bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell–cell coupling and DNA methylation abnormal phenotypes in the after-hours mice
Authors: Tinarelli Federico , Ivanova Elena , Colombi Ilaria , Barini Erica , Balzani Edoardo , Garcia Celina Garcia , Gasparini Laura , Chiappalone Michela , Kelsey Gavin , Tucci Valter 
Published: January 2021

Abstract
Background
DNA methylation has emerged as an important epigenetic regulator of brain processes, including circadian rhythms. However, how DNA methylation intervenes between environmental signals, such as light entrainment, and the transcriptional and translational molecular mechanisms of the cellular clock is currently unknown. Here, we studied the after-hours mice, which have a point mutation in the Fbxl3 gene and a lengthened circadian period.

Methods
In this study, we used a combination of in vivo, ex vivo and in vitro approaches. We measured retinal responses in Afh animals and we have run reduced representation bisulphite sequencing (RRBS), pyrosequencing and gene expression analysis in a variety of brain tissues ex vivo. In vitro, we used primary neuronal cultures combined to micro electrode array (MEA) technology and gene expression.

Results
We observed functional impairments in mutant neuronal networks, and a reduction in the retinal responses to light-dependent stimuli. We detected abnormalities in the expression of photoreceptive melanopsin (OPN4). Furthermore, we identified alterations in the DNA methylation pathways throughout the retinohypothalamic tract terminals and links between the transcription factor Rev-Erbα and Fbxl3.

Conclusions
The results of this study, primarily represent a contribution towards an understanding of electrophysiological and molecular phenotypic responses to external stimuli in the Afh model. Moreover, as DNA methylation has recently emerged as a new regulator of neuronal networks with important consequences for circadian behaviour, we discuss the impact of the Afh mutation on the epigenetic landscape of circadian biology.
DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna
Authors: Hearn Jack , Plenderleith Fiona , Little Tom J. 
Published: January 2021

AbstractBackgroundPatterns of methylation influence lifespan, but methylation and lifespan may also depend on diet, or differ between genotypes. Prior to this study, interactions between diet and genotype have not been explored together to determine their influence on methylation. The invertebrateDaphnia magnais an excellent choice for testing the epigenetic response to the environment: parthenogenetic offspring are identical to their siblings (making for powerful genetic comparisons), they are relatively short lived and have well-characterised inter-strain life-history trait differences. We performed a survival analysis in response to caloric restriction and then undertook a 47-replicate experiment testing the DNA methylation response to ageing and caloric restriction of two strains ofD. magna.ResultsMethylated cytosines (CpGs) were most prevalent in exons two to five of gene bodies. One strain exhibited a significantly increased lifespan in response to caloric restriction, but there was no effect of food-level CpG methylation status. Inter-strain differences dominated the methylation experiment with over 15,000 differently methylated CpGs. One gene, Me31b, was hypermethylated extensively in one strain and is a key regulator of embryonic expression. Sixty-one CpGs were differentially methylated between young and old individuals, including multiple CpGs within the histone H3 gene, which were hypermethylated in old individuals. Across all age-related CpGs, we identified a set that are highly correlated with chronological age.ConclusionsMethylated cytosines are concentrated in early exons of gene sequences indicative of a directed, non-random, process despite the low overall DNA methylation percentage in this species. We identify no effect of caloric restriction on DNA methylation, contrary to our previous results, and established impacts of caloric restriction on phenotype and gene expression. We propose our approach here is more robust in invertebrates given genome-wide CpG distributions. For both strain and ageing, a single gene emerges as differentially methylated that for each factor could have widespread phenotypic effects. Our data showed the potential for an epigenetic clock at a subset of age positions, which is exciting but requires confirmation.
Clinical outcomes of patients with giant cell arteritis treated with tocilizumab in real-world clinical practice: decreased incidence of new visual manifestations
Authors: Unizony Sebastian , McCulley Timothy J. , Spiera Robert , Pei Jinglan , Sidiropoulos Paris N. , Best Jennie H. , Birchwood Christine , Pavlov Andrey , Stone John H. 
Published: January 2021

Abstract
Background
Placebo-controlled clinical trials have demonstrated the efficacy of tocilizumab (TCZ) for remission maintenance and glucocorticoid sparing in patients with giant cell arteritis (GCA). However, limited data exist on the effectiveness and safety of TCZ for GCA in real-world clinical practice.

Methods
This was a retrospective, single-center analysis of patients with GCA treated with intravenous or subcutaneous TCZ (2010–2018). Outcomes evaluated before and after TCZ initiation included occurrence of flare, time to flare, annualized flare rate, flare characteristics (i.e., polymyalgia rheumatica [PMR] symptoms, cranial manifestations), prednisone use, and safety. Flare was defined as the recurrence of unequivocal GCA manifestations requiring treatment intensification. Subgroup analyses of patients with PMR or visual manifestations at GCA diagnosis were performed.

Results
Sixty patients with GCA were included. The median (IQR) disease duration before and after the start of TCZ was 0.6 (0.2–1.6) and 0.5 (0.3–1.4) years, respectively. At least 1 flare was observed in 43 patients (71.7%) before and in 18 (30.0%) after TCZ initiation. Median (IQR) time to flare was 0.5 (0.3–0.7) years before TCZ treatment and 2.1 (0.6–2.6) years after TCZ initiation (HR 0.22; 95% CI 0.10–0.50; p = 0.0003). The annualized flare rate significantly decreased following TCZ use (before TCZ 1.4 [95% CI 1.0–2.1]; after TCZ 0.6 [95% CI 0.3–1.0] events/year; p < 0.001). Similar improvements were observed in patients with visual manifestations or PMR symptoms at GCA diagnosis. TCZ reduced the incidence of new visual manifestations, and no flares associated with permanent vision loss occurred while patients were receiving TCZ. Mean (SD) prednisone dose at TCZ onset and at the end of follow-up was 30 (18.3) and 5 (6.9) mg/day, respectively (p < 0.0001). After TCZ initiation, 46.6% of patients successfully discontinued prednisone. The incidence of adverse events, primarily attributed to glucocorticoids, was similar before and after TCZ initiation.

Conclusions
In this real-world setting, TCZ improved GCA clinical outcomes significantly and demonstrated effectiveness in the subgroups of patients with PMR symptoms and GCA-related visual manifestations at GCA diagnosis. No new cases of blindness occurred after TCZ initiation. Adverse events, many attributable to glucocorticoids, were comparable before and after TCZ treatment.
Comparison of the effects of introducing the CRISPR/Cas9 system by microinjection and electroporation into porcine embryos at different stages
Authors: Le Quynh Anh , Tanihara Fuminori , Wittayarat Manita , Namula Zhao , Sato Yoko , Lin Qingyi , Takebayashi Koki , Hirata Maki , Otoi Takeshige 
Published: January 2021

Abstract
Objective
Cytoplasmic microinjection and electroporation of the CRISPR/Cas9 system into zygotes are used for generating genetically modified pigs. However, these methods create mosaic mutations in embryos. In this study, we evaluated whether the gene editing method and embryonic stage for gene editing affect the gene editing efficiency of porcine embryos.

Results
First, we designed five guide RNAs (gRNAs) targeting the B4GALNT2 gene and evaluated mutation efficiency by introducing each gRNA with Cas9 protein into zygotes by electroporation. Next, the optimized gRNA with Cas9 protein was introduced into 1-cell and 2-cell stage embryos by either microinjection or electroporation. The sequence of gRNA affected the bi-allelic mutation rate and mutation efficiency of blastocysts derived from electroporated embryos. Microinjection significantly decreased the cleavage rates in each embryonic stage and blastocyst formation rates in 2-cell stage embryos compared with electroporation (p < 0.05). However, the bi-allelic mutation rate and mutation efficiency of blastocysts from the 1-cell stage embryos edited using microinjection were significantly higher (p < 0.05) than those of blastocysts from the 2-cell stage embryos edited by both methods. These results indicate that the gene editing method and embryonic stage for gene editing may affect the genotype and mutation efficiency of the resulting embryos.
Antimicrobial sensitivity patterns of Staphylococcus species isolated from mobile phones and implications in the health sector
Authors: Shiluli Clement , Achok Caroly , Nyaswa Philip , Ogwai Susan , Aroko Arthur , Obila James , Koigi George , Ridhwana Mustafa , Okwayo Bildad , Wanjiru Dorcas , Lukeba Linda , Ryckaert Eline , Van Durme Arne , Walschaerts Verena , De Preter Vicky 
Published: January 2021

AbstractObjectivesThe aim of this research was to determine drug sensitivity profiles ofStaphylococcusspecies isolated from mobile phones of students in Microbiology and Biomedical Laboratory Sciences from UZIMA University, Kisumu (Kenya) and the University Colleges Leuven-Limburg, Leuven (Belgium), respectively.ResultsAll mobile phones (16/16, 100%) had gram-positive bacteria. 3/8 (37.5%) mobile devices hadStaphylococcus aureus. 2/3 (67%)Staphylococcus aureusstrains were resistant to ampicillin, oxacillin, ceftazidime, vancomycin and amoxicillin. Guidelines for disinfection of mobile phones need to be developed urgently to stop transmission of resistant bacteria.
The complete genome sequence of Hafnia alvei A23BA; a potential antibiotic-producing rhizobacterium
Authors: Awolope Opeyemi K. , O’Driscoll Noelle H. , Di Salvo Alberto , Lamb Andrew J. 
Published: January 2021

Abstract
Objectives
The urgent need for novel antibiotics cannot be overemphasized. Hafnia alvei A23BA was isolated from plant rhizosphere as part of an effort to recover novel antibiotic-producing bacterial strains from soil samples. The genome of the isolate was sequenced to facilitate mining for potential antibiotic-encoding biosynthetic gene clusters and to gain insights into how these gene clusters could be activated.

Data description
Here, we report the complete genome sequence of H. alvei A23BA obtained from the hybrid assembly of Illumina HiSeq and GridION reads. The genome, consisting of a circular chromosome and a circular plasmid, is 4.77 Mb in size with a GC content of 48.77%. The assembly is 99.5% complete with genomic features including 4,217 CDSs, 125 RNAs, and 30 pseudogenes. Thiopeptide, beta-lactone, siderophore, and homoserine lactone biosynthetic gene clusters were also identified. Other gene clusters of interest include those associated with bioremediation, biocontrol, and plant growth promotion- all of which are reported for H. alvei for the first time. This dataset serves to expedite the exploration of the biosynthetic and metabolic potentials of the species. Furthermore, being the first published genome sequence of a soil isolate, this dataset enriches the comparative genomics study of H. alvei strains.
Variations in cervico-vaginal microbiota among HPV-positive and HPV-negative asymptomatic women in Peru
Authors: Carrillo-Ng Hugo , Becerra-Goicochea Lorena , Tarazona-Castro Yordi , Pinillos-Vilca Luis , del Valle Luis J. , Aguilar-Luis Miguel Angel , Tinco-Valdez Carmen , Silva-Caso Wilmer , Martins-Luna Johanna , Peña-Tuesta Isaac , Aquino-Ortega Ronald , del Valle-Mendoza Juana 
Published: January 2021

Abstract
Objective
To characterize the cervicovaginal microbiota of HPV-positive and HPV-negative asymptomatic Peruvian women, by identifying the presence of 13 representative bacteria genus.

Results
A total of 100 HPV-positive and 100 HPV-negative women were matched by age for comparison of microbiota. The following bacteria were more frequently identified in HPV-positive patients compared to HPV-negative: Eubacterium (68 vs 32%), Actinobacteria (46 vs 33%), Fusobacterium (11 vs 6%) and Bacteroides (20 vs 13%). A comparison between high-risk and low-risk genotypes was performed and differences were found in the detection of Actinobacteria (50 vs 33.33%), Bifidobacterium (50 vs 20.83%) and Enterococcus (50 vs 29.17%).
Identification and characterization of a silent mutation in RNA binding domain of N protein coding gene from SARS-CoV-2
Authors: Zolfaghari Emameh Reza , Eftekhari Mahyar , Nosrati Hassan , Heshmatnia Jalal , Falak Reza 
Published: January 2021

Abstract
Objective
This study describes the occurrence of a silent mutation in the RNA binding domain of nucleocapsid phosphoprotein (N protein) coding gene from SARS-CoV-2 that may consequence to a missense mutation by onset of another single nucleotide mutation.

Results
In the DNA sequence isolated from severe acute respiratory syndrome (SARS-CoV-2) in Iran, a coding sequence for the RNA binding domain of N protein was detected. The comparison of Chinese and Iranian DNA sequences displayed that a thymine (T) was mutated to cytosine (C), so “TTG” from China was changed to “CTG” in Iran. Both DNA sequences from Iran and China have been encoded for leucine. In addition, the second T in “CTG” in the DNA or uracil (U) in “CUG” in the RNA sequences from Iran can be mutated to another C by a missense mutation resulting from thymine DNA glycosylase (TDG) of human and base excision repair mechanism to produce “CCG” encoding for proline, which consequently may increase the affinity of the RNA binding domain of N protein to viral RNA and improve the transcription rate, pathogenicity, evasion from human immunity system, spreading in the human body, and risk of human-to-human transmission rate of SARS-CoV-2.
Collaborative offloading for UAV-enabled time-sensitive MEC networks
Authors: Li Wen-Tao , Zhao Mingxiong , Wu Yu-Hui , Yu Jun-Jie , Bao Ling-Yan , Yang Huan , Liu Di 
Published: January 2021

AbstractRecently, unmanned aerial vehicle (UAV) acts as the aerial mobile edge computing (MEC) node to help the battery-limited Internet of Things (IoT) devices relieve burdens from computation and data collection, and prolong the lifetime of operating. However, IoT devices can ONLY ask UAV for either computing or caching help, and collaborative offloading services of UAV are rarely mentioned in the literature. Moreover, IoT device has multiple mutually independent tasks, which make collaborative offloading policy design even more challenging. Therefore, we investigate a UAV-enabled MEC networks with the consideration of multiple tasks either for computing or caching. Taking the quality of experience (QoE) requirement of time-sensitive tasks into consideration, we aim to minimize the total energy consumption of IoT devices by jointly optimizing trajectory, communication and computing resource allocation at UAV, and task offloading decision at IoT devices. Since this problem has highly non-convex objective function and constraints, we first decompose the original problem into three subproblems named as trajectory optimization ($$\mathbf {P}_{\mathbf {T}}$$

P
T

), resource allocation at UAV ($$\mathbf {P}_{\mathbf {R}}$$

P
R

) and offloading decisions at IoT devices ($$\mathbf {P}_{\mathbf {O}}$$

P
O

) and then propose an iterative algorithm based on block coordinate descent method to cope with them in a sequence. Numerical results demonstrate that collaborative offloading can effectively reduce IoT devices’ energy consumption while meeting different kinds of offloading services, and satisfy the QoE requirement of time-sensitive tasks at IoT devices.
A QoS-based joint user association and resource allocation scheme in ultra-dense networks
Authors: Si Zhiwei , Chuai Gang , Gao Weidong , Zhang Jinxi , Chen Xiangyu , Zhang Kaisa 
Published: January 2021

AbstractUltra-dense networks (UDNs) have become an important architecture for the fifth generation (5G) networks. A large number of small base stations (SBSs) are deployed to provide high-speed and seamless connections for users in the network. However, the advantage of increasing the system capacity brought by the dense distribution of SBSs comes at the cost of severe inter-cell interference. Although the user-centric virtual cell method has been proposed to solve the interference problem, some challenges have been encountered in practical applications. For example, inter-cell interference still exists to a certain extent, and the cell load may be imbalance. Hence, under the virtual cell architecture, we propose a quality of service (QoS)-based joint user association and resource allocation scheme in UDNs. In order to mitigate the interference, balance cell load and improve the system throughput, a non-convex NP-hard problem is formulated. To effectively solve this problem, we decouple the formulated problem into three sub-problems: user association, physical resource block (PRB) allocation and power allocation. First, we consider the QoS requirements of user equipment (UE) and perform user association based on the PRB estimation method. Then, based on the overlapped virtual cells constructed, we propose a graph-based PRB allocation scheme for reducing virtual inter-cell interference. Moreover, we solve power allocation sub-problem by using the difference of concave (DC) programing method. The simulation results show that our proposed scheme is superior to other schemes in terms of user rates, cell load and system throughput.
Hopf bifurcation in a delayed reaction–diffusion–advection equation with ideal free dispersal
Authors: Liu Yunfeng , Hui Yuanxian 
Published: January 2021

AbstractIn this paper, we investigate a delay reaction–diffusion–advection model with ideal free dispersal. The stability of positive steady-state solutions and the existence of the associated Hopf bifurcation are obtained by analyzing the principal eigenvalue of an elliptic operator. By the normal form theory and the center manifold reduction, the stability and bifurcation direction of Hopf bifurcating periodic solutions are obtained. Moreover, numerical simulations and a brief discussion are presented to illustrate our theoretical results.
Detecting recurrent prostate Cancer using multiparametric MRI, influence of PSA and Gleason grade
Authors: Venkatesan Aradhana M. , Mudairu-Dawodu Eniola , Duran Cihan , Stafford R. Jason , Yan Yuanqing , Wei Wei , Kundra Vikas 
Published: January 2021

Abstract
Background
The utility of multiparametric MRI (mpMRI) in detecting suspected local recurrence post radical prostatectomy (RP) may be associated with PSA and Gleason grade. The purpose of the study was to evaluate the likelihood of detecting locally recurrent prostate cancer utilizing mpMRI in patients with suspected recurrence following radical prostatectomy (RP) parsed by PSA and Gleason grade.

Methods
One hundred ninety five patients with suspected local recurrence were imaged on a 1.5 T MRI with torso array and endorectal coil in this retrospective study. mpMRI interpretations were stratified by PSA and lower (Gleason < 7) vs. higher grade tumors (Gleason 8–10). Recursive partitioning was used to determine whether mpMRI interpretations could be classified as positive or negative.

Results
The majority of mpMRI interpretations in patients with lower Gleason grade tumors and PSA < 0.5 ng/mL were negative (68/78, 87.2%, p = 0.004). The majority of mpMRI interpretations in patients with higher Gleason grade tumors and PSA > 1.5 ng/mL were positive (8/9, 88.9%, p = 0.003). Findings were corroborated by recursive partitioning, which identified a PSA = 0.5 ng/ml in patients with lower grade tumors and a PSA = 1.5 ng/mL in patients with higher grade tumors as differentiating negative and positive mpMRIs.

Conclusion
In the setting of suspected recurrence after RP, mpMRI results are associated with PSA and Gleason grade, both of which can help guide when mpMRI may find utility. mpMRI is likely to be low diagnostic yield and negative for recurrence (87%) in the setting of lower Gleason grade tumors and PSA < 0.5 ng/mL. mpMRI is likely to be of low diagnostic value and positive for recurrence (89%) in the setting of PSA > 1.5 ng/mL and higher grade tumors; in this case, mpMRI findings may be more useful for directing biopsy and local therapy. Between these extremes, PSA > 0.5 ng/mL and lower grade tumors or PSA < 1.5 ng/mL and higher grade tumors, mpMRI results are less predictable, suggesting greater diagnostic value for detecting recurrence post prostatectomy.
Validation of the brief scale for the evaluation of acculturation stress in migrant population (EBEA)
Authors: Urzúa Alfonso , Henríquez Diego , Caqueo-Urízar Alejandra , Smith-Castro Vanessa 
Published: January 2021

Abstract
Background
Acculturation stress is associated with poorer physical and mental health and a lower level of psychological well-being. The causes of acculturation stress are diverse, but most are similar in the migrant population. Despite the importance of evaluating this variable, few studies have reported culturally adapted and validated instruments for specific populations. Based on this, the aim of this study was to evaluate the psychometric properties of a short scale for the evaluation of acculturation stress (EBEA).

Methods
Two studies were conducted, involving 1725 first-generation Colombian and Peruvian migrants living in Chile, between the ages of 18 and 60 years. In addition to the EBEA and as evidence of validity, the Beck Anxiety Scale and the WHOQOL-BREF psychological health domain were applied. A confirmatory factor analysis was carried out, and the reliability and nomological validity were evaluated.

Results
The results in both studies indicated that the scale presents a factorial structure of three dimensions: (a) the stress derived from the preparation and departure from the country of origin, (b) the stress produced by socioeconomic concerns in the host country, and (c) the tensions typical of adaptation to sociocultural changes or Chilean society. The reliability coefficients and the analysis of their nomological validity were very good.

Conclusions
The EBEA is a measure that offers quick, useful screening for researchers who need a short measure for research among migrants. This tool contributes to the work of education, prevention, and intervention in the field of general health and migrants’ mental health.