bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the potential incidence of COVID-19 and effectiveness of containment measures in Spain: a data-driven approach
Authors: Aleta Alberto , Moreno Yamir 
Published: May 2020

Abstract
Background
We are currently experiencing an unprecedented challenge, managing and containing an outbreak of a new coronavirus disease known as COVID-19. While China—where the outbreak started—seems to have been able to contain the growth of the epidemic, different outbreaks are nowadays present in multiple countries. Nonetheless, authorities have taken action and implemented containment measures, even if not everything is known.

Methods
To facilitate this task, we have studied the effect of different containment strategies that can be put into effect. Our work referred initially to the situation in Spain as of February 28, 2020, where a few dozens of cases had been detected, but has been updated to match the current situation as of 13 April. We implemented an SEIR metapopulation model that allows tracing explicitly the spatial spread of the disease through data-driven stochastic simulations.

Results
Our results are in line with the most recent recommendations from the World Health Organization, namely, that the best strategy is the early detection and isolation of individuals with symptoms, followed by interventions and public recommendations aimed at reducing the transmissibility of the disease, which, although might not be sufficient for disease eradication, would produce as a second order effect a delay of several days in the raise of the number of infected cases.

Conclusions
Many quantitative aspects of the natural history of the disease are still unknown, such as the amount of possible asymptomatic spreading or the role of age in both the susceptibility and mortality of the disease. However, preparedness plans and mitigation interventions should be ready for quick and efficacious deployment globally. The scenarios evaluated here through data-driven simulations indicate that measures aimed at reducing individuals’ flow are much less effective than others intended for early case identification and isolation. Therefore, resources should be directed towards detecting as many and as fast as possible the new cases and isolate them.
Molecular detection of porcine reproductive and respiratory syndrome virus, porcine circovirus 2 and hepatitis E virus in oral fluid compared to their detection in faeces and serum
Authors: Plut Jan , Jamnikar-Ciglenecki Urska , Stukelj Marina 
Published: May 2020

AbstractBackgroundPorcine Reproductive and Respiratory Syndrome Virus (PRRSV), Porcine Circovirus Type 2 (PCV2) and Hepatitis E virus (HEV) are common and economically important viral disease causative agents detected in pig oral fluid (OF), faeces and serum at some infection stages. The purpose of this study was to detect PRRSV, PCV2 and HEV on six pig farms to determine which of the three sample types, OF, faeces or serum is appropriate for the diagnosis of these viruses in different pig categories.The following pig categories were included: 5 weeks-old (w/o), 7 w/o, 9 w/o, 11 w/o weaners, fatteners and breeding sows. Pursuant to the preliminary detection of each pathogen at the selected farms, OF samples, faeces, serum pools and 10 individual sera were examined, using PCR, for each age category. If any of the viruses were found in pools of faeces and OF, then faeces and OF from positive farms were tested separately for each pig category. The viral nucleic acids were detected using RT-PCR, PCR and real-time RT-PCR, for PRRSV, PCV2 and HEV respectively.ResultsPRRSV and HEV were detected on one farm and PCV2 on three others, positive results being more often obtained from the OF than from the faeces of the same animals. Ten individual serum samples from pigs from the same group of animals were also tested. The viruses were detected in almost all individual sera and OF in the same pig category with some exceptions: PRRSV was detected in the OF of fatteners but was absent in their sera; on Farm 2, PCV2 was detected in sera of 11 w/o pigs and fatteners but absent in group samples of their OF and, vice versa, in case of 9 w/o animals; HEV was detected in the OF of the youngest, 5 w/o weaners and absent in sera of the same age group.ConclusionsThe primary finding of the study is that OF is a welfare-friendly, non-invasive and highly efficient matrix for pathogen detection, thus evidencing the usefulness of pig OF as a matrix in which each of the three viruses considered can be detected with the highest probability.
Measuring the impact of sea surface temperature on the human incidence of Vibrio sp. infection in British Columbia, Canada, 1992–2017
Authors: Galanis Eleni , Otterstatter Michael , Taylor Marsha 
Published: May 2020

Abstract
Background
Vibrio growth in the environment is related to sea surface temperature (SST). The incidence of human Vibrio illness increased sharply in British Columbia (BC) between 2008 and 2015 for unknown reasons, culminating in the largest outbreak of shellfish-associated Vibrio parahaemolyticus (Vp) in Canadian history in 2015. Our objective was to assess the relationship between SST and Vibrio illness in BC, Canada during 1992–2017 and assess the role of SST and other environmental factors in the 2015 Vp outbreak.

Methods
Cases of Vibrio infection reported to the BC Centre for Disease Control during 1992–2017 were used. SST data were obtained from NOAA and NASA. We assessed changes in incidence trend of annual Vibrio cases during 1992–2017 using a Poisson regression. We assessed the correlation between annual Vibrio cases and the average annual maximum SST using a Spearman rank-order correlation. We modeled the association between weekly Vp case counts, SST and other environmental factors during 2007–2017 using a Poisson regression.

Results
There was a significant increase in Vibrio cases between 2008 and 2015 (annual slope = 0.163, P < 0.001). Increased Vibrio incidence was observed in most El Niño years. There was a significant correlation between annual Vibrio cases and maximum SST from 1992 to 2017 (r = 0.46, P = 0.018). Our model captured observed seasonal variation in shellfish-associated Vp in most years, but underestimated the 2015 Vp outbreak.

Conclusions
Vibrio incidence has been increasing concurrently with increasing SST in BC during 2008–2015. The 2015 Vp outbreak was not fully explained by climatic factors and may in part have been associated with other factors. Vp subtyping would be useful in the future to understand the combined effects of SST changes and strain emergence.
Long non-coding RNAs towards precision medicine in gastric cancer: early diagnosis, treatment, and drug resistance
Authors: Yuan Li , Xu Zhi-Yuan , Ruan Shan-Ming , Mo Shaowei , Qin Jiang-Jiang , Cheng Xiang-Dong 
Published: May 2020

AbstractGastric cancer is a deadly disease and remains the third leading cause of cancer-related death worldwide. The 5-year overall survival rate of patients with early-stage localized gastric cancer is more than 60%, whereas that of patients with distant metastasis is less than 5%. Surgical resection is the best option for early-stage gastric cancer, while chemotherapy is mainly used in the middle and advanced stages of this disease, despite the frequently reported treatment failure due to chemotherapy resistance. Therefore, there is an unmet medical need for identifying new biomarkers for the early diagnosis and proper management of patients, to achieve the best response to treatment. Long non-coding RNAs (lncRNAs) in body fluids have attracted widespread attention as biomarkers for early screening, diagnosis, treatment, prognosis, and responses to drugs due to the high specificity and sensitivity. In the present review, we focus on the clinical potential of lncRNAs as biomarkers in liquid biopsies in the diagnosis and prognosis of gastric cancer. We also comprehensively discuss the roles of lncRNAs and their molecular mechanisms in gastric cancer chemoresistance as well as their potential as therapeutic targets for gastric cancer precision medicine.
Cigarette smoking is associated with high level of ferroptosis in seminal plasma and affects semen quality
Authors: Ou Zhanhui , Wen Qirong , Deng Yu , Yu Yang , Chen Zhiheng , Sun Ling 
Published: May 2020

Abstract
Purpose
The effects of cigarette smoking on male semen quality are controversial, and the molecular mechanisms underlying how cigarette smoking affects semen quality are not clear yet.

Methods
In this study, semen samples from 70 heavy smokers and 75 non-smokers receiving infertility treatment were included. Basic semen parameters in non-smokers and heavy smokers were evaluated. Levels of glutathione (GSH), lipid reactive oxygen species (ROS), iron and GSH-dependent peroxidase 4 (GPX4) protein level were observed in human seminal plasma and in GC-2Spd cells exposed to cigarette smoke condensate (CSC).

Results
Heavy smokers had significantly higher abnormalities (sperm viability and sperm progressive motility) than non-smoking counterparts. Comparing non-smokers group, GSH level was reduced in the group of heavy smokers (P < 0.05). However, the level of lipid ROS and iron were significantly increased (P < 0.05). Besides, GSH level was reduced following treatment with CSC for 24 h, while lipid ROS and iron levels were increased (P < 0.05). However, the levels were reduced after being co-cultured with Ferrostatin-1 (Fer-1) (P < 0.05). The level of GPX4 protein was reduced after being treated with CSC in 24 h, and increased after being co-cultured with Fer-1(P < 0.05).

Conclusion
Cigarette smoking is associated with high level of ferroptosis in seminal plasma and affect semen quality.
Influence of extracorporeal membrane oxygenation on the pharmacokinetics of ceftolozane/tazobactam: an ex vivo and in vivo study
Authors: Mané Camille , Delmas Clément , Porterie Jean , Jourdan Géraldine , Verwaerde Patrick , Marcheix Bertrand , Concordet Didier , Georges Bernard , Ruiz Stéphanie , Gandia Peggy 
Published: May 2020

Abstract
Background
Extracorporeal membrane oxygenation (ECMO) is increasingly used in intensive care units and can modify drug pharmacokinetics and lead to under-exposure associated with treatment failure. Ceftolozane/tazobactam is an antibiotic combination used for complicated infections in critically ill patients. Launched in 2015, sparse data are available on the influence of ECMO on the pharmacokinetics of ceftolozane/tazobactam. The aim of the present study was to determine the influence of ECMO on the pharmacokinetics of ceftolozane-tazobactam.

Methods
An ex vivo model (closed-loop ECMO circuits primed with human whole blood) was used to study adsorption during 8-h inter-dose intervals over a 24-h period (for all three ceftolozane/tazobactam injections) with eight samples per inter-dose interval. Two different dosages of ceftolozane/tazobactam injection were studied and a control (whole blood spiked with ceftolozane/tazobactam in a glass tube) was performed. An in vivo porcine model was developed with a 1-h infusion of ceftolozane–tazobactam and concentration monitoring for 11 h. Pigs undergoing ECMO were compared with a control group. Pharmacokinetic analysis of in vivo data (non-compartmental analysis and non-linear mixed effects modelling) was performed to determine the influence of ECMO.

Results
With the ex vivo model, variations in concentration ranged from − 5.73 to 1.26% and from − 12.95 to − 2.89% respectively for ceftolozane (concentrations ranging from 20 to 180 mg/l) and tazobactam (concentrations ranging from 10 to 75 mg/l) after 8 h. In vivo pharmacokinetic exploration showed that ECMO induces a significant decrease of 37% for tazobactam clearance without significant modification in the pharmacokinetics of ceftolozane, probably due to a small cohort size.

Conclusions
Considering that the influence of ECMO on the pharmacokinetics of ceftolozane/tazobactam is not clinically significant, normal ceftolozane and tazobactam dosing in critically ill patients should be effective for patients undergoing ECMO.
Three-dimensional morphological analysis of the femoral neck torsion angle—an anatomical study
Authors: Zhang Ru-Yi , Su Xiu-Yun , Zhao Jing-Xin , Li Jian-Tao , Zhang Li-Cheng , Tang Pei-Fu 
Published: May 2020

Abstract
Background
The femoral neck torsion angle (FNTA) is an important but often neglected parameter in assessments of the anatomical morphology of the femoral neck, which is often confused with the femoral neck anteversion angle (FNAA) in the current literature. Currently, the measurement methods reported in the literature all adopt the naked eye or two-dimensional (2D) visualization method, and the measurement parameters and details are not clearly defined. The objection of this research was to provide a reliable 3D method for determining the femoral neck axis, to improve the measurement method of the FNTA, and to analyze the anatomical and clinical significance of the results.

Methods
Computed tomography (CT) data of 200 patients who received a lower extremity CT angiography examination were selected, and the bilateral femurs were reconstructed with three dimensional CT (3D CT). First, the 3D axis of the femoral neck was built. Second, the long axis of the cross section the femoral neck isthmus (FNI) and femoral neck basilar part (FNB) were confirmed by the “inertia axes” method, and the plane consisting of the long axis of the cross-section and the center of the femoral head was defined as the long axial plane. Third, the coronal plane of the proximal femur was determined through the long axis of the proximal femur and the femoral coronal. Finally, the FNTAs (the angles between the long axial planes and the coronal plane of the proximal femur) of FNI and FNB were measured. The size of FNTA was compared between the sexes and sides and different locations, the correlation between the parameters and age, height, and weight were evaluated.

Results
The difference in FNTA was statistically significant between the isthmus and the basilar part (isthmus 30.58 ± 8.90° vs. basilar part 23.79 ± 3.98°; p < 0.01). Significant difference in the FNTA was observed between the sexes (males 31.99 ± 9.25° vs. females 27.49 ± 7.19°; p < 0.01). The increase in FNTA from the basilar part to the isthmus was 6.79 ± 8.06°, and the male (7.87 ± 8.57°) was greater than the female (4.44 ± 6.23°, p < 0.01). However, no significant difference in the values was observed between sides. Height exerted the greatest effect on the FNTA according to the correlation analysis (r = 0.255, p< 0.001).

Conclusions
This study found a reliable 3D method for the determination of the femoral neck axis improved the measurement method of the FTNTA and made it more accurate and repeatable. The results provided a methodological basis and theoretical support for the research and development of internal fixation device for femoral neck fracture and the spatial configuration of implants in treatment. And the optimal opening point of the femoral medullary cavity was recommended to locate at the posterior position of the top of the femoral neck cross-section during hip replacement.
Learning curve associated with thoraco-laparoscopic esophagectomy for esophageal cancer patients in the prone position
Authors: Wang Tao , Ma Mu-yuan , Wu Bo , Zhao Yang , Ye Xiao-feng , Li Tao 
Published: May 2020

Abstract
Objective
To observe the surgical index at the different learning stages of thoraco-laparoscopic esophagectomy in the prone position for esophageal cancer and to investigate the learning curve of this surgical procedure.

Methods
Sixty thoraco-laparoscopic esophagectomies in the prone position for esophageal cancer conducted by the same group of surgeons between January 2014 and December 2015 were retrospectively analyzed. The surgeries were divided into 5 groups, A, B, C, D, and E, in chronological order. The duration of surgery, intraoperative blood loss, total number of lymph nodes removed, rate of the intraoperative conversion to open surgery, complication rate, and length of postoperative hospitalization were recorded and analyzed.

Results
The general information of the patients did not significantly differ among the 5 groups (P > 0.05). The duration of surgery, intraoperative blood loss, number of lymph node removed, rate of intraoperative conversion to open surgery, and number of injuries to the recurrent laryngeal nerve all significantly differed (P < 0.05). The rates of postoperative pulmonary infection, anastomotic fistula, pneumothorax, and hospitalization did not significantly differ (P > 0.05).

Conclusion
Thoracic physicians with some endoscopic experience can meet the requirements of the thoraco-laparoscopic esophagectomy in the prone position for esophageal cancer after completing 24–30 surgeries.
Molecular delineation of small supernumerary marker chromosomes using a single nucleotide polymorphism array
Authors: Zhou Lili , Zheng Zhaoke , Wu Lianpeng , Xu Chenyang , Wu Hao , Xu Xueqin , Tang Shaohua 
Published: May 2020

AbstractBackgroundDefining the phenotype-genotype correlation of small supernumerary marker chromosomes (sSMCs) remains a challenge in prenatal diagnosis. We karyotyped 20,481 amniotic fluid samples from pregnant women and explored the molecular characteristics of sSMCs using a single nucleotide polymorphism (SNP) array.ResultsOut of the 20,481 samples, 15 abnormal karyotypes with sSMC were detected (frequency: 0.073%) and the chromosomal origin was successfully identified by SNP array in 14 of them. The origin of sSMCs were mainly acrocentric-derived chromosomes and the Y chromosome. Two cases of sSMC combined with uniparental disomy (UPD) were detected, UPD(1) and UPD(22). More than half of the cases of sSMC involved mosaicism (8/15) and pathogenicity (9/15) in prenatal diagnosis. A higher prevalence of mosaicism for non-acrocentric chromosomes than acrocentric chromosomes was also revealed. One sSMC derived from chromosome 3 with a neocentromere revealed a 24.99-Mb pathogenic gain of the 3q26.31q29 region on the SNP array, which presented as an abnormal ultrasound indicating nasal bone hypoplasia.ConclusionThe clinical phenotypes of sSMCs are variable and so further genetic testing and parental karyotype analysis are needed to confirm the characteristics of sSMCs. The SNP array used here allows a detailed characterisation of the sSMC and establishes a stronger genotype-phenotype correlation, thus allowing detailed genetic counselling for prenatal diagnosis.
Microbiota-driven interleukin-17 production provides immune protection against invasive candidiasis
Authors: Li Mengmeng , Li Congya , Wu Xianan , Chen Tangtian , Ren Lei , Xu Banglao , Cao Ju 
Published: May 2020

Abstract
Background
The intestinal microbiota plays a crucial role in human health, which could affect host immunity and the susceptibility to infectious diseases. However, the role of intestinal microbiota in the immunopathology of invasive candidiasis remains unknown.

Methods
In this work, an antibiotic cocktail was used to eliminate the intestinal microbiota of conventional-housed (CNV) C57/BL6 mice, and then both antibiotic-treated (ABX) mice and CNV mice were intravenously infected with Candida albicans to investigate their differential responses to infection. Furthermore, fecal microbiota transplantation (FMT) was applied to ABX mice in order to assess its effects on host immunity against invasive candidiasis after restoring the intestinal microbiota, and 16S ribosomal RNA gene sequencing was conducted on fecal samples from both uninfected ABX and CNV group of mice to analyze their microbiomes.

Results
We found that ABX mice displayed significantly increased weight loss, mortality, and organ damage during invasive candidiasis when compared with CNV mice, which could be alleviated by FMT. In addition, the level of IL-17A in ABX mice was significantly lower than that in the CNV group during invasive candidiasis. Treatment with recombinant IL-17A could improve the survival of ABX mice during invasive candidiasis. Besides, the microbial diversity of ABX mice was significantly reduced, and the intestinal microbiota structure of ABX mice was significantly deviated from the CNV mice.

Conclusions
Our data revealed that intestinal microbiota plays a protective role in invasive candidiasis by enhancing IL-17A production in our model system.
Efficacy of neoadjuvant endocrine therapy compared with neoadjuvant chemotherapy in pre-menopausal patients with oestrogen receptor-positive and HER2-negative, lymph node-positive breast cancer
Authors: Kim Hee Jeong , Noh Woo Chul , Lee Eun Sook , Jung Yong Sik , Kim Lee Su , Han Wonshik , Nam Seok Jin , Gong Gyung -Yub , Kim Hwa Jung , Ahn Sei Hyun 
Published: May 2020

Abstract
Introduction
Neoadjuvant endocrine therapy (NET) has demonstrated efficacy in post-menopausal patients with hormone-responsive breast cancer. This trial was designed to compare the efficacy of neoadjuvant chemotherapy (NCT) with NET in pre-menopausal breast cancer.

Patients and methods
In this prospective, randomised, phase III study, oestrogen receptor (ER)-positive, HER2-negative, and lymph node-positive pre-menopausal breast cancer patients were recruited from 7 hospitals in South Korea. Enrolled patients were randomly assigned (1:1) to receive 24 weeks of either NCT or NET with goserelin and tamoxifen. The primary purpose was to evaluate the non-inferiority of NET compared to NCT using clinical response, assessed by MRI. Besides, pathological complete response rate (pCR), changes in Ki-67 expression, breast conservation surgery (BCS) rate, and quality of life were included as secondary endpoints.

Results
A total of 187 patients were assigned to receive NCT (n = 95) or NET (n = 92), and 87 patients in each group completed treatments. More NCT patients had complete response or partial response than NET patients using MRI (NCT 83.7% vs. NET 52.9%, 95% CI 17.6–44.0, p < 0.001) and callipers (NCT 83.9% vs. NET 71.3%, 95% CI 0.4–24.9, p = 0.046). Three NCT patients (3.4%) and one NET patient (1.2%) showed pCR (p < 0.005). No difference existed in the conversion rate of BCS (13.8% for NCT vs. 11.5% for NET, p = 0.531) and Ki-67 change (p = 0.114) between the two groups. Nineteen NCT patients had treatment-related grade 3 or worse events compared with none in the NET group.

Conclusions
Better clinical responses were observed in pre-menopausal patients after 24 weeks of NCT compared to those observed after NET.

Trial registration
Clinicaltrials.gov, NCT01622361. Registration June 19, 2012.