bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining Several Substitution Cipher Algorithms using Circular Queue Data Structure
Authors: Ibraheem Noor , Hasan Mokhtar
Published: December 2020

With the revolutionized expansion of the Internet, worldwide information increases the application of communication technology, and the rapid growth of significant data volume boosts the requirement to accomplish secure, robust, and confident techniques using various effective algorithms. Lots of algorithms and techniques are available for data security.  This paper presents a cryptosystem that combines several Substitution Cipher Algorithms along with the Circular queue data structure. The two different substitution techniques are; Homophonic Substitution Cipher and Polyalphabetic Substitution Cipher in which they merged in a single circular queue with four different keys for each of them, which produces eight different outputs for every single incoming letter. The present work can be applied efficiently for personal information security and network communication security as well, and the time required for ciphering and deciphering a message is less than 0.1 sec.
Detection of Suicidal Ideation on Twitter using Machine Learning & Ensemble Approaches
Authors: Rabani Syed Tanzeel , Khan Qamar Rayees , Khanday Akib Mohi UD Din
Published: December 2020

Suicidal ideation is one of the most severe mental health issues faced by people all over the world. There are various risk factors involved that can lead to suicide. The most common & critical risk factors among them are depression, anxiety, social isolation and hopelessness. Early detection of these risk factors can help in preventing or reducing the number of suicides. Online social networking platforms like Twitter, Redditt and Facebook are becoming a new way for the people to express themselves freely without worrying about social stigma. This paper presents a methodology and experimentation using social media as a tool to analyse the suicidal ideation in a better way, thus helping in preventing the chances of being the victim of this unfortunate mental disorder. The data is collected from Twitter, one of the popular Social Networking Sites (SNS). The Tweets are then pre-processed and annotated manually. Finally, various machine learning and ensemble methods are used to automatically distinguish Suicidal and Non-Suicidal tweets. This experimental study will help the researchers to know and understand how SNS are used by the people to express their distress related feelings and emotions. The study further confirmed that it is possible to analyse and differentiate these tweets using human coding and then replicate the accuracy by machine classification. However, the power of prediction for detecting genuine suicidality is not confirmed yet, and this study does not directly communicate and intervene the people having suicidal behaviour.
Sea-ice retreat may decrease carbon export and vertical microbial connectivity in the Eurasian Arctic basins
Authors: Fadeev Eduard , Rogge Andreas , Ramondenc Simon , Nöthig Eva-Maria , Wekerle Claudia , Bienhold Christina , Salter Ian , Waite Anya , Hehemann Laura , Boetius Antje , Iversen Morten
Published: December 2020

Arctic Ocean sea-ice cover is shrinking due to warming. Long-term sediment trap data show higher export efficiency of particulate organic carbon in regions with seasonal sea-ice compared to regions without sea-ice. To investigate this sea-ice enhanced export, we compared how different phytoplankton communities in seasonally ice-free and ice-covered regions of the Fram Strait affect carbon export and vertical dispersal of microbes. In situ collected aggregates, combined with microbial source tracking revealed that larger aggregates from sea-ice and under-ice diatom blooms were responsible for higher export efficiency and vertical microbial connectivity. During early summer, Phaeocystis aggregates dominated the ice-free regions and exported two-fold less carbon than diatom aggregates in ice-covered regions, and also less surface-born microbial clades to the deep-sea. This suggests that continuous ice-loss will further decrease pelagic-benthic coupling, impacting the quantity and quality of food input due to formation of slow-settling aggregates, with potential repercussions for Arctic deep-sea ecosystems.
Out-of-plane emission of trions in monolayer WSe2 revealed by whispering gallery modes of dielectric microresonators
Authors: Andres-Penares Daniel , Hábil Mojtaba Karimi , Molina-Sánchez Alejandro , Zapata-Rodríguez Carlos , Martinez-Pastor Juan , Sánchez-Royo Juan
Published: December 2020

The manipulation of light emitted by two-dimensional semiconductors grounds forthcoming technologies in the field of on-chip communications. However, these technologies require from the so elusive out-of-plane photon sources to achieve an efficient coupling of radiated light into planar devices. Here we propose a versatile spectroscopic method that enables the identification of the out-of-plane component of dipoles due to the selective coupling of light emitted by in-plane and out-of-plane dipoles to the whispering gallery modes of spherical dielectric microresonators, in close contact to them. We have applied this method to demonstrate the existence of dipoles with an out-of-plane orientation in monolayer WSe2 at room temperature, by means of micro-photoluminescent measurements, numerical simulations based on finite element methods, and ab-initio calculations. Experimental results and ab-initio calculations identify trions as the source responsible for this out-of-plane emission, opening new routes for realizing on-chip integrated systems with applications in information processing and quantum communications.
The Role of Undegraduate Medical Students Training in Respect for Patient Confidentiality
Authors: Beltran-Aroca Cristina M , Ruiz-Montero Rafael , Labella Fernando , Girela-López Eloy
Published: December 2020

IntroductionEncouraging professional integrity is vital in providing a standard of excellence in the quality of medical care and education, promoting a culture of respect and responsibility. The main objective of this work consisted of studying the relationship of medical students with the right to privacy of patients in Spain, specifically analysing the conditions of accessing patients’ Clinical History (CH).MethodsA questionnaire was sent to final-year students at 41 Spanish universities. It had 14 multiple choice questions framed in 3 large blocks. The first one addressed basic general knowledge issues on the right to privacy and the obligation of confidentiality. The two remaining blocks were made up of questions directed towards evaluating the frequency with which certain requirements and steps of action related to the students in attending the patient were performed, and regarding the guarantees in accessing and handling their CH both on paper and in the Electronic Medical Record.ResultsA total of 245 valid replies was considered. 67.8% of participants were women, with an average age of 24.05±3.49 years. Up to 90.6% were aware that confidentiality affected the data in CHs, although 43.3% possessed non-anonymized photocopies of patients’ clinical reports outside healthcare context, and only 49.8% of the students were always adequately identified. 59.2% accessed patients’ CHs on some occasions by using passwords of healthcare professionals and 77.2% of them did not have patients’ express consent and 71.9% accessed a CH that was not anonymised.ConclusionsThe role of healthcare institutions and universities is considered to be fundamental in implementing educational measures regarding the risks and ethical and legal problems arising from the use of CHs among professionals and students. A profound study of medical ethics is needed through the analysis of clinical cases, and direct exposure to situations in which the patient’s confidentiality is questioned.
Microwave-Assisted One Pot Three-Component Synthesis of Novel Bioactive Thiazolyl-pyridazinediones As Potential Antimicrobial Agents against Antibiotic-Resistant Bacteria
Authors: Abu-Melha Saraa , Gomha Sobhi , Abouzid Amr , Edrees Mastoura , Dena Ahmed Abo , Muhammad Zeinab
Published: December 2020

Novel 2-thiazolyl-pyridazinedione derivatives were prepared via multicomponent synthesis under microwave irradiation as ecofriendly energy source and using the eco-friendly naturally occurring chitosan basic catalyst with high/efficient yields and short reaction time. All the prepared compounds were fully characterized by spectroscopic methods, and their in-vitro biological activities were investigated. The obtained results were compared with those of standard antibacterial/antifungal agents. DFT calculations and molecular docking studies were used to investigate the electronic properties and molecular interactions with specific microbial receptors.
Accurate Detection and Quantification of Seasonal Abundance of American Bullfrog (Lithobates Catesbeianus) Using ddPCR eDNA Assays
Authors: Everts Teun , Halfmaerten David , Neyrinck Sabrina , De Regge Nico , Jacquemyn Hans , Brys Rein
Published: December 2020

The invasive American bullfrog (Lithobates catesbeianus) imperils freshwater biodiversity worldwide. Effective management includes rapid detection and response to incipient invasions, as established populations are extremely difficult to eradicate. Although environmental DNA (eDNA) approaches provide a highly sensitive alternative to conventional surveillance techniques, extensive testing is paramount to generate reliable output. Here, we tested and compared the performance of two primer/probe assays to detect and quantify the abundance of bullfrogs in silico and in situ using digital droplet PCR. Although both assays proved to be equally specific and sensitive, one outperformed the other in detection resolution (i.e. distinguishing target and non-target droplets), and hence was selected for further analyses. Mesocosm experiments using density series of larval and juvenile bullfrogs revealed that eDNA concentrations could explain 99% of the larval abundance and biomass. Per individual eDNA emission rates did not differ significantly among life stages, indicating that eDNA concentrations can be used as a reliable proxy to asses bullfrog abundance in natural populations. Seasonal eDNA patterns in three infested ponds showed parallel fluctuations in bullfrog eDNA concentrations. A peak in late summer (August, September or October), coinciding with the breeding season, was followed by continuously low eDNA concentrations in winter and spring. These findings demonstrate that eDNA analyses can be used as a solid and reliable tool to detect the early stages of bullfrog invasions and to quantify temporal changes in abundance that will be useful in coordinating and evaluating large-scale bullfrog eradication programs.
Effect of six weeks 1000 mg/day Vitamin C supplementation and healthy training in elderly women on genes expression associated with immune response - a randomized controlled trial
Authors: Żychowska Małgorzata , Grzybkowska Agata , Zasada Mariusz , Piotrowska Anna , Dworakowska Danuta , Czerwinska-Ledwig Olga , Pilch Wanda , Antosiewicz Jędrzej
Published: December 2020

BackgroundIn this study we investigated the effects of supplementation and exercise on the expression of genes associated with inflammation like CCL2, CRP, IL1, IL6, IL10 mRNA in elderly women.MethodsTwenty four participants divided randomly into two groups were subjected to 6 weeks of the same health training program (three times per week). SUP group (supplemented, n = 12, mean age 72.8 ± 5.26 years and mean body mass 68.1 ± 8.3 kg) received 1000 mg of Vitamin C/day during training period, while CON group (control, n = 12, mean age 72.4 ± 5.5 years and body mass 67.7 ± 7.5 kg) received placebo.ResultsNo significant changes in IL-1, IL-6, IL-10 and CRP mRNA were observed within and between groups. However, there was a clear tendency of a decrease in IL-6 (two-way ANOVA, significant for time) and an increase in IL-10 mRNA noted in the supplemented group. A significant decrease in CCL2 mRNA was observed only in the CON group (from 2^0.2 to 2^0.1, p = 0.01).ConclusionsIt can be concluded, that 6 weeks of supplementation and exercise was too short to obtain significant changes in gene expression in leukocytes, but supplementation of 1000 mg vitamin C positively affected IL-6 and IL-10 expression – which are key changes in the adaptation to training. However, changes in body mass, IL1 and CCL2 was positive in CON group. It is possible that Vitamin C during 6 weeks of supplementation could have different effects on the expression of individual genes involved in immune response.Trial registration: retrospectively registered.
Network machine learning maps phytochemically-rich “Hyperfoods” to fight COVID-19
Authors: Laponogov Ivan , Gonzalez Guadalupe , Shepherd Madelen , Qureshi Ahad , Veselkov Dennis , Charkoftaki Georgia , Vasiliou Vasilis , Youssef Jozef , Mirnezami Reza , Bronstein Michael , Veselkov Kirill
Published: December 2020

In this paper, we introduce a network machine learning method to identify potential bioactive anti-COVID-19 molecules in foods based on their capacity to target the SARS-CoV-2-host gene-gene (protein-protein) interactome. Our experiments were run using a supercomputing DreamLab App platform, harnessing the idle computational power of thousands of smartphones. Machine learning models were initially calibrated by demonstrating that the proposed method can predict anti-COVID-19 candidates among experimental and clinically approved drugs (5658 in total) targeting COVID-19 interactomics with the balanced classification accuracy of 80-85% in 5-fold cross-validated settings. This identified the most promising drug candidates that can be potentially “repurposed” against COVID-19 including common drugs used to combat cardiovascular and metabolic disorders, such as simvastatin, atorvastatin and metformin. A database of 7694 bioactive food-based molecules was run through the calibrated machine-learning algorithm, which identified 52 biologically active molecules, from varied chemical classes, including flavonoids, terpenoids, coumarins and indoles predicted to target SARS-CoV-2-host interactome networks. This in turn was used to construct a “food map” with the theoretical anti-COVID-19 potential of each ingredient estimated based on the diversity and relative levels of candidate compounds with antiviral properties. We expect this in-silico predicted food map to play an important role in future clinical studies of precision nutrition interventions against COVID-19 and other viral diseases.
The Long Noncoding RNA Differential Expression in Peripheral Blood Leukocyte from Schizophrenia Patients by RNA Sequencing
Authors: Wu Jie , Liu Zijun , Zhang Yunqiao , Teng Zhaowei , You Xu , Ruan Ye , Gao Changqing , Zeng Yong , Teng Zhaowei
Published: December 2020

Background: The diagnosis of schizophrenia (SCZ) depends on the evaluation of clinical symptoms, and there is no objective biomarker. Surveys have found that long non-coding RNA (lncRNA) may be affected in the pathogenesis of SCZ. There are also different genes in the expression of peripheral blood (PBL) in SCZ patients.Methods: We profiled transcriptome analysis of PBL in 50 patients with schizophrenia and 50 controls without psychiatric diagnoses, reconstructed PBL transcriptome information using RNA-seq, predicted lncRNA-mRNA interaction via “RNAplex”, a hierarchical classification-Spielman correlation coefficient approach was used to analyze the correlation between lncRNA and protein-coding gene expression among samples, and used systematic bioinformatics methods (Go/Pathway) to perform lncRNA functional annotation and qPCR experimental verification. Predicting functional sites for sequences using the database PROSITE, NCBI, UCSC, JASPAR.Results: We screened 94 lncRNA and 1179 mRNA differential expressions in PBL, of which 46 new lncRNAs were identified for the first time. Enrichment into lncRNA involves biological processes and signaling pathways related to the neutrophil activation involved in immune response. According to Spearman correlation coefficient analysis, 81 lncRNA and 410 mRNA have expression correlation (p<0.01 and |r|≥0.4), QPCR in independent samples verified that the core node of the lncRNA-mRNA co-expression network IL1RAP-TCONS_00138311 variable shear is indeed highly expressed in SCZ patients, 2^-△△Ct is 0.56, the area under the ROC curve is 0.924. The top four ranked transcription factors were predicted to be HSF1, HSF2, HSF4, and FOXA1.Conclusions: Combined with sequence function analysis, it showed that the transcription factors FOXA1, HSF1, HSF2, HSF4, etc. may mediate the activation of IL1B-induced NF-kβ pathway and other inflammatory pathways through the regulation of IL1RAP alternative splicing transcripts TCONS_00138311, thereby participating in the pathogenesis of SCZ. We propose that the frequency of Differential lncRNA in peripheral blood could be used as novel biomarker for distinguishing SCZ from health.
Exploiting the Anticancer Effects of a Nitrogen Bisphosphonate Nanomedicine for Glioblastoma Multiforme
Authors: Jena Lynn , Bennie Lindsey , McErlean Emma , Pentlavalli Sreekanth , Thakur Raj , Burrows James , Kett Vicky , Buckley Niamh , Coulter Jonathan , Dunne Nicholas , McCarthy Helen O
Published: December 2020

Glioblastoma multiforme (GBM) is an incurable aggressive brain cancer in which current treatment strategies have demonstrated limited survival benefit. In recent years, nitrogen-containing bisphosphonates (N-BPs) have demonstrated direct anticancer effects in a number of tumour types including GBM. In this study, a nano-formulation with the RALA peptide was used to complex the N-BP, alendronate (ALN) into nanoparticles (NPs) <200 nm for optimal endocytic uptake. Fluorescently labelled AlexaFluor®647 Risedronate was used as a fluorescent analogue to visualise the intracellular delivery of N-BPs in both LN229 and T98G GBM cells. RALA NPs were effectively taken up by GBM where a dose-dependent response was evidenced with potentiation factors of 14.96 and 13.4 relative to ALN alone after 72 h in LN229 and T98G cells, respectively. Furthermore, RALA/ALN NPs at the IC50, significantly decreased colony formation, induced apoptosis and slowed spheroid growth in vitro. In addition, H-Ras membrane localisation was significantly reduced in the RALA/ALN groups compared to ALN or controls, indicative of prenylation inhibition. The RALA/ALN NPs were lyophilised to enhance stability without compromising the physiochemical properties necessary for functionality, highlighting the suitability of the NPs for scale-up and in vivo application. Collectively, these data show the significant potential of RALA/ALN NPs as novel therapeutics in the treatment of GBM.
Simultaneous acquisition of current and lateral force signals during atomic force microscopy for characterising the piezoelectric and triboelectric effects of ZnO nanorods
Authors: Yang Yijun , Kim Kwanlae
Published: December 2020

Atomic force microscopy (AFM) is central to investigating the piezoelectric potentials of one-dimensional nanomaterials. The AFM probe is used to deflect individual piezoelectric nanorods and to measure the resultant current. However, the torsion data of AFM probes have not been exploited to elucidate the relationship between the applied mechanical force and resultant current. In this study, the effect of the size of ZnO nanorods on the efficiency of conversion of the applied mechanical force into current was investigated by simultaneously acquiring the conductive AFM and lateral force microscopy signals. The conversion efficiency was calculated based on linear regression analysis of the scatter plot of the data. This method is suitable for determining the conversion efficiencies of all types of freestanding piezoelectric nanomaterials grown under different conditions. A pixel-wise comparison of the current and lateral force images elucidated the mechanism of current generation from dense arrays of ZnO nanorods. The current signals generated from the ZnO nanorods by the AFM probe originated from the piezoelectric and triboelectric effects. The current signals contributed by the triboelectric effect were alleviated by using an AFM probe with a smaller spring constant and reducing the normal force.
Analysis of miRNA-mediated Regulation of Flowering Induction in Lilium × formolongi
Authors: Zhang Qian , Zhao Yu-Qian , Gao Xue , Jia Guixia
Published: December 2020

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

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

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

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 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

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

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

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

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

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

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

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.
Clinical Predictors for Deep Vein Thrombosis on Admission in Patients with Intertrochanteric Fractures: A Retrospective Study
Authors: Fan Jixing , Zhou Fang , Xu Xiangyu , Zhang Zhishan , Tian Yun , Ji Hongquan , Guo Yan , Lv Yang , Yang Zhongwei , Hou Guojin
Published: December 2020

Background Limited studies are available to investigate the prevalence of preoperative deep vein thrombosis (DVT) in elderly patients with intertrochanteric fractures. The aim of present study was to evaluate risk factors and the prevalence of pre-admission DVT in elderly patients with intertrochanteric fractures.Methods This retrospective study included 788 elderly patients with intertrochanteric fracture who were eligible for this study from January 1, 2010, to December 31, 2019. Color doppler ultrasonography was performed for DVT detection at admission. All patients’ clinical data were collected. Cumulative incidence plots were calculated to assess the overall DVT risk and the median time from injury to admission. A stepwise multiple logistic regression analysis was used to identify the risk factors contributing to the occurrence of DVT.Results The overall prevalence of pre-admission DVT in patients with intertrochanteric fractures was 20.81% (164 of 788 patients). Univariate analysis showed that significantly elevated risk of DVT were found in patients with longer time from injury to admission, high energy injury, higher BMI, diabetes, chronic obstructive pulmonary disease (COPD), atrial fibrillation, dementia, varicose veins, higher age-adjusted CCI, higher ASA class and A3 type intertrochanteric fractures (P<0.05). The adjusted multivariate logistic regression analysis demonstrated that longer time from injury to admission, high energy trauma, COPD, atrial fibrillation, varicose veins and A3 type intertrochanteric fractures were independent risk factors of pre-admission DVT.Conclusions A high prevalence of pre-admission DVT was found in elderly Chinese patients with intertrochanteric fractures. Therefore, routine DVT screening before admission was necessary for elderly patients with intertrochanteric fractures in order to prevent intraoperative and postoperative PE and other lethal complications.
Mitochondrial dysfunction-induced KDM5A degradation impairs adult hippocampal neurogenesis in Alzheimer’s disease
Authors: Kim Dong Kyu , Jeong Hyobin , Bae Jingi , Cha Moon-Yong , Kang Moonkyung , Shin Dongjin , Ha Shinwon , Hyeon Seung Jae , Kim Hokeun , Suh Kyujin , Choi Mi-Sun , Ryu Hoon , Yu Seong-Woon , Kim Jong-Il , Kim Yeon-Soo , Lee Sang-Won , Hwang Daehee , Mook-Jung Inhee
Published: December 2020

Background Adult hippocampal neurogenesis (AHN) is a process of continuously generating functional mature neurons from neural stem cells in the dentate gyrus. In Alzheimer’s disease (AD) brains, amyloid pathology has deleterious effects on AHN, but molecular mechanisms for dysregulated AHN are unclear. Mitochondria of neural stem/progenitor cells play crucial roles in determining cell fate. Since mitochondrial dysfunction by amyloid pathology is the typical symptom of AD pathogenesis, we aim to study whether mitochondrial dysfunction of neural stem/progenitor cells by amyloid pathology causes the impairment of AHN, and elucidate the molecular mechanism of the phenomenon. Methods To investigate the effect of mitochondrial dysfunction of neural stem/progenitor cells on neuronal differentiation, we expressed mitochondria-targeted amyloid beta (mitoAβ) in neural stem/progenitor cells in vitro and in vivo. Proteomic analysis of the hippocampal tissue implicated mitochondrial dysfunction by mitoAβ as a cause of AHN deficits. We identified epigenetic regulators of neural progenitor cells that are regulated by mitoAβ expression or drug-induced mitochondrial toxicity and proposed a link between mitochondria and AHN. Results Amyloid pathology characteristically inhibited the neuronal differentiation stage, not the proliferation of neural stem/progenitor cells during AHN in early AD model mice. Mitochondrial dysfunction in neural stem/progenitor cells by expressing mitoAβ inhibited the neuronal differentiation and AHN with cognitive impairment. Mechanistic studies revealed that lysine demethylase 5A (KDM5A) was involved in the neuronal differentiation and could be degraded by mitochondrial dysfunction in neural progenitor cells, thereby inhibiting the differentiation and cognitive functions. Conclusions These results reveal the new role of KDM5A as a mediator of retrograde signaling, reflecting mitochondrial status, and that the decrease of KDM5A in neural progenitor cells by mitochondrial dysfunction impairs the neuronal differentiation and AHN, finally leading to memory deficits. These findings and its relationship to mitochondrial dysfunction suggest that mitochondrial failure in neural progenitor cells by amyloid pathology closely associates with reduced AHN in AD.