bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leveraging phylogenetic signal to unravel microbial community function and assembly rules
Authors: de Carcer Daniel Aguirre , Parras Marcos , Talavera-Marcos Silvia 
Published: December 2022

Abstract
Clarifying the general rules behind microbial community assembly will foster the much-anticipated microbiome-based technological revolution. We followed the cue of the existence of phylogenetic signal in microbial communities, and knowledge that ecological function shows some degree of phylogenetic conservatism, to explore community assembly rules. The strategy gravitated around the computational analysis of phylogenetic core groups (PCGs); discrete portions of the phylogeny characteristic of an ecosystem. We first show that PCGs are a prevalent and predominant feature of microbial ecosystems. Then, we re-analyzed an experimental dataset drawing only from its community composition data and freely available genomic databases. Using mainly genome scale metabolic models and population dynamics modeling, we obtained ecological insights on metabolic niche structure and population dynamics comparable to those gained after canonical experimentation. Leveraging phylogenetic signal to help unravel microbiome function and assembly rules offers an inexpensive avenue to gain insights into Earth’s microbial ecosystems.
The development and breeding practice of molecular markers for peach skin blush
Authors: Guo Tianfa , Wang Jiao , Lu Xinxin , jinlong wu , Wang Lirong 
Published: December 2022

Abstract
Peach is an economically important fruit tree crop worldwide. The external color of fruit impairs peach price, especially fruits with different degrees blush. Developing varied skin color cultivars by molecular breeding is expected to satisfy the market demands for diverse peach fruits. Although, the variations in key genes regarding whether the skin is colored have been found, their markers have not really been widely used in the breeding process, and the molecular marker development of peach skin blush awaits promotion and application. The goal of this study was to explore the variations related to peach skin color, and to develop molecular markers for breeding based on variations. By analyzing the expression of anthocyanin synthesis-related and regulatory genes, we confirmed that the MYB10.1 is a key gene control skin color. We further found that 5243 bp insertion and 483 bp deletion in MYB10.1 promoter were closely related to peach skin color phenotype. In addition, we identified one transposon insertion mutation at the − 2706 bp position of MYB10.1 promoter related to non-red fruit skin trait and developed a marker for validation. The size of the insertion amplified from the ShiYuBaiTao genome DNA was approximately 3.5 kb. However, it does not completely explain the phenomenon of non-red skin of peach just as MYB10.1-2/MYB10.1-2 and accuracy were 36.1% in this study. Based on the results of this work, we propose that MYB10.1-2/MYB10.1-2 should not only be a genotype of non-red skin, but also should be combined with other makers to predict the color of peach skin color.
DOS attack Network Traffic Monitoring in Software Defined Networking using Mininet and RYU Controller
Authors: Jaiswal Amit Kumar 
Published: December 2022

Abstract
Software Defined Networking (SDN) is a revolutionary networking design that isolates forwarding hardware from control decisions. The separation of the control plane from the data plane creates a number of issues, including security, dependability, load balancing, and traffic engineering. Dreadful security concerns in SDNs include denial of service (DoS) and distributed denial of service (DDoS) attacks. In SDNs, for example, DoS/DDoS attacks might overwhelm the control plane, data plane, or communication channel. In this study The SDN setup and installation approach used is a Mininet emulator with a controller Ryu with switching hub component, OpenFlow switches, and nodes. In SDN, we will use several Dos and DDos attack methods such as (simple ping, force ping, and aggressive ping) to generate traffic in various topology such as (single, linear, and tree). We will discuss the intensity of effect in all distinct ping topology. Furthermore, we examine the various methodologies and tools used to execute the improved solutions. Finally, we discuss potential future research approaches for dealing with DoS/DDoS assaults in SDNs.
Involvement of relatives during End Of Life care in Emergency Departments: comparison between the perceptions of physicians and nurses
Authors: Roussel Mélanie , Fourcade Claire , Douplat Marion , Conte Philippe Le , Freund Yonathan , Truchot Jennifer 
Published: December 2022

Abstract
Background: There is a lack of research focused on the management and involvement of relatives of patients admitted for End Of Life (EOL) in the Emergency Department (ED). Relatives should be included in the decision process of withholding or withdrawing life support however whether the relatives should be involved in the specific palliative care in the ED is not known. Healthcare workers (HCW) may have mixed feelings and therefore behaviors regarding their participation
Aim: This study aims to evaluate HCW perceptions regarding the patients’ relative’s involvement during EOL care in the ED. The secondary objective was to assess the acceptability of analgesia controlled by patients’ relative through an opioid patient-controlled analgesia (PCA) pump.
Design: An online survey designed by a panel of emergency physicians and experts in palliative care was shared to HCW from 3 countries.
Results: A total of 1408 HCW from 145 EDs answered the survey, including 758 (54%) physicians and 650 (46%) nurses. Only 185 responders (13%) considered that relatives were spontaneously willing to participate in EOL care. Only 10% of ED HCW responders declared that they used PCA over continuous intravenous infusion, compared to 68% in palliative care.
Conclusions: The variety of current practices regarding the involvement of relatives in the care of EOL patients in the ED warrants future research to improve EOL care.
Structure-based design of biocatalytic panels for pharmaceuticals synthesis
Authors: Yu Yuqi , Casamajo Arnau Rue , Finnigan William , Schnepel Christian , Barker Rhys , Morrill Charlotte , Heath Rachel , De Maria Leonardo , Turner Nicholas , Scrutton Nigel 
Published: December 2022

AbstractBiocatalysis is emerging as an attractive option for manufacturing pharmaceuticals. However, the identification of enzymes for target transformations of interest requires major screening efforts. Here we report a structure-based computational workflow to prioritize protein sequences by a score based on predicted activities on substrates, thereby reducing resource intensive laboratory-based biocatalyst screening. We selected imine reductases (IREDs) as a class of biocatalysts to illustrate the application of the computational workflow termed IREDFisher. Validation by using published data showed that IREDFisher can retrieve the best enzymes and increase the hit rate by identifying the top 20 ranked sequences. The power of IREDFisher is confirmed by computationally screening 1,400 sequences to identify suitable biocatalysts for five selected reductive amination reactions. IREDFisher is available as a user-friendly web interface that will enable rapid identification of biocatalysts for applications in synthesis and directed evolution studies with minimal time and resource expenditure.
Classification of age-related macular degeneration using very deep learning neural network based on transfer learning
Authors: Le Ngoc Thien , Le Truong Thanh , Itthipanichpong Rath , Pongsachareonnont Pear Ferreira , Mavichak Apivat , Suwajanakorn Disorn , Benjapolakul Watit 
Published: December 2022

Abstract
Background: Detecting and classifying the age-related macular degeneration (AMD) at the elderly people is one of the main concerns of the national public health program in Thailand. Within this research purview, accurate and sensitive performance is highly desirable, and a variety of proposed models have been developed toward this end. Deep learning neural networks have recently been shown to have advantage over existing approaches for the task of classifying the level of eye disease. Despite of these advances, there is still significant potential for development, regarding model classification accuracy, and sensitive values.
Results: Six very deep learning neural networks (DLNN), named as InceptionV3, ResNet152V2, DenseNet201, EfficientNetB7, InceptionResNetV2, and NASNetLarge are proposed for training to detect and classify the AMD disease from fundus images. The training process with AMD images is implemented based on the transfer learning technique through Google Colab Pro platform. The experiments showed that, for 3-classes AMD classification (Normal, Dry AMD, and Wet AMD), the overall classification accuracy of DenseNet201 is highest and is about 88% with the testing dataset. Furthermore, for the inferred 2-class AMD classification (Normal vs. AMD), the most accuracy values obtained from EfficientNetB7 and InceptionResNetV2 about 93.5% and 95.06%, respectively.
Conclusions: The experimental results have shown that, after applying transfer learning technique, the DenseNet201 model had higher accuracy performance in 3-class AMD classification of fundus images than other very deep learning neural networks and other state-of-the-art proposed deep learning models in the literature. Furthermore, the trained EfficientNetB7 and InceptionResNetV2 showed the advantages for the 2-class AMD classification over other existing models.
Miniaturization Design of Power-Receiving Module for Cavity Resonance-Enabled Wireless Power Transfer
Authors: Akai Suzuka , Saeki Hiromasa , Tamura Masaya 
Published: December 2022

Abstract
Wireless sensor networks (WSNs) are a candidates for data collection in factories. WSNs possess the problem of securing power for each sensor. Cavity resonance-enabled wireless power transfer (CR-WPT) has attracted attention as a solution to the abovementioned problem. This study proposes a design methodology for a miniaturized power-receiving module for the CR-WPT. The optimum matching circuit for the compact power-receiving modules are designed by considering the transmitter, cavity resonator, and receiver as a single system. The power-receiving module for a transmission frequency of 119 MHz is reduced from 280 x 59 x 67 mm3 to 100 x 30 x 30 mm3, which means a 92% reduction in volume. The compact power-receiving module obtains an efficiency similar to that of a previous power-receiving module.
Umbilical artery thrombosis and maternal positive autoimmune antibodies: Two case reports and a literature review
Authors: Li Xin , Chen Wei , Liu Tianjiao , Cai Jian , Wei Sumei , Du Yuhua , Liu Chunyan , Gong Zhaolin , Cheng Linbo , Zhou Xiaoling , Xiong Min , Wang Tao , Li Yalan , Lai Fan , Yang Xiao 
Published: December 2022

Abstract
Background: Previous studies have shown that abnormal increases in autoimmune antibodies in pregnant women may increase the risk of maternal thrombosis. However, at our hospital, two pregnant women presented with umbilical artery thrombosis and positive maternal autoantibodies were detected in both, which led us to consider whether maternal autoantibodies also played a role in umbilical artery thrombosis.
Case presentation: Case 1: Fetal ultrasound of a 34-year-old pregnant woman at 30+4 weeks gestation showed two umbilical arteries, with an inner diameter of approximately 0.15 cm for the smaller was artery. However, only a single umbilical artery blood flow signal was detected. Due to fetal distress, which was noted on abnormal cardiotocography and Doppler ultrasound, an emergency cesarean section was performed at 31+1 weeks gestation. The Apgar score of the newborn was 3-8-8. Umbilical cord examination detected thrombosis in the two umbilical arteries. Moreover, blood test results during pregnancy showed nRNP/Sm antibody (+) and SS antibody (+++).
Case 2: The first systematic ultrasound of a 33-year-old twin pregnancy at 24+3 weeks gestation was normal, but routine fetal ultrasound at 27+1 weeks gestation showed only one umbilical artery between fetus A and the placenta. Blood test results showed that the patient was anti-nRNP/Sm antibody (+) in the rheumatoid immune activity test at 27+3 weeks gestation. An emergency cesarean section was performed at 34+6 weeks gestation because of the single umbilical artery and abnormal maternal coagulation. Both umbilical cords of fetus A and B blood test results showed anti-nRNP/Sm antibody (++). The pathological examination of the umbilical cord and placenta showed the presence of old thrombosis in one of the umbilical arteries of fetus A.
Conclusions: Abnormal maternal autoantibodies may be a risk factor for umbilical artery thrombosis. For these pregnant women, anticoagulation therapy with heparin and aspirin was used in a timely manner, which could possibly have avoided the occurrence of adverse pregnancy outcomes.
Epidural lidocaine, butorphanol, and butorphanol – lidocaine combination in dromedary camels
Authors: Nahas Ayman El , Almubarak Adel Ibrahim , Hagag Usama 
Published: December 2022

Abstract

Background Hazard of decubitus constrains practicing of general anesthesia in dromedary camels. Caudal epidural analgesia is an appropriate substitute providing loco-regional analgesia for numerous invasive and noninvasive painful conditions. Lidocaine is the most popular local anesthetic in veterinary practice, but of limited analgesic merits. Epidural administration of an opioid - local anesthetic mixture would improve the quality and length of analgesia and minimize the adverse motor effects provoked by local anesthetics. Epidural butorphanol (an opioid) and lidocaine (local anesthetic) mixture was used to improve analgesia in certain animal species, but not in camels. Therefore, our purpose was to investigate the analgesic effects as well as the clinical and hemato-biochemical profiles produced by the epidural administration of butorphanol (0.04 mg/kg), lidocaine (0.22 mg/ kg), and butorphanol-lidocaine (0.04 mg/kg − 0.22 mg/ kg) mixture in nine adult dromedary camels through a crossover experimental study. Results The beginning of analgesia was not significantly different between lidocaine (6.5 ± 2.3 min) and butorphanol-lidocaine (7.3 ± 1.5 min) mixture. Delayed onset of analgesia was reported after butorphanol administration (14.7 ± 3.5 min). Butorphanol-lidocaine mixture produced significant longer duration (175 ± 8.7 min) than lidocaine (55 ± 6.8 min) and butorphanol (158 ± 5.3 min). Butorphanol–lidocaine treated animals showed mild sedation and slight locomotor disturbances. A transient significant rise in glucose levels was observed after all treatments. Conclusions Epidural administration of butorphanol augments the analgesic effects and duration of lidocaine with minimal adverse effects.
Risk of Arrhythmia with Exposure to Anthracyclines: A Systematic Review, Meta-Analysis, and Network Meta-Analysis
Authors: Li Hongzheng , Yang Wenwen , Yu Zikai , Peng Yuxuan , Huang Mingyan , Long Linzi , Lu Aimei , Tan Ling , Deng Mi , Qu Hua , Fu Changgeng 
Published: December 2022

Abstract
Objective
Whether clinical application of anthracyclines is associated with increasing arrhythmic risk remains controversial. In order to evaluate the arrhythmic risk of anthracyclines as a class, and the comparative risk for each individual drug, we conducted a systematic review, meta-analysis, and network meta-analysis.
Methods
Pubmed, Web of Science, EMBASE and the Cochrane Library were searched, up to March 2022, for randomized controlled trials, cohort studies, and case control studies that investigated the association between anthracyclines treatment and the risk of arrhythmia. We followed the PRISMA 2020 guidelines for data selection and extraction. Outcomes were pooled using fixed effects models in cohort studies and randomized controlled studies, and random models in single-arm studies. Direct and indirect comparisons in network meta-analysis were performed using frequentist methods.
Results
4 cohort studies, 8 RCTs, and 18 single-arm studies were included in our analysis. Anthracyclines use was associated with a statistically significant 90% increase in the risk for arrhythmia (odds ratio [OR] 1.90; 95% confidence interval [CI] 1.62–2.24) and 114% increase in the risk for supraventricular arrhythmia (OR 2.14; 95% CI 1.18–3.89). And the single-arm studies also indicated that incidence of arrhythmia rate is 20%, 95%CI is 15/100 − 25/100. Epirubicin ranked most likely to have the highest risk for arrhythmia compared with non-anthracycline antineoplastic drugs in the analysis (OR 43.07 [95% CI 2.80-2105.83]) by network meta-analysis.
Conclusions
Our findings show a significant association between anthracyclines use and an increased risk for arrhythmia, especially supraventricular arrhythmia. Epirubicin ranked with the highest probability for arrhythmia. These results indicated cardiac rhythm should be strictly monitored during the application of anthracyclines in clinical practice, and possible therapy for anthracyclines associated arrhythmia should be explored.
A cuproptosis-related gene cluster in prediction of ovarian cancer prognosis and chemotherapeutic response
Authors: Zou Qiaojian , Wang Shuyi , Chen Yili , Du Qiqiao , Zhang Chunyu , Liu Junxiu , Yao Shuzhong 
Published: December 2022

Abstract
Background
Ovarian cancer (OC) is a common gynecological malignancy correlated with a poor prognosis. Cuproptosis is a newly discovered form of cell death and has a close relationship with cancers, but the relationship between OC and cuproptosis remains unclear.
Results
In this study, we explored cuproptosis-related genes (CRGs) in public databases and found most CRGs are closely related to survival, and the potential roles of FDX1, LIAS and SLC31A1 in proliferation and migration were discovered in OC cell line. Afterwards, all 791 OC patients were divided into 2 clusters and the pathway enrichment and survival time showed obvious difference. 70 differentially expressed genes between 2 clusters were utilized to construct a gene signature. Significant difference was found in survival time and tumor-infiltrating immune cells among different risk groups. Finally, sensitivity of 12 commonly-used chemotherapeutic drugs was predicted closely correlating with risk score, which may provide a new strategy for clinical practice.
Conclusion
In conclusion, our study suggests that cuproptosis may play an important role in the progression of OC. We combinedly analyze cuproptosis-related differentially-associated genes in TCGA and GEO database and construct a risk model, which may provide new understandings to the treatment of OC.
Exogenous Female Sex Steroid Hormones and New-Onset Asthma in Women: A Matched Case-Control Study
Authors: Zhang Guo-Qiang , Basna Rani , Mathur Maya , Lässer Cecilia , Mincheva Roxana , Ekerljung Linda , Wennergren Göran , Rådinger Madeleine , Lundbäck Bo , Kankaanranta Hannu , Nwaru Bright 
Published: December 2022

Abstract
Background
Evidence on the role of exogenous female sex steroid hormones in asthma development in women remains conflicting. We sought to quantify the potential causal role of hormonal contraceptives and menopausal hormone therapy (MHT) in the development of asthma in women.
Methods
We conducted a matched case-control study based on the West Sweden Asthma Study, nested in a representative cohort of 15,003 women aged 16–75 years, with 8-year follow-up (2008–2016). Data were analyzed using Frequentist and Bayesian conditional logistic regression models.
Results
We included 114 cases and 717 controls. In Frequentist analysis, the odds ratio (OR) for new-onset asthma with ever use of hormonal contraceptives was 2.13 (95% confidence interval [CI] 1.03–4.38). Subgroup analyses showed that the OR increased consistently with older baseline age. The OR for new-onset asthma with ever MHT use among menopausal women was 1.17 (95% CI 0.49–2.82). In Bayesian analysis, the ORs for ever use of hormonal contraceptives and MHT were, respectively, 1.11 (95% posterior interval [PI] 0.79–1.55) and 1.18 (95% PI 0.92–1.52). The respective probability of each OR being larger than 1 was 72.3% and 90.6%.
Conclusions
Although use of hormonal contraceptives was associated with an increased risk of asthma, this may be explained by selection of women by baseline asthma status, given the upward trend in the effect estimate with older age. This indicates that use of hormonal contraceptives may in fact decrease asthma risk in women. Use of MHT may increase asthma risk in menopausal women.
The natural history study of preclinical genetic Creutzfeldt-Jakob Disease (CJD): A prospective longitudinal study protocol
Authors: Noa Bregman , Tamara Shiner , Gitit Kavé , Roy Alcalay , Mali Gana-Weisz , Orly Goldstein , Tal Glinka , Orna Aizenstein , Dafna Ben Bashat , Yifat Alcalay , Anat Mirelman , Avner Thaler , Nir Giladi , Nurit Omer 
Published: December 2022

Abstract
Background
Creutzfeldt-Jakob Disease (CJD) is the most common prion disease in humans causing a rapidly progressive neurological decline and dementia and is invariably fatal. The familial forms (genetic CJD, gCJD) are caused by mutations in the PRNP gene encoding for the prion protein (PrP). In Israel, there is a large cluster of gCJD cases, carriers of an E200K mutation in the PRNP gene, and therefore the largest population of at-risk individuals in the world. The mutation is not necessarily sufficient for the formation and accumulation of the pathological prion protein (PrPsc), suggesting that other, genetic and non-genetic factors affect the age at symptoms onset. Here we present the protocol of a cross-sectional and longitudinal natural history study of gCJD patients and first-degree relatives of gCJD patients, aiming to identify biological markers of preclinical CJD and risk factors for phenoconversion.
Methods
The study has two arms: A cross-sectional protocol for patients diagnosed with gCJD, and a longitudinal protocol for first-degree healthy relatives (HR) (both carriers and non-carriers of the E200K mutation in the PRNP gene) of patients diagnosed with gCJD. At baseline, and at the end of every year, participants are invited for an “in-depth” visit, which includes a clinical evaluation, blood and urine collection, gait assessment, brain MRI, lumbar puncture (LP), and PSG. At 6 months from baseline, and then halfway through each year, participants are invited for a “brief” visit, which includes a clinical evaluation, short cognitive assessment, and blood and urine collection.
Discussion
This continuous follow-up of the participants and the frequent assessments will allow early identification and diagnosis in case of conversion into disease. The knowledge generated from this study is likely to advance the understanding of the underlying clinicopathological processes that occur at the very beginning of CJD, as well as potential genetic and environmental risk factors for the development of the disease, therefore advancing the development of safe and efficient interventions.