bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study on the influence of sand liquefaction caused by earthquake on the floating of underground structures
Authors: Wang Kaiping , Yang Lingqiang , Yao Jifei 
Published: March 2020

Abstract
The effective stress of the soil decreases and the pore water stress increases under the earthquake, which causes the sand to liquefy. The vertical deformation of the ground caused by the liquefaction of sand causes serious damage to the ground and the buried structure, which seriously threatens the safety of underground lifeline engineering. In order to study the impacts of sand liquefaction, the language FORTRAN was used to establish a finite element model under the earthquakes. The floating of various locations of the underground structure under different earthquakes was studied, and the factors affecting the floating were discussed. The results show that during the earthquake, the liquefaction of sand occurs, which causes the underground structure moves up due to buoyancy, and the soil mass from the structure collapses. The liquefied sand diffuses to the surrounding area after the earthquake, causing the sand beneath the underground structure to be lost, and the building will return to its original position or even collapse. The results provide references for the anti-floating research of underground structures.
Application of time-frequency image feature extraction method based on gray level co-occurrence matrix in coal mine pipeline leakage detection
Authors: Han Wenbei , Zhao Hongliang , Zhao Ziwei , Gu Fengshou , Zhen Dong 
Published: March 2020

Abstract
The underground mining environment of coal mine is complex. Once the water supply or gas supply pipes leak, the location and time of leakage are unpredictable. If the leakage can not be found in time, it will seriously threaten the life safety of underground workers. Therefore, it is very necessary to automatically detect the pipeline leakage. In order to solve the problem of automatic detection of coal mine pipeline leakage, this paper proposes an image processing method based on gray level co-occurrence matrix to extract the features of time-frequency image of vibration signal. Firstly, the data in a relatively short time is divided into one frame to reduce the amount of calculation. Secondly, each frame of signal is processed by SPWVD to get the time-frequency image. Then, the time-frequency image after time-frequency analysis is transformed into gray-scale image, and the gray-scale co-occurrence matrix (GLCM) of the image is extracted. Finally, the energy, contrast and correlation of the co-occurrence matrix are extracted and input to SVM for learning and training. Through the design and build of the experimental pipeline to test the algorithm proposed in this paper, the detection result of SVM is 96.67%, which shows that this method can effectively detect the pipeline leakage.
The Impact of Delayed Switch to Second-Line Antiretroviral Therapy on Mortality, Depending on Definition of Failure Time and CD4 Count at Failure
Authors: Bell-Gorrod Helen , Fox Matthew P , Boulle Andrew , Prozesky Hans , Wood Robin , Tanser Frank , Davies Mary-Ann , Schomaker Michael 
Published: March 2020

Abstract
Little is known about the functional relationship of delaying second-line treatment initiation for human immunodeficiency virus–positive patients and mortality, given a patient’s immune status. We included 7,255 patients starting antiretroviral therapy during 2004–2017, from 9 South African cohorts, with virological failure and complete baseline data. We estimated the impact of switch time on the hazard of death using inverse probability of treatment weighting of marginal structural models. The nonlinear relationship between month of switch and the 5-year survival probability, stratified by CD4 count at failure, was estimated with targeted maximum likelihood estimation. We adjusted for measured time-varying confounding by CD4 count, viral load, and visit frequency. Five-year mortality was estimated to be 10.5% (95% CI: 2.2, 18.8) for immediate switch and to be 26.6% (95% CI: 20.9, 32.3) for no switch (51.1% if CD4 count was &lt;100 cells/mm3). The hazard of death was estimated to be 0.37 (95% CI: 0.30, 0.46) times lower if everyone had been switched immediately compared with never. The shorter the delay in switching, the lower the hazard of death—delaying 30–59 days reduced the hazard by 0.53 (95% CI: 0.43, 0.65) times and 60–119 days by 0.58 (95% CI: 0.49, 0.69) times, compared with no switch. Early treatment switch is particularly important for patients with low CD4 counts at failure.
Myths of the Odyssey in the British Museum (and beyond): Jane Ellen Harrison’s museum talks and their audience
Authors: Baker Abigail 
Published: March 2020

AbstractJane Ellen Harrison’s early work giving tours and lectures in London’s museums offers an unusual window on visitor experience in the late nineteenth century. This article examines the composition and motivations of her audience, looking at how Harrison’s lectures addressed gendered and class-based anxieties about their access to education and ability to respond appropriately to prestigious objects. Harrison used Greek vases to tell stories from ancient Greek literature. She made the case for the value of Greek vases as a repository of stories that could be understood through comparisons with literature but which also stood as evidence in their own right, hinting at lost stories and the perspectives of ordinary people. Her museum talks demonstrate a belief that Greek vases offered an alternative to Classical literature, one which had been made by ordinary people in the past and could be ‘read’ by ordinary people in the present.
Are Patients with Inflammatory Bowel Disease at Increased Risk for Covid-19 Infection?
Authors: Monteleone Giovanni , Ardizzone Sandro 
Published: March 2020

Abstract
Crohn’s disease [CD] and ulcerative colitis [UC], the main inflammatory bowel diseases [IBD] in humans, are chronic, immune-inflammatory diseases, the pathogenesis of which suggests a complex interaction between environmental factors and genetic susceptibility. These disabling conditions affect millions of individuals and, together with the drugs used to treat them, can put patients at risk of developing complications and other conditions. This is particularly relevant today, as coronavirus disease [Covid-19] has rapidly spread from China to countries where IBD are more prevalent, and there is convincing evidence that Covid-19-mediated morbidity and mortality are higher in subjects with comorbidities. The primary objectives of this Viewpoint are to provide a focused overview of the factors and mechanisms by which the novel severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] infects cells and to illustrate the link between such determinants and intestinal inflammation. We also provide clues about the reasons why the overall IBD population might have no increased risk of developing SARS-CoV-2 infection and highlight the potential of cytokine blockers, used to treat IBD patients, to prevent Covid-driven pneumonia.
The effect of facemask in patients with unilateral cleft lip and palate: a systematic review and meta-analysis
Authors: Palikaraki Georgia , Makrygiannakis Miltiadis A , Zafeiriadis Anastasios A , Benetou Vassiliki , Sanoudos Mattheos , Bitsanis Ilias , Tsolakis Apostolos I 
Published: March 2020

Summary

Background
Patients with cleft lip and palate usually present a Class III skeletal pattern. Facemask (FM) is one of the conventional orthodontic treatment modalities used to address the skeletal discrepancy in cleft patients.

Objective
To investigate the potential effectiveness of FM in unilateral cleft lip and palate (UCLP) patients.

Search methods
Search without restrictions except language in seven databases since inception and hand searching until January 2019 was conducted. Detailed search strategies were developed for each database which were based on the PubMed strategy and adapted accordingly.

Selection criteria
Controlled studies assessing the effect of FM in UCLP patients were to be included.

Data collection and analysis
After retrieval and selection of the studies, data extraction was performed. Both angular and linear cephalometric measurements were collected. Weighted mean differences (WMDs) and 95% confidence intervals (CΙs) between treated and untreated UCLP patients concerning the pre- and post-treatment angular measurements of each group were calculated using a random-effects meta-analysis model. The risk of bias in individual studies was assessed using the ROBINS-I tool.

Results
From nine eligible studies, five were included in the meta-analysis investigating the use of FM in patients and controls with UCLP (with and without maxillary expansion). Statistically significant differences were evident for SNA/S–N–ss, SNB/S–N–sm, ANB/ss–N–sm, and SN–MP. FM was found to induce an increase of SNA (WMD = 2.12 degrees, 95% CI: 1.58 to 2.66), ANB (WMD = 4.17 degrees, 95% CI: 3.60 to 4.74), and SN–MP angles (WMD = 2.60 degrees, 95% CI: 1.10 to 4.10) and a decrease of SNB angle (WMD = −1.94 degrees, 95% CI: −2.48 to −1.40) in UCLP patients. Low to moderate heterogeneity was observed.

Limitations
They emerge due to risk of bias, exclusion of non-English papers and methodological characteristics of the included papers.

Conclusions
According to the available data, FM seems to improve the sagittal skeletal relationships in UCLP patients, increasing the SNA and ANB angles and decreasing the SNB angle. Moreover, in the vertical dimension, FM increases the SN–MP angle. Regarding dental measurements, there are controversial results. More high-quality studies need to be conducted in order to further clarify the impact of FM on UCLP patients.

Registration number
PROSPERO: CRD42019131619.
Comparison of in-hospital outcomes and readmissions for valve-in-valve transcatheter aortic valve replacement vs. reoperative surgical aortic valve replacement: a contemporary assessment of real-world outcomes
Authors: Hirji Sameer A , Percy Edward D , Zogg Cheryl K , Malarczyk Alexandra , Harloff Morgan T , Yazdchi Farhang , Kaneko Tsuyoshi 
Published: March 2020

Abstract

Aims
We sought to perform a head-to-head comparison of contemporary 30-day outcomes and readmissions between valve-in-valve transcatheter aortic valve replacement (VIV-TAVR) patients and a matched cohort of high-risk reoperative surgical aortic valve replacement (re-SAVR) patients using a large, multicentre, national database.

Methods and results
We utilized the nationally weighted 2012–16 National Readmission Database claims to identify all US adult patients with degenerated bioprosthetic aortic valves who underwent either VIV-TAVR (n = 3443) or isolated re-SAVR (n = 3372). Thirty-day outcomes were compared using multivariate analysis and propensity score matching (1:1). Unadjusted, VIV-TAVR patients had significantly lower 30-day mortality (2.7% vs. 5.0%), 30-day morbidity (66.4% vs. 79%), and rates of major bleeding (35.8% vs. 50%). On multivariable analysis, re-SAVR was a significant risk factor for both 30-day mortality [adjusted odds ratio (aOR) of VIV-SAVR (vs. re-SAVR) 0.48, 95% confidence interval (CI) 0.28–0.81] and 30-day morbidity [aOR for VIV-TAVR (vs. re-SAVR) 0.54, 95% CI 0.43–0.68]. After matching (n = 2181 matched pairs), VIV-TAVR was associated with lower odds of 30-day mortality (OR 0.41, 95% CI 0.23–0.74), 30-day morbidity (OR 0.53, 95% CI 0.43–0.72), and major bleeding (OR 0.66, 95% CI 0.51–0.85). Valve-in-valve TAVR was also associated with shorter length of stay (median savings of 2 days, 95% CI 1.3–2.7) and higher odds of routine home discharges (OR 2.11, 95% CI 1.61–2.78) compared to re-SAVR.

Conclusion
In this large, nationwide study of matched high-risk patients with degenerated bioprosthetic aortic valves, VIV-TAVR appears to confer an advantage over re-SAVR in terms of 30-day mortality, morbidity, and bleeding complications. Further studies are warranted to benchmark in low- and intermediate-risk patients and to adequately assess longer-term efficacy.
piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions
Authors: Kofler Robert 
Published: March 2020

AbstractpiRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. Moreover, larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high, and TE insertions are recessive. If piRNA clusters are too small, the load of deleterious TE insertions that accumulate during a TE invasion may drive populations extinct before an effective piRNA-based defense against the TE can be established. Our findings are solely based on three well-supported assumptions: 1) TEs multiply within genomes, 2) TEs are mostly deleterious, and 3) piRNA clusters act as transposon traps, where a single insertion in a cluster silences all TE copies in trans. Interestingly, the piRNA clusters of some species meet our observed minimum size requirements, whereas the clusters of other species do not. Species with small piRNA clusters, such as humans and mice, may experience severe fitness reductions during invasions of novel TEs, which is possibly even threatening the persistence of some populations. This work also raises the important question of how piRNA clusters evolve. We propose that the size of piRNA clusters may be at an equilibrium between evolutionary forces that act to expand and contract piRNA clusters.
Reflection on modern methods: trial emulation in the presence of immortal-time bias. Assessing the benefit of major surgery for elderly lung cancer patients using observational data
Authors: Maringe Camille , Benitez Majano Sara , Exarchakou Aimilia , Smith Matthew , Rachet Bernard , Belot Aurélien , Leyrat Clémence 
Published: March 2020

Abstract
Acquiring real-world evidence is crucial to support health policy, but observational studies are prone to serious biases. An approach was recently proposed to overcome confounding and immortal-time biases within the emulated trial framework. This tutorial provides a step-by-step description of the design and analysis of emulated trials, as well as R and Stata code, to facilitate its use in practice. The steps consist in: (i) specifying the target trial and inclusion criteria; (ii) cloning patients; (iii) defining censoring and survival times; (iv) estimating the weights to account for informative censoring introduced by design; and (v) analysing these data. These steps are illustrated with observational data to assess the benefit of surgery among 70–89-year-old patients diagnosed with early-stage lung cancer. Because of the severe unbalance of the patient characteristics between treatment arms (surgery yes/no), a naïve Kaplan-Meier survival analysis of the initial cohort severely overestimated the benefit of surgery on 1-year survival (22% difference), as did a survival analysis of the cloned dataset when informative censoring was ignored (17% difference). By contrast, the estimated weights adequately removed the covariate imbalance. The weighted analysis still showed evidence of a benefit, though smaller (11% difference), of surgery among older lung cancer patients on 1-year survival. Complementing the CERBOT tool, this tutorial explains how to proceed to conduct emulated trials using observational data in the presence of immortal-time bias. The strength of this approach is its transparency and its principles that are easily understandable by non-specialists.
HIV Modifies the Effect of Tobacco Smoking on Oral Human Papillomavirus Infection
Authors: Alli Babatunde Y , Burk Robert D , Fatahzadeh Mahnaz , Kazimiroff Julie , Grossberg Robert M , Smith Richard V , Ow Thomas J , Wiltz Mauricio , Polanco Jacqueline , Rousseau Marie-Claude , Nicolau Belinda , Schlecht Nicolas F 
Published: March 2020

Abstract

Background
People living with HIV (PLWH) are more likely to smoke and harbor oral human papillomavirus (HPV) infections, putting them at higher risk for head and neck cancer. We investigated effects of HIV and smoking on oral HPV risk.

Methods
Consecutive PLWH (n = 169) and at-risk HIV-negative individuals (n = 126) were recruited from 2 US health centers. Smoking history was collected using questionnaires. Participants provided oral rinse samples for HPV genotyping. We used multivariable logistic regression models with interaction terms for HIV to test for smoking effect on oral HPV.

Results
PLWH were more likely to harbor oral HPV than HIV-negative individuals, including α (39% vs 28%), β (73% vs 63%), and γ-types (33% vs 20%). HIV infection positively modified the association between smoking and high-risk oral HPV: odds ratios for smoking 3.46 (95% confidence interval [CI], 1.01–11.94) and 1.59 (95% CI, .32–8.73) among PLWH and HIV-negative individuals, respectively, and relative excess risk due to interaction (RERI) 3.34 (95% CI, −1.51 to 8.18). RERI for HPV 16 was 1.79 (95% CI, −2.57 to 6.16) and 2.78 for β1-HPV (95% CI, −.08 to 5.65).

Conclusion
Results show tobacco smoking as a risk factor for oral HPV among PLWH.
Combining Hepatitis B Virus RNA and Hepatitis B Core–Related Antigen: Guidance for Safely Stopping Nucleos(t)ide Analogues in Hepatitis B e Antigen–Positive Patients With Chronic Hepatitis B
Authors: Fan Rong , Peng Jie , Xie Qing , Tan Deming , Xu Min , Niu Junqi , Wang Hao , Ren Hong , Chen Xinyue , Wang Maorong , Sheng Jifang , Tang Hong , Bai Xuefan , Wu Yaobo , Zhou Bin , Sun Jian , Hou Jinlin ,   for the Chronic Hepatitis B Study Consortium, Ning Qin , Shi Guangfeng , Wan Mobin , Chen Shijun , Yu Yanyan , Ma Hong , Cheng Jun , Zhang Hongfei , Liu Huimin , Gao Zhiliang 
Published: March 2020

Abstract

Background
Safe nucleos(t)ide analogue discontinuation in chronic hepatitis B (CHB) is an unmet need. We aimed to investigate whether combining hepatitis B virus (HBV) RNA and hepatitis B core–related antigen (HBcrAg) could perform satisfactorily in predicting off-treatment outcomes.

Methods
The evaluation cohort included 127 hepatitis B e antigen (HBeAg)–positive patients from a multicenter prospective trial who stopped telbivudine-based therapy after achieving HBeAg seroconversion and HBV DNA &lt; 50 IU/mL for &gt; 48 weeks. As validation, 59 patients treated with entecavir or tenofovir before discontinuation were analyzed.

Results
At the end of treatment (EOT), HBV RNA and HBcrAg were significant independent predictors of the clinical relapse risk. In the evaluation cohort, no clinical relapse occurred among patients with negative HBV RNA and HBcrAg &lt; 4 log10 U/mL at EOT (low-risk group), whereas 46.8% patients with positive HBV RNA and HBcrAg ≥ 4 log10 U/mL (high-risk group) experienced clinical relapse during 4-year posttreatment follow-up (P &lt; .001); the corresponding incidences in the validation cohort were 0% and 69.4% (P &lt; .001), respectively. More patients in the low-risk group achieved HBsAg loss than the other patients after treatment cessation (16.1% vs 1.3%, P = .002).

Conclusions
Combining HBV RNA and HBcrAg performed satisfactorily in predicting clinical relapse and HBsAg loss after treatment cessation in HBeAg-positive patients with CHB.
The combination of hepatitis B virus RNA and hepatitis B core–related antigen performed satisfactorily in predicting clinical relapse and hepatitis B surface antigen loss after stopping nucleos(t)ide analogue treatment among noncirrhotic hepatitis B e antigen–positive patients with chronic hepatitis B and could be used to guide safe discontinuation.
Using word embeddings to improve the privacy of clinical notes
Authors: Abdalla Mohamed , Abdalla Moustafa , Rudzicz Frank , Hirst Graeme 
Published: March 2020

Abstract

Objective
In this work, we introduce a privacy technique for anonymizing clinical notes that guarantees all private health information is secured (including sensitive data, such as family history, that are not adequately covered by current techniques).

Materials and Methods
We employ a new “random replacement” paradigm (replacing each token in clinical notes with neighboring word vectors from the embedding space) to achieve 100% recall on the removal of sensitive information, unachievable with current “search-and-secure” paradigms. We demonstrate the utility of this paradigm on multiple corpora in a diverse set of classification tasks.

Results
We empirically evaluate the effect of our anonymization technique both on upstream and downstream natural language processing tasks to show that our perturbations, while increasing security (ie, achieving 100% recall on any dataset), do not greatly impact the results of end-to-end machine learning approaches.

Discussion
As long as current approaches utilize precision and recall to evaluate deidentification algorithms, there will remain a risk of overlooking sensitive information. Inspired by differential privacy, we sought to make it statistically infeasible to recreate the original data, although at the cost of readability. We hope that the work will serve as a catalyst to further research into alternative deidentification methods that can address current weaknesses.

Conclusion
Our proposed technique can secure clinical texts at a low cost and extremely high recall with a readability trade-off while remaining useful for natural language processing classification tasks. We hope that our work can be used by risk-averse data holders to release clinical texts to researchers.
Brevipalpus Species Vectoring Citrus Leprosis Virus (Cilevirus and Dichorhavirus)
Authors: Ferreira Leticia M , Nunes Maria A , Sinico Thaís E , Soares Alex J , Novelli Valdenice M 
Published: March 2020

Abstract
Citrus leprosis (CL) is one of the most devastating viral diseases of orchards, and industries correspondingly invest highly in the management and control of the virus vector. In Brazil, the disease is caused most predominantly by the citrus leprosis virus C (CiLV-C, Kitaviridae: Cilevirus), and also by citrus leprosis virus N (CiLV-N, Rhabdoviridae: Dichorhavirus). Both viruses are transmitted by false spider mites and at least three different species, Brevipalpus yothersi Baker, B. papayensis Baker, and B. phoenicis (Geijskes) sensu stricto, have been reported in citrus orchards. The main goal of this study was to evaluate the capacity of three Brevipalpus species to transmit citrus leprosis virus (cytoplasmic and nuclear types). The capacity of false spider mites to acquire the virus was accomplished using RT–PCR and the ability to inoculation the virus to host plants (common bean and sweet orange) was assessed via viral transmission assays. Common beans infested with B. yothersi and B. papayensis showed symptoms of CiLV-C in 87.5 and 17% of the plants assessed, respectively. In sweet orange, B. yothersi was exclusively able to inoculate CiLV-C, and around 83% of samples were symptomatic. Host plants infected with CiLV-N showed symptoms only when infested with B. phoenicis sensu stricto (s.s.). All the Brevipalpus species (Acari: Tenuipalpidae) were able to acquire both viruses (CiLV-C and CiLV-N), but not infect plants. These results suggest the existence of virus-vector specificity in the leprosis pathosystem, and this information will be critical for enhancing our further understanding of epidemiological features and disease management.