bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analysis of SARS‐CoV‐2 antibody dynamics in New Zealand
Authors: Whitcombe Alana L , McGregor Reuben , Craigie Alyson , James Alex , Charlewood Richard , Lorenz Natalie , Dickson James MJ , Sheen Campbell R , Koch Barbara , Fox‐Lewis Shivani , McAuliffe Gary , Roberts Sally A , Morpeth Susan C , Taylor Susan , Webb Rachel H , Jack Susan , Upton Arlo , Ussher James E , Moreland Nicole J 
Published: March 2021

AbstractObjectivesCirculating antibodies are important markers of previous infection and immunity. Questions remain with respect to the durability and functionality of SARS‐CoV‐2 antibodies. This study explored antibody responses in recovered COVID‐19 patients in a setting where the probability of re‐exposure is effectively nil, owing to New Zealand's successful elimination strategy.MethodsA triplex bead‐based assay that detects antibody isotype (IgG, IgM and IgA) and subclass (IgG1, IgG2, IgG3 and IgG4) responses against Nucleocapsid (N) protein, the receptor binding domain (RBD) and Spike (S) protein of SARS‐CoV‐2 was developed. After establishing baseline levels with pre‐pandemic control sera (n = 113), samples from PCR‐confirmed COVID‐19 patients with mild–moderate disease (n = 189) collected up to 8 months post‐infection were examined. The relationship between antigen‐specific antibodies and neutralising antibodies (NAbs) was explored with a surrogate neutralisation assay that quantifies inhibition of the RBD/hACE‐2 interaction.ResultsWhile most individuals had broad isotype and subclass responses to each antigen shortly after infection, only RBD and S protein IgG, as well as NAbs, were relatively stable over the study period, with 99%, 96% and 90% of samples, respectively, having responses over baseline 4–8 months post‐infection. Anti‐RBD antibodies were strongly correlated with NAbs at all time points (Pearson's r ≥ 0.87), and feasibility of using finger prick sampling to accurately measure anti‐RBD IgG was demonstrated.ConclusionAntibodies to SARS‐CoV‐2 persist for up to 8 months following mild‐to‐moderate infection. This robust response can be attributed to the initial exposure without immune boosting given the lack of community transmission in our setting.
Buffering and prioritization in switches for fast processing table‐miss packets in software‐defined networks
Authors: Lai Yuan‐Cheng , Legese Hailemariam Zelalem , Chen Yen‐Hung , Kuo Yi‐Ting 
Published: March 2021

SummaryIn software‐defined networks, the switch forwards incoming packets according to forwarding rules recorded in the flow entries. When a switch receives a table‐miss packet, meaning no match with any flow entry, it sends this packet as a Packet‐In message to the controller for its further processing. Many Packet‐In messages will cause large overhead and long packet delay. This paper proposes a novel method, Packet‐In Buffering and Prioritization (PIBP), which buffers Packet‐In messages and prioritizes these messages to reduce the number of Packet‐In messages and accelerate their processing, respectively. The concept of PIBP is sending only the first table‐miss packet of each flow to the controller. The other table‐miss packets belonging to the same flow are temporarily stored in the switch. Moreover, these messages have a higher priority. That is, after the packet sent from the controller has been forwarded from the switch, the buffered packets belonging to the same flow are also immediately forwarded. We formally analyze the performance of PIBP with queuing theory. The analytical and simulation results show that PIBP can decrease the average delay of table‐miss packets compared with two typical methods, Priority Queue and Mismatched Packets Table.
Implementation and comparative analysis of evolutionary algorithms for energy optimization in wireless sensor networks
Authors: Kundaliya Brijesh , Hadia Sarman K. 
Published: March 2021

SummaryWireless sensor networks will be at the epitome of applications in near future. It is going through tremendous positive changes. Although it suffers from some limitations and it sorts out its limitations day by day. The biggest limitation of wireless sensor networks is the limited energy of the nodes. Most of the energy is used during the routing of the data. An optimized way of routing will save the valuable energy of the node and helpful for increasing the network's lifetime. The optimization algorithms are indeed utterly helpful in many applications across the different fields to optimize the resources. In the proposed worked we have applied Adaptive Particle Swarm Optimization (APSO), Ant Colony Optimization (ACO), Genetic Algorithms (GA), and Simulated Annealing (SA) to a Modified Rendezvous Point Selection Scheme and observed the effect on the network lifetime and energy consumption in the network. We have made an exhaustive comparison of all the optimization algorithms with considerable simulations.
Synthesis and characterization of new pyrazole–tetrazole derivatives as new vasorelaxant agents
Authors: Cherfi Mounir , Dib Ikram , Harit Tarik , Ziyyat Abderrahim , Malek Fouad 
Published: March 2021

AbstractThe synthesis of new functionalized tetrazole–pyrazole compounds is reported. They were fully characterized by spectroscopy and spectrometry methods. The vasorelaxant potency of these molecules was also investigated. All compounds showed a good vasorelaxant activity but the Compound 6 “ethyl 1‐((2‐(3‐bromopropyl)‐2H‐tetrazol‐5‐yl)methyl)‐5‐methyl‐1H‐pyrazole‐3‐carboxylate” seems to have the highest effect, which reached 70% at 10−4 M concentration. This effect was partially endothelium‐dependent; also, the vasorelaxant pattern of this compound was quite similar to that of the verapamil.
Eya2 expression during mouse embryonic development revealed by Eya2lacZ knockin reporter and homozygous mice show mild hearing loss
Authors: Zhang Ting , Xu Jinshu , Xu Pin‐Xian 
Published: March 2021

AbstractBackgroundEya2 expression during mouse development has been studied by in situ hybridization and it has been shown to be involved skeletal muscle development and limb formation. Here, we generated Eya2 knockout (Eya2−) and a lacZ knockin reporter (Eya2lacZ) mice and performed a detailed expression analysis for Eya2lacZ at different developmental stages to trace Eya2lacZ‐positive cells in Eya2‐null mice. We describe that Eya2 is not only expressed in cranial sensory and dorsal root ganglia, retina and olfactory epithelium, and somites as previously reported, but also Eya2 is specifically detected in other organs during mouse development.ResultsWe found that Eya2 is expressed in ocular and trochlear motor neurons. In the inner ear, Eya2lacZ is specifically expressed in differentiating hair cells in both vestibular and cochlear sensory epithelia of the inner ear and Eya2−/− or Eya2lacZ/lacZ mice displayed mild hearing loss. Furthermore, we detected Eya2 expression during both salivary gland and thymus development and Eya2‐null mice had a smaller thymus.ConclusionsAs Eya2 is coexpressed with other members of the Eya family genes, these results together highlight that Eya2 as a potential regulator may act synergistically with other Eya genes to regulate the differentiation of the inner ear sensory hair cells and the formation of the salivary gland and thymus.
Lessons learned through listening to biology students during a transition to online learning in the wake of the COVID‐19 pandemic
Authors: Humphrey Eve A. , Wiles Jason R. 
Published: March 2021

AbstractDuring the Spring Semester of 2020, an outbreak of a novel coronavirus (SARS‐CoV‐2) and the illnesses it caused (COVID‐19) led to widespread cancelling of on‐campus instruction at colleges and universities in the United States and other countries around the world. Response to the pandemic in university settings included a rapid and unexpected shift to online learning for faculty and students. The transition to teaching and learning online posed many challenges, and the experiences of students during this crisis may inform future planning for distance learning experiences during the ongoing pandemic and beyond. Herein, we discuss the experiences of first‐ and second‐year university students enrolled in a biology seminar course as their classes migrated to online environments. Drawing on reported student experiences and prior research and resources, we discuss the ways we will adjust our own teaching for future iterations of the course while offering recommendations for instructors tasked with teaching in online environments.
Food resource partitioning between juvenile and mature weatherfish Misgurnus fossilis
Authors: Pyrzanowski Kacper , Zięba Grzegorz , Leszczyńska Joanna , Adamczuk Małgorzata , Dukowska Małgorzata , Przybylski Mirosław 
Published: March 2021

AbstractThis study represents a description of the diet composition of one of the largest European cobitids, the weatherfish Misgurnus fossilis. Specimens were collected in a drainage canal, representing a typical habitat for weatherfish, and with gut content analysis conducted with regard to individual total length and maturity stage. Overall, the weatherfish diet mainly consisted of Copepoda, Cladocera, Ostracoda, Oligochaeta, Asellus aquaticus, Chironomidae and Coleoptera larvae, Gastropoda, and detritus. To evaluate size‐related patterns of resource use, fish were assigned to two size classes, defined according to size at first maturation. ANOSIM analyses revealed major ontogenetic shifts in feeding strategy, which were related to size and maturity, with a significant ontogenetic shift in feeding pattern, marked by differences in the proportions of the main taxonomic groups of prey consumed. Copepoda and Cladocera dominated in the diet of small and immature individuals, while large weatherfish primarily fed on detritus. Similarly, cluster analysis of diet classified into these food types showed distinct two groups comprising juvenile and mature fish. The weatherfish is a food opportunist using all available resources, but spatially showed a change in feeding sites. Smaller and sexually immature individuals more often use prey caught in the water column and among macrophytes, while larger (sexually mature) individuals occupying the bottom, much more often use detritus as a food base.
Identifying the patterns of changes in α‐ and β‐diversity across Dacrydium pectinatum communities in Hainan Island, China
Authors: Liu Haodong , Liu Hua , Chen Yongfu , Xu Zhiyang , Dai Yunchuan , Chen Qiao , Ma Yongkang 
Published: March 2021

AbstractExploring vegetation distribution spatial patterns facilitates understanding how biodiversity addresses the potential threat of future climate variability, especially for highly diverse and threatened tropical plant communities, but few empirical studies have been performed. Dacrydium pectinatum is a constructive and endangered species in the tropical mountain forests of Hainan Island, China. In this study, sixty‐eight 30 m × 30 m permanent plots of D. pectinatum were investigated, and species‐based and phylogenetic‐based methods were used to analyze the α‐ and β‐diversity pattern variation and its key drivers. Our study showed that species and phylogenetic α‐diversity patterns are different on a local scale. However, on a regional scale, the variations in the two α‐diversity patterns tend to converge, and they decrease with increasing elevation. The phylogenetic structure changes from overdispersion to convergence with increasing elevation. Soil (SOM, TP, AP), topography (EL, SL), and stand (CD) factors and α‐diversity showed close correlations. Species and phylogenetic β‐diversity have significant positive correlations with changing environmental distance and geographical distance; however, as a representative form of habitat heterogeneity, elevation distance has a greater impact on β‐diversity changes than geographical distance. In conclusion, the α‐ and β‐diversity patterns of the D. pectinatum community are mainly related to habitat filtering, especially in high‐elevation areas, and the colonization history of various regions also affects the formation of diversity patterns. Species‐based and phylogenetic‐based methods robustly demonstrated the key role of the habitat filtering hypothesis in community assembly. We believe that more plant diversity patterns need to be explored to understand the biodiversity formation mechanisms in tropical forests. We also recommend strengthening the construction and management of nature reserves to help address the biodiversity loss crisis in endangered tropical plant communities.
An online target and rapid screening method for α‐glucosidase inhibitors based on capillary electrophoresis
Authors: Zhang Ying , Zhong Hai‐Yang , Nsanzamahoro Stanislas , Yao Xiao‐Jun , Wang Wei‐Feng , Yang Jun‐Li 
Published: March 2021

AbstractScreening enzymatic active compounds is one of the important fields in drug research. α‐Glucosidase can hydrolyze carbohydrates to monosaccharides after meals and lead to the rise of blood glucose levels in human body. Thus, the inhibition of α‐glucosidase activity is an effective approach for the diabetes treatment. In this work, we developed a new method to simultaneously screen multiple bioactive compounds within a single CE running. The affect factors on the method performance, including injection, mixing, incubation, separation and detection, were carefully analyzed and discussed. Under the optimum, the mixture consisting of two internal standards (DMSO and 4‐nitrophenol) and five compounds (lyoniresinol, hydroxytyrosol, rutin, kaempferol, and quercetin) was simultaneously screened, and kaempferol and quercetin showed stronger activity and this conclusion was also supported by offline assay. Furthermore, molecular docking was employed for investigating its interaction mechanism. Eventually, the established method has been applied to screen potential α‐glucosidase inhibitors from an extract of Lycium barbarum and the peak area of rutin, taxifolin, quercetin, and chlorogenic acid in L. barbarum samples changed before and after the enzymatic reaction, confirming that these four compounds had potential inhibitory activities, which was consistent with the literature data. The present work provides a promising method for the target and rapid discovery of bioactive compounds from a plant extract or mixture.
Micro‐aerobic production of isobutanol with engineered Pseudomonas putida
Authors: Ankenbauer Andreas , Nitschel Robert , Teleki Attila , Müller Tobias , Favilli Lorenzo , Blombach Bastian , Takors Ralf 
Published: March 2021

AbstractPseudomonas putida KT2440 is emerging as a promising microbial host for biotechnological industry due to its broad range of substrate affinity and resilience to physicochemical stresses. Its natural tolerance towards aromatics and solvents qualifies this versatile microbe as promising candidate to produce next generation biofuels such as isobutanol. In this study, we scaled‐up the production of isobutanol with P. putida from shake flask to fed‐batch cultivation in a 30 L bioreactor. The design of a two‐stage bioprocess with separated growth and production resulted in 3.35 gisobutanol L–1. Flux analysis revealed that the NADPH expensive formation of isobutanol exceeded the cellular catabolic supply of NADPH finally causing growth retardation. Concomitantly, the cell counteracted to the redox imbalance by increased formation of 2‐ketogluconic thereby providing electrons for the respiratory ATP generation. Thus, P. putida partially uncoupled ATP formation from the availability of NADH. The quantitative analysis of intracellular pyridine nucleotides NAD(P)+ and NAD(P)H revealed elevated catabolic and anabolic reducing power during aerobic production of isobutanol. Additionally, the installation of micro‐aerobic conditions during production doubled the integral glucose‐to‐isobutanol conversion yield to 60 mgisobutanol gglucose–1 while preventing undesired carbon loss as 2‐ketogluconic acid.
DNA Methylation Signatures Reveal the Diversity of Processes Remodeling Hepatocellular Carcinoma Methylomes
Authors: Meunier Léa , Hirsch Théo Z. , Caruso Stefano , Imbeaud Sandrine , Bayard Quentin , Roehrig Amélie , Couchy Gabrielle , Nault Jean‐Charles , Llovet Josep M. , Blanc Jean‐Frédéric , Calderaro Julien , Zucman‐Rossi Jessica , Letouzé Eric 
Published: March 2021

Background and Aims
DNA methylation patterns are highly rearranged in HCCs. However, diverse sources of variation are intermingled in cancer methylomes, precluding the precise characterization of underlying molecular mechanisms. We developed a computational framework (methylation signature analysis with independent component analysis [MethICA]) leveraging independent component analysis to disentangle the diverse processes contributing to DNA methylation changes in tumors.

Approach and Results
Applied to a collection of 738 HCCs, MethICA unraveled 13 stable methylation components preferentially active in specific chromatin states, sequence contexts, and replication timings. These included signatures of general processes associated with sex and age but also signatures related to specific driver events and molecular subgroups. Catenin beta 1 mutations were major modulators of methylation patterns in HCC, characterized by a targeted hypomethylation of transcription factor 7–bound enhancers in the vicinity of Wnt target genes as well as a widespread hypomethylation of late‐replicated partially methylated domains. By contrast, demethylation of early replicated highly methylated domains was a signature of replication stress, leading to an extensive hypomethylator phenotype in cyclin‐activated HCC. Inactivating mutations of the chromatin remodeler AT‐rich interactive domain‐containing protein 1A were associated with epigenetic silencing of differentiation‐promoting transcriptional networks, also detectable in cirrhotic liver. Finally, a hypermethylation signature targeting polycomb‐repressed chromatin domains was identified in the G1 molecular subgroup with progenitor features.

Conclusions
This study elucidates the diversity of processes remodeling HCC methylomes and reveals the epigenetic and transcriptional impact of driver alterations.
Construction and validation of a machine learning‐based nomogram: A tool to predict the risk of getting severe coronavirus disease 2019 (COVID‐19)
Authors: Yao Zhixian , Zheng Xinyi , Zheng Zhong , Wu Ke , Zheng Junhua 
Published: March 2021

AbstractBackgroundIdentifying patients who may develop severe coronavirus disease 2019 (COVID‐19) will facilitate personalized treatment and optimize the distribution of medical resources.MethodsIn this study, 590 COVID‐19 patients during hospitalization were enrolled (Training set:n = 285; Internal validation set:n = 127; Prospective set:n = 178). After filtered by two machine learning methods in the training set, 5 out of 31 clinical features were selected into the model building to predict the risk of developing severe COVID‐19 disease. Multivariate logistic regression was applied to build the prediction nomogram and validated in two different sets. Receiver operating characteristic (ROC) analysis and decision curve analysis (DCA) were used to evaluate its performance.ResultsFrom 31 potential predictors in the training set, 5 independent predictive factors were identified and included in the risk score: C‐reactive protein (CRP), lactate dehydrogenase (LDH), Age, Charlson/Deyo comorbidity score (CDCS), and erythrocyte sedimentation rate (ESR). Subsequently, we generated the nomogram based on the above features for predicting severe COVID‐19. In the training cohort, the area under curves (AUCs) were 0.822 (95% CI, 0.765–0.875) and the internal validation cohort was 0.762 (95% CI, 0.768–0.844). Further, we validated it in a prospective cohort with the AUCs of 0.705 (95% CI, 0.627–0.778). The internally bootstrapped calibration curve showed favorable consistency between prediction by nomogram and the actual situation. And DCA analysis also conferred high clinical net benefit.ConclusionIn this study, our predicting model based on five clinical characteristics of COVID‐19 patients will enable clinicians to predict the potential risk of developing critical illness and thus optimize medical management.
Epigenetic targeting of SLC30A3 by HDAC1 is related to the malignant phenotype of glioblastoma
Authors: Zhang Longzhou , Liu Zengjin , Dong Yang , Kong Lingchang 
Published: March 2021

AbstractThe epigenetic abnormality is believed as a major driver for cancer initiation. Histone modification plays a vital role in tumor formation and progression. Particularly, alteration in histone acetylation has been highly associated with gene expression, cell cycle, as well as carcinogenesis. By analyzing glioblastoma (GBM)‐related microarray from the GEO database and conducting chromatin immunoprecipitation‐sequencing (ChIP‐seq), we discovered that solute carrier family 30 member 3 (SLC30A3), a super enhancer (SE)‐regulated factor, was significantly reduced in GBM tissues. Furthermore, histone deacetylase 1 (HDAC1), overexpressed in GBM tissues, could inhibit SLC30A3 expression by promoting histone H3K27ac deacetylation modification of the SE region of SLC30A3. Our functional validation revealed that SLC30A3 can inhibit the growth and metastatic spread of GBM cells in vitro and in vivo, and can activate the MAPK signaling pathway to promote apoptosis of GBM cells. Moreover, overexpression of HDAC1 resulted in a significant increase in DNA replication activity, a significant decline in apoptosis and cell cycle arrest in GBM cells. In a word, these findings indicate that combined epigenetic targeting of SLC30A3 by HDAC1 and SE is potentially therapeutically feasible in GBM.
Netrin‐1 and clusterin: Innovative potential diagnostic biomarkers for early renal damage in β‐thalassemia major children
Authors: Abd El‐Khalik Sarah Ragab , Sharaby Radwa Mahmoud , Nasif Elham , Hamza Mohamed Bassiony , Ibrahim Rowida Raafat 
Published: March 2021

AbstractBackgroundChildren with β‐thalassemia major (β‐TM) suffer from tubular dysfunction even before the onset of any renal impairment symptoms and/or clinical signs. Therefore, identifying innovative biomarkers allowing early renal damage detection has focused attention.AimThis study aims to preliminary assess Netrin‐1(NTN‐1) and clusterin (CLU) in β‐TM children and explore their possible roles as surrogate noninvasive biomarkers of renal tubular dysfunction.Subjects and methodsIn this study, 40 β‐TM children and 30 healthy children were enrolled. Routine serum and urinary biochemical variables were determined. Urinary NTN‐1 and CLU levels were measured using ELISA and their mRNA expression in PBMCs were assayed using real‐time PCR. Serum TNF‐α, MDA levels and GST activity were measured.ResultsUrinary NTN‐1 and CLU concentrations and mRNA relative expression levels in PBMCs were significantly increased in β‐TM children relative to controls. Oxidative stress and inflammatory markers revealed significant elevation in β‐TM children compared to controls. The change in these parameters correlated significantly with other renal parameters. ROC curves analysis showed that urinary NTN‐1 and CLU levels are of promising diagnostic performance.ConclusionOur results suggest that NTN‐1 and CLU are qualified as new noninvasive biomarker panels for early detection of renal injury in β‐TM children. Moreover, urinary NTN‐1 is recommended as a precise one during the clinical practices.