcriptome mapping data. We identified SNP sites with at least four reads on 25,462 unigenes. They were anchored on eight A. cepa chromosomes. A single SNP site was identified on 3,278 unigenes and multiple SNPs were identified on 22,184 unigenes. The chromosome marker information was made public via the web database Allium TDB (http://alliumtdb.kazusa.or.jp/). To map these markers, we gathered RNA sequence data from 96 lines of a DHA × doubled haploid bulb onion A. cepa common onion group (DHC) mapping population. After selecting co-dominant SNP sites, 16,872 SNPs were identified in 5,339 unigenes. Of these, at least two SNPs with identical genotypes were found in 1,435 unigenes. We developed a linkage map using genotype information from these unigenes. All unigene markers mapped onto the eight chromosomes and graphical genotyping was conducted based on the unigene order information. Another 2,963 unigenes were allocated onto the eight chromosomes. To confirm the accuracy of this transcriptome-based genetic linkage map, conventional PCR-based markers were used for linkage analysis. All SNP - and PCR-based markers were mapped onto the expected linkage groups and no inconsistency was found among these chromosomal locations.ConclusionsEffective transcriptome analysis with unique Allium resources successfully associated numerous chromosome markers with unigene information and an ultrahigh-density A. cepa linkage map. The information on these unigene markers is valuable in genome sequencing and useful trait detection in Allium.
Predicting Progress in Word Learning for Children With Autism and Minimal Verbal Skills
Authors: Brady Nancy , Kosirog Christine , Fleming Kandace K. , Williams Lindsay 
Published: December 2020

Abstract
Background: Approximately 30 % children diagnosed with autism remain minimally verbal past age 5. Interventions are often effective in increasing spoken communication for some of these children. Clinical and research decisions would be facilitated by identifying early indicators of progress in interventions. The purpose of this study is to investigate the relationship between speech sound measures obtained from the early phases of treatment and later treatment outcomes in children with autism and minimal verbal skills. Mehtods: Twenty-three children (18 boys) between 5-9 years of age participated. We compared scores reflecting the phonemic features of word attempts produced during probes, and the number of correct words after 4 weeks of intervention to later word learning outcomes. Results: Correlational analyses showed that both predictors were positively correlated with outcomes, but the phonemic scores were more strongly related than number of correct words. Conclusion: We conclude that phonemic scoring may be a useful measure to determine proximal gains in a spoken word learning intervention. Proximal measures are particularly helpful when trying to decide if the current course of intervention should be maintained or altered.
Incidence and Prognostic Factors of Primary Thyroid Lymphoma and Construction of Prognostic Models for Post-chemotherapy and Postoperative Patients: A Population-based Study
Authors: Xiang Nan , Dong Fangyuan , Zhan Xuebing , Wang Shuhan , Wang Junjie , Sun Entao , Chen Bing 
Published: December 2020

Abstract
Background: Primary thyroid lymphoma (PTL) is a rare thyroid malignancy, there are few large sample studies on PTL and no standardized treatment regimen has been established due to the rarity. Objective: The aims of this study were to explore the incidence and prognostic factors of PTL and construct visual prognostic prediction models for post-chemotherapy and postoperative patients.Methods: The incidence of PTL in 1975-2017 was extracted from the US Surveillance, Epidemiology, and End Results (SEER) database, then assessed using joinpoint regression software. A total of 1,616 eligible PTL patients diagnosed in 1998-2016 were brought into prognostic analysis. Multivariate Cox regression analyses were carried out to reveal independent prognostic elements for overall survival (OS) and cancer-specific survival (CSS).Results: PTL incidence showed a relatively steady increase in 1975-1994, which annual percent change (APC) was 4.0%, and steady decreasing in 1994-2017(APC -2.4%). Age, marital status, lymphoma Ann Arbor stage, histological subtypes, surgery, chemotherapy, and radiation were significantly correlated to OS and CSS. The combination of radiotherapy with chemotherapy or surgery was beneficial to the prognosis of patients. Nomograms were constructed to predict OS and CSS in post-chemotherapy and postoperative PTL patients separately, and were verified to have good reliability.Conclusions: The incidence of PTL increased and subsequently decreased. We revealed the prognostic implications and constructed reliable nomograms for post-chemotherapy and postoperative PTL patients.
Mental Health Problems Are the Leading Cause of Hospitalization Among Adolescents Accessing a Pediatric Emergency Department in Italy.
Authors: Cozzi Giorgio , Passaglia Lisa , Agrusti Anna , Giangreco Manuela , Giorgi Rita , Rabach Ingrid , Germani Claudio , Barbi Egidio 
Published: December 2020

Abstract
AimDescribe the use of the pediatric emergency department of a tertiary-level children’s hospital in Italy by adolescents. MethodsThis retrospective study was based on the medical records of patients aged 13 to 17 years, who accessed the pediatric emergency department of the Institute for Maternal and Child Health IRCCS Burlo Garofolo, from 1 January to 31 December 2018. For each patient, we reported: age, gender, triage category, chief complaint, diagnosis, admission status, and hospital ward of destination. The primary outcome was to describe the use of the department in terms of leading causes of access, diagnoses, and outcomes. ResultsDuring the study period, 3062 adolescents accessed to the department, for a total of 3895 unscheduled visits. The principal causes of access were trauma (45.3%) and organic diseases (38.8%). 249 adolescents (6.4%) had mental health problems. One-hundred-forty-two adolescents (3.6%) were admitted to the hospital, 54 of whom to the neuropsychiatric ward, for mental health problems. Compared to younger patients entering the department, adolescents were admitted to the neuropsychiatric ward more frequently (p <0.001). Conclusions﻿In this series, mental health problems were a frequent cause of urgent access to the hospital and the leading cause of urgent hospitalization among adolescents.