bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization
Authors: von Sydow Anita Koskela , Lindqvist Carl Mårten , Naveed Asghar , Johansson Magnus , Sundqvist Martin , Mölling Paula , Stenmark Bianca 
Published: October 2022

Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) worldwide pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14–30 were run using three different protocols: the Twist Bioscience SARS‑CoV‑2 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The ARTIC and Midnight protocol produced an even coverage across samples, and almost all reads were mapped to the SARS-CoV-2 reference. ARTIC and Midnight represent robust, cost-effective, and highly scalable methods that are appropriate in a clinical environment. Lineage designations were uniform across methods, representing the dominant lineages in Sweden during the period of collection. This study provides insights into methodological differences in SARS‑CoV‑2 sequencing and guidance in selecting suitable methods for various purposes.
Influence of cementite coarsening on the corrosion resistance of high strength low alloy steel
Authors: Liu Chao , Li Qinglin , Li Xuan , Yang Shufeng , Liu Zhiyong , Cheng Xuequn 
Published: October 2022

Abstract
A detailed study was carried out on how heat treatment affects the initiation and evolution of localized corrosion on E690 steel in a simulated marine environment. Localized corrosion was mainly induced by the inclusions and initiated by dissolution of the distorted matrix surrounding the inclusions. In this early corrosion initiation stage, localized corrosion induced by inclusions is the main form of corrosion. The chemical and electrochemical processes of matrix deformation and localized corrosion induced by inclusions are explained in detail. With the immersion time increased, galvanic contributions at the ferrite-austenite interfaces and the coarsened carbides reduced the polarization resistance in the annealed specimen and therefore accelerated corrosion compared to the as-received specimen. Hence, the heat-treated specimen showed a lower charge transfer resistance than the one without heat treatment. This promoted a shift from localized to uniform corrosion. Lastly, a corrosion initiation and evolution model has been established to explain the corrosion process of E690 steel in the marine environment.
Estimation of optimal tilt angles for photovoltaic panels in Egypt with experimental verifications
Authors: Abdelaal Ashraf , El-Fergany Attia 
Published: October 2022

Abstract
The principal target of this work is to compute the optimal tilt angle (OTA) for Photovoltaic (PV) panels. To perform this task, comprehensive simulations are done starting from altering the tilt angle (TA) daily, to use one fixed TA for all the year. The mathematical models for extra-terrestrial radiation (ETR) of both horizontal and inclined surfaces are presented firstly. At a later stage, the optimization formulation for the maximizing the solar radiation (SR) is adapted, and then the daily, monthly, seasonally, half-yearly and optimal fixed TAs are obtained. Although, the daily OTA produces the maximum SR, it is costly and impractical. It is found that altering the TA twice a year at optimal values that are computed as 5o and 50o for Suez city, gives the best results that are very near to the daily altering of the OTA. The difference between the two methods is 1.56% which is very small. Also, the two OTAs has SR better than that of the fixed OTA which is 28o by 7.77%. Also, it is found that the yearly fixed OTA (28o) is nearly equal to the latitude angle of Suez city which is 30o. The two OTAs method of this paper is different from the commonly used method that suggests two TAs. The first TA is used for winter months which is obtained by adding 15o to the latitude angle while the second TA is obtained by subtracting 15o from the latitude angle for the summer months. This commonly used method produces lesser SR than the two OTAs method of this paper. The theoretical work has been proved by an experimental work on two PV systems constructed at 25o and 30o TAs. The results of the experimental work agree with the theoretical results.
A Retrospective Study of the Contraceptive Use and Pregnancy Outcome of Women With Familial Mediterranean Fever in Turkey
Authors: Bilge Nazife Sule Yasar , Kilic Seda , Bilge Ugur , Balcioglu Huseyin , Kasifoglu Timucin 
Published: October 2022

Abstract
Background: Familial Mediterranean fever (FMF) is an autoinflammatory disease. Because FMF commonly affects people of childbearing ages, the effect of the disease and its treatment on fertility and pregnancy outcomes is under consideration. This study aimed to evaluate pregnancy outcomes and contraception methods of FMF patients.
Results: The records of 62 female FMF patients were retrospectively evaluated. Intrauterine devices and tubal ligation are the most common contraception methods. Of the 62 patients, 25 patients had 39 pregnancies. Of the 39 pregnancies, miscarriages were miscarriage, two had abortus, one was ectopic, and the remaining 26 were delivered. Two of the deliveries were preterm and the remaining were term. All patients received colchicine treatment, and the dose of colchicine had no effect on the pregnancy results (chi-square: 5.475, p = 0.708).
Conclusion: Colchicine treatment is safe during pregnancy. Furthermore, having FMF or receiving colchicine therapy does not affect the contraception habits of patients.
Ppe.CR.1 DNA test for predicting chilling requirement in peach
Authors: Demirel Gizem , Calle Alejandro , Lawton John Mark , Atagul Omer , Fu Wanfang , Gasic Ksenija 
Published: October 2022

Abstract
Chilling requirement (CR) is an important agronomic trait controlling the floral bud break for proper flowering in peach. Even though it has been widely researched and several peach CR quantitative trait loci (QTLs) have been identified, no diagnostic DNA tests validated in the U.S. peach breeding germplasm are available for this trait. Breeders and growers need a simple DNA test to predict the CR of peach cultivars for their particular environment. Therefore, we developed a quick and reliable Kompetitive Allele Specific PCR (KASP) DNA test using haplotype information from 9K IPSC genotype data of the U.S. peach germplasm integrating four CR-associated SNP markers from the previously reported CR QTL region on linkage group 1. Four KASP assays (Ppe.CR.1–1 to -4) were developed and validated on 77 peach cultivars, and nine accessions from two F2 populations, with 96 and 74% accuracy in predicting correct CR genotype and phenotype, respectively. Furthermore, the Ppe.CR.1 showed 80% accuracy in predicting the precise CR phenotype in the Clemson University peach breeding material. Only one Ppe.CR.1 KASP assay (Ppe.CR.1–1) is needed to distinguish between haplotypes with CR lower and higher than 800 chilling hours, and two Ppe.CR.1 assays (Pp.CR.1–1 and − 4), are capable of distinguishing low, moderate, and high CR alleles. Coupled with the crude DNA extraction, the Ppe.CR.1 DNA test provides a low-cost option for breeders and growers to predict CR in peach material with more than 70% accuracy.
Post-resolution macrophage-derived lipids shapes long-term tissue immunity and integrity
Authors: Feehan Karen , Bridgewater Hannah , Stenkiewicz-Witeska Jan , Ferguson John , Mack Matthias , BROWN JEREMY , Ercoli Giuseppe , Mawer Connar , Akbar Arne , Jalali Parinaaz , Bracken Olivia , Glanville James , Nicolaou Anna , Kendall Alexandra , Sugimoto Michelle , Gilroy Derek 
Published: October 2022

Abstract

Resolving inflammation is thought to return the affected tissue back to homeostasis. However, we show that within days following resolution of Streptococcus pneumonia-triggered lung inflammation there is an influx of antigen specific lymphocytes with a memory and tissue-resident phenotype as well as macrophages bearing an alveolar or interstitial phenotype. Transcriptomic analysis revealed that macrophages are enriched with genes that drive T cell chemotaxis and differentiation as well as prostaglandin biosynthesis.
Therapeutic depletion of post-resolution macrophages or inhibition of PGE2/EP4 signalling reduced numbers of lung CD4+/CD44+/CD62L+ and CD4+/CD44+/CD62L-/CD27+ T cells as well as their expression of the alpha-integrin, CD103. This intervention resulted in a failure of these cells to reappear and reactivate upon secondary challenge up to six weeks following primary infection. Concomitantly, EP4 inhibition caused accumulation of lung macrophages and marked tissue fibrosis.
Hence, resolving inflammation triggers a second wave of immune activity controlled, in part, by PGE2, which through EP4, drives local tissue-resident T cell development on the one hand, whilst limiting tissue injury on the other.
Internet Engagement and its’ Association with Weight Parameters and Academic Performance among Malaysian Adolescents
Authors: MY Nurul Haniza , Majid Hazreen Abdul , Thangiah Nithiah , Jalaludin Muhammad Yazid , Chinna Karuthan , Su Tin Tin 
Published: October 2022

Abstract
BACKGROUND: This study identifies the association of internet engagement with weight-related parameters and academic performance among adolescents in Malaysia.
METHODS: This is a cross-sectional study which collected primary data on academic performance and used secondary data from the second wave of the Malaysian Health and Adolescents Longitudinal Research Team (MyHeARTs) Study cohort. The participants comprised 720 students attending year three public secondary schools from the states of Selangor, Perak and Federal Territory of Kuala Lumpur in Malaysia. Sampling was done using a two-stage cluster sampling design.
RESULTS: The prevalence of adolescents who engage on the Internet regularly was 85.3% (n=614). Among those who regularly engaged with the Internet, 53.9% (n=331) spent an average of ≥3 hours per day on the Internet while 46.1% (n=283) of them spent an average of < 3 hours per day on the Internet. Of the total participants, 57.6% (n=415) have a mobile phone or tablet with a data plan. Participants who regularly engaged on the internet were more likely to have better overall academic performance (OR=2.319, CI=1.118-4.810) than those who rarely engaged on the internet. However, participants who spent an average of ≥ 3 hours per day on the Internet had less likelihood of getting average in aggregate (overall academic performance) (OR=0.899, CI=0.811-0.996) compared to participants who spent an average of < 3 hours per day on the Internet. Participants who spent an average of ≥ 3 hours per day on the Internet had less likelihood of having excess body fat compared to the participants who spent < 3 hours daily on the Internet (OR=0.701, CI=0.493-0.997).
CONCLUSION: Generally, time spent on the Internet is not associated with all weight-related parameters. It could be said that since majority of participants use mobile phone for internet engagement, thus it may not affect ones’ body composition. On the other hand, regular engagement on the internet was associated to better academic performance but it was found that spending more time on the internet resulted in poorer academic performances. As such, close monitoring, supervision, and guidance on Internet engagement among adolescents is crucial.
The OptiBreech Care Pathway: evaluating the feasibility and acceptability of team care for women seeking to plan a vaginal breech birth (OptiBreech 1) – a mixed methods implementation feasibility study
Authors: Walker Shawn , Spillane Emma , Stringer Kate , Meadowcroft Amy , Dasgupta Tisha , Davies Siân , Sandall Jane , Shennan Andrew , Collaborative OptiBreech 
Published: October 2022

Abstract
Background
OptiBreech Care is a care pathway for breech presentation at term, including where chosen, physiological breech birth attended by professionals with advanced training and/or proficiency. We aimed to assess the feasibility of implementing OptiBreech team care to test it in trial-within-a-cohort study.
Methods
Our design was a mixed methods trial feasibility assessment across England and Wales, January 2021 – June 2022. Our objectives were to determine whether Trusts could provide attendants with advanced training (implementation feasibility), who deliver protocol-consistent care (fidelity), in a way acceptable to women and staff (acceptability), within existing resources (costs), while maintaining low neonatal admission rates (safety) and adequate recruitment rates (trial feasibility). Participants were women > 37 weeks pregnant with a breech-presenting fetus, requesting support for a vaginal breech birth following standard counselling, and the staff involved in the study. No randomisation occurred in this first stage of feasibility work.
Results
Thirteen National Health Service sites recruited. A total of 82 women planned births on the study, and 21 staff were interviewed. Sites with a breech specialist midwife and/or dedicated clinic recruited 1 woman/month, while sites without recruited an average of 2 women every 3 months. Referrals into the study came from midwives (46%), obstetricians (34%) and women themselves (20%). Vaginal births were attended by staff with OptiBreech training at 87.5% (35/40) and by staff who met stricter proficiency criteria at 67.5% (27/40). Fidelity criteria were met more consistently by staff who met proficiency criteria. There were four neonatal admissions (4.9%, 4/82), including one serious adverse outcome (1.2%, 1/82); these outcomes compare well with previous breech research. Women found the model of care highly acceptable compared to standard care, and staff providing care generally found the OptiBreech model acceptable. However, staffing shortages throughout the pandemic and persistent negative views of vaginal breech birth outside the teams created challenges.
Conclusions
A large prospective observational cohort of OptiBreech Care, which could potentially support nested or cluster randomisation, appears feasible in sites willing to establish a dedicated clinic and develop further proficient members of staff strategically, with back-up plans for supporting rapidly progressing births. Randomisation procedures remain to be feasibility-tested. Funded by the NIHR (300582).
Defining the Learning Curve of Robotic Portal Segmentectomy in Small Pulmonary Lesions: A Prospective Observational Study
Authors: Yang Mu-Zi , Tan Zi-Hui , Abbas Abbas , Li Ji-Bin , Xie Chu-Long , Long Hao , Zhang Lan-Jun , Fu Jian-Hua , Lin Peng , Yang Hao-Xian 
Published: October 2022

Abstract
Although robotic segmentectomy has been applied for the treatment of small pulmonary lesions for many years, studies on the learning curve of robotic segmentectomy are quite limited. Thus, we aim to investigate the learning curve of robotic portal segmentectomy with 4 arms (RPS-4) using prospectively collected data in patients with small pulmonary lesions. One hundred consecutive patients with small pulmonary lesions who underwent RPS-4 between June 2018 and April 2021 were included in the study. Da Vinci Si/Xi systems were used to perform RPS-4. The mean operative time, console time, and docking time for the entire cohort were 119.2 ± 41.6, 85.0 ± 39.6, and 6.6 ± 2.8 minutes, respectively. The learning curve of RPS-4 can be divided into three different phases: 1–37 cases (learning phase), 38–78 cases (plateau phase), and > 78 cases (mastery phase). Moreover, 64 cases were required to ensure acceptable surgical outcomes. The total operative time (P < 0.001), console time (P < 0.001), blood loss (P < 0.001), and chest tube duration (P = 0.014) were reduced as experience increased. In conclusion, the learning curve of RPS-4 could be divided into three phases. 37 cases were required to pass the learning phase, and 78 cases were needed to truly master this technique.
Milk-derived exosomes carrying siRNA-KEAP1 promote diabetic wound healing by improving oxidative stress
Authors: Xiang Xuejiao , Chen Jing , Jiang Tao , Yan Chengqi , Kang Yu , Zhang Maojie , Xiang Kaituo , Guo Jiahe , Jiang Guoyong , Wang Cheng , Xu Xiang , Yang Xiaofan , Chen Zhenbing 
Published: October 2022

Abstract
Diabetic wound, as a serious complication of diabetes mellitus (DM), leads to persistent infection, amputation and even death. Prolonged oxidative stress has been widely recognized as the main cause of diabetic wound and is considered as hopeful therapeutic target. In the present study, Keap1/Nrf2 signaling was confirmed to be activated in streptozotocin (STZ)-induced diabetic mice and methylglyoxal (MGO)-treated human umbilical vein endothelial cells (HUVEC). Knockdown of Keap1 by siRNA attenuated the raised Keap1 level, promoted the nuclear transfer of Nrf2, and then facilitated the expression of HO-1, an antioxidant protein. Then the milk-derived exosomes (mEXOs) were developed as a novel, efficient and non-toxic siRNA carrier. SiRNA-Keap1 (siKeap1) was loaded into mEXOs through ultrasonic technique, which promoted HUVEC proliferation, migration and relieved oxidative stress in MGO-treated HUVEC. In the meantime, the injection of mEXOs-siKeap1 significantly accelerated the diabetic wound healing with enhanced collagen formation and neovascularization in mice models. Totally, the present study puts forward a potential treatment for diabetic wound and proved the feasibility of mEXOs as a scalable, biocompatible, and cost-effective siRNA delivery system.
Evolutionary Combination of Subplot Patterns into Meaningful Plots
Authors: Gervás Pablo , Méndez Gonzalo , Concepción Eugenio 
Published: October 2022

Abstract
Purpose: Many of the stories we are exposed to are built from small patterns of connected events involving a set of characters -- boy meets girl leads to a relationship or crime leads to revenge. The present paper studies the computational constraints that apply to the task of putting together a story by combining a set of such patterns. This approach presents three challenges: how to mix up the elements in the different patterns,how to instantiate the characters across the patterns andhow to tell acceptable combinations from the rest.
Methods: The present paper applies an evolutionary solution that relies on a genetic representation for these combinations of patterns, and applies as fitness functions a set of metrics on compatibility constraints across pattern combinations. Outputs of this procedure are evaluated by human judges in comparison with baseline solutions.
Results: The proposed solution generates a population of story drafts that resemble plot descriptions for simple stories. A comparative evaluation by human judges against baselines based on random gene assignment yields positive results.
Conclusion: The genetic representation of pattern combinations and the metrics on compatibility across pattern pairs provide a valid evolutionary solution for constructing simple plots.
Evaluating the one-time chair stand test for predicting the coronavirus disease severity in patients during hospital admission: A cohort study in Japan
Authors: Ishihara Atsushi , Yoshizane Takashi , Mori Teruki , Sasaki Yui , Hosokawa Takahiro , Suzuki Jun , Tsuzuku Akifumi , Asano Fumihiro , Noda Toshiyuki 
Published: October 2022

Abstract
Background: This study aimed to understand whether the one-time chair stand test (CS-1) is useful for predicting the severity of coronavirus disease (COVID-19) in 101 patients admitted to the hospital with acute respiratory failure.
Methods: This single-centered, prospective observational cohort study enrolled 101 critically ill adult patients hospitalized with COVID-19 who underwent the CS-1 as a dynamic evaluation tool in clinical practice between late April 2020 and October 2021. Data on demographic characteristics, symptoms, laboratory values, computed tomography findings, and clinical course after admission were collected. Furthermore, the data was compared and the association between the intubation and non-intubation groups was determined. We also calculated the cut-off point, area under the curve (AUC), and 95% confidence interval (CI) of the change in oxygen saturation (ΔSpO2) during the CS-1.
Results: Thirty-three out of 101 patients (33%) were intubated during hospitalization. There was no significant difference in the resting SpO2 (93.3% versus 95.2%, P=0.22), but there was a significant difference in ΔSpO2 during the CS-1 between the intubation and non-intubation groups (10.8% versus 5.5%, P<0.01). In addition, there was a significant correlation between hospitalization and ΔSpO2 during the CS-1 (ρ=0.60, P<0.01). The generated cut-off point was calculated as 9.5% (AUC=0.94, 95% CI=0.88–1.00).
Conclusion: For COVID-19 patients with acute respiratory failure, the CS-1 performed on admission was useful for predicting the severity of COVID-19. Furthermore, the CS-1 can be utilized as a remote and simple evaluation parameter. Thus, it could have potential clinical application in the future.
Cost-Effective Bio-Synthesis and characterization of Encapsulated Cu, Ag, and Magnetic Cu-Ag Bimetallic Nanoparticles
Authors: Shamim Mahadi Hasan , Kabir Md. Faysal , Ferdousy Jannatul , Ullah A. K. M. Atique , Tareq Rayhan , Islam Razzakul , Rahman Md. Mizanur 
Published: October 2022

Abstract

Since this work's goal is to create magnetic monometallic and magnetic bimetallic nanoparticles will proceed without using any chemicals. This study reports the green synthesis of Cu, Ag, and Cu-Ag nanoparticles at room temperature using Musa paradisiaca (banana) leaf extract. Our current study also focuses on determining how effective the leaf extract of Musa paradisiaca (commonly known as banana) is as a reducing and stabilizing agent. After adding the Musa paradisiaca (banana) leaf extract to the solution containing the metal salt, constant stirring was performed until the reaction was finished. X-ray Diffraction (XRD) and the Fourier transform infrared spectroscopy (FTIR) was used to examine the synthesized nanoparticles. The major types of equipment for our characterization were Energy Dispersive X-ray Spectroscopy (EDS), Field Emission Scanning Electron Microscopy (FESEM), Thermogravimetric Analysis (TGA), and Vibrating Sample Magnetometer (VSM). The analyses revealed that Musa paradisiaca (Banana) leaf extract efficiently reduced the Cu, Ag, and magnetic Cu-Ag nanoparticles. Biomolecules from Musa paradisiaca (banana) leaves were adsorbed on nanoparticle surfaces, producing a capping layer and stabilizing the nanoparticles. The average crystalline sizes of Cu, Ag and Ag-Cu nanoparticles were about 19 nm, 13 nm, and 23.15 nm, respectively. Surface morphology and particle size distribution were also observed using a modern FESEM device. ImageJ software was used to compute the average particle size and the distribution of particle sizes. The calculated particle size range was (5nm - 35 nm), (10 nm – 60 nm), and (20 nm – 90 nm) for Cu NPS, Ag NPs, and Cu-Ag NPs, respectively. Simultaneously, the presence of elements in our synthesized nanoparticles was also investigated with the help of EDX tools. Organic functional groups were confirmed using FTIR analysis. In the last part, the magnetic behavior of our synthesis Cu-Ag bimetallic nanoparticles was analyzed using a VSM machine, and we found saturation magnetization (Ms) was 0.58 emu g-1. The coercivity (Hc) was 153 Oe. According to the findings, Musa paradisiaca (banana) leaf extract is a promising reducing and stabilizing agent.