bluuebunny/crossref_metadata_2025_split huggingface dataset:
An effective method to resolve ambiguous bisulfite-treated reads
Authors: Liu Mengya , Xu Yun 
Published: May 2021

Abstract
Background
The combination of the bisulfite treatment and the next-generation sequencing is an important method for methylation analysis, and aligning the bisulfite-treated reads (BS-reads) is the critical step for the downstream applications. As bisulfite treatment reduces the complexity of the sequences, a large portion of BS-reads might be aligned to multiple locations of the reference genome ambiguously, called multireads. These multireads cannot be employed in the downstream applications since they are likely to introduce artifacts. To identify the best mapping location of each multiread, existing Bayesian-based methods calculate the probability of the read at each position by considering how does it overlap with unique mapped reads. However, $$\sim 25$$

∼
25

% of multireads are not overlapped with any unique reads, which are unresolvable for existing method.

Results
Here we propose a novel method (EM-MUL) that not only rescues multireads overlapped with unique reads, but also uses the overall coverage and accurate base-level alignment to resolve multireads that cannot be handled by current methods. We benchmark our method on both simulated datasets and real datasets. Experimental results show that it is able to align more than 80% of multireads to the best mapping position with very high accuracy.

Conclusions
EM-MUL is an effective method designed to accurately determine the best mapping position of multireads in BS-reads. For the downstream applications, it is useful to improve the methylation resolution on the repetitive regions of genome. EM-MUL is free available at https://github.com/lmylynn/EM-MUL.
Knowledge, attitudes and practices regarding tuberculosis amongst healthcare workers in Moyen-Ogooué Province, Gabon
Authors: Vigenschow Anja , Edoa Jean Ronald , Adegbite Bayode Romeo , Agbo Pacome Achimi , Adegnika Ayola A. , Alabi Abraham , Massinga-Loembe Marguerite , Grobusch Martin P. 
Published: May 2021

AbstractBackgroundIn countries with a high tuberculosis incidence such as Gabon, healthcare workers are at enhanced risk to become infected with tuberculosis due to their occupational exposure. In addition, transmission can occur between patients and visitors, if a tuberculosis infection is not suspected in time. Knowledge about tuberculosis and correct infection control measures are therefore highly relevant in healthcare settings.MethodsWe conducted an interviewer-administered knowledge, attitude and practice survey amongst healthcare workers in 20 healthcare facilities at all levels in the Moyen-Ogooué province, Gabon. Correctly answered knowledge questions were scored and then categorised into four knowledge levels. Additionally, factors associated with high knowledge levels were identified. Fisher’s Exact test was used to identify factors associated with high knowledge levels.ResultsA total of 103 questionnaires were completed by various healthcare personnel. The most-frequently scored category was ‘intermediate knowledge’, which was scored by 40.8% (42/103), followed by ‘good knowledge’ with 28.2% (29/103) and ‘poor knowledge’ with 21.4% (22/103) of participating healthcare workers, respectively. ‘Excellent knowledge’ was achieved by 9.7% (10/103) of the interviewees. Apart from the profession, education level, type of employing healthcare facility, as well as former training on tuberculosis were significantly associated with high knowledge scores.Attitudes were generally positive towards tuberculosis infection control efforts. Of note, healthcare workers reported that infection control measures were not consistently practiced; 72.8% (75/103) of the participants were scared of becoming infected with tuberculosis, and 98.1% saw a need for improvement of local tuberculosis control.ConclusionsThe survey results lead to the assumption that healthcare workers in the Moyen-Ogooué province are at high risk to become infected with tuberculosis. There is an urgent need for improvement of tuberculosis infection control training for local healthcare personnel, particularly for less trained staff such as assistant nurses. Furthermore, the lack of adequate infection control measures reported by staff could possibly be correlated with a lack of adequate facility structures and protective equipment and requires further investigation.
Real-life cost-effectiveness of benralizumab in patients with severe asthma
Authors: Padilla-Galo A. , García-Ruiz A. J. , Levy Abitbol R. Ch. , Olveira C. , Rivas-Ruiz F. , García-Agua Soler N. , Pérez Morales M. , Valencia Azcona B. , Tortajada-Goitia B. , Moya-Carmona I. , Levy-Naon A. 
Published: May 2021

Abstract
Background
Availability of clinically effective and cost-effective treatments for severe asthma would be beneficial to patients and national healthcare systems. The aim of this study was to evaluate clinical outcomes and healthcare expenditure after incorporating benralizumab into the standard treatment of refractory eosinophilic asthma.

Methods
This was a cross-sectional multicentre study of consecutive patients with refractory eosinophilic asthma who received treatment with benralizumab during at least 12 months. Patient follow-up was performed in specialised severe asthma units. The main effectiveness parameters measured were: the avoidance of one asthma exacerbation, a 3-point increase in the asthma control test (ACT) score, and the difference in utility scores (health-related quality of life) between a 1-year baseline treatment and 1-year benralizumab treatment. The health economic evaluation included direct costs and incremental cost-effectiveness ratios (ICERs).

Results
After 1 year of treatment with benralizumab, patients with refractory eosinophilic asthma showed an improvement in all the effectiveness parameters analysed: improvement of asthma control and lung function, and decrease in the number of exacerbations, oral corticosteroid (both as corticosteroid courses and maintenance therapy), and inhaled corticosteroid use. The total annual cost per patient for the baseline and benralizumab treatment periods were €11,544 and €14,043, respectively, reflecting an increase in costs due to the price of the biological agent but a decrease in costs for the remaining parameters. The ICER was €602 per avoided exacerbation and €983.86 for every 3-point increase in the ACT score.

Conclusions
All the pharmacoeconomic parameters analysed show that treatment with benralizumab is a cost-effective option as an add-on therapy in patients with refractory eosinophilic asthma.
Evaluating endophenotypes for bipolar disorder
Authors: Guglielmo Riccardo , Miskowiak Kamilla Woznica , Hasler Gregor 
Published: May 2021

Abstract
Background
Phenotypic heterogeneity is a major impediment to the elucidation of the neurobiology and genetics of bipolar disorder. Endophenotype could help in reducing heterogeneity by defining biological traits that are more direct expressions of gene effects. The aim of this review is to examine the recent literature on clinical, epidemiological, neurobiological, and genetic findings and to select and evaluate candidate endophenotypes for bipolar disorder. Evaluating putative endophenotype could be helpful in better understanding the neurobiology of bipolar disorder by improving the definition of bipolar-related phenotypes in genetic studies. In this manner, research on endophenotypes could be useful to improve psychopathological diagnostics in the long-run by dissecting psychiatric macro phenotypes into biologically valid components.

Main body
The associations among the psychopathological and biological endophenotypes are discussed with respect to specificity, temporal stability, heritability, familiarity, and clinical and biological plausibility. Numerous findings regarding brain function, brain structure, neuropsychology and altered neurochemical pathways in patients with bipolar disorder and their relatives deserve further investigation. Overall, major findings suggest a developmental origin of this disorder as all the candidate endophenotypes that we have been able to select are present both in the early stages of the disorder as well as in subjects at risk.

Conclusions
Among the stronger candidate endophenotypes, we suggest circadian rhythm instability, dysmodulation of emotion and reward, altered neuroimmune state, attention and executive dysfunctions, anterior cingulate cortex thickness and early white matter abnormalities. In particular, early white matter abnormalities could be the result of a vulnerable brain on which new stressors are added in young adulthood which favours the onset of the disorder. Possible pathways that lead to a vulnerable brain are discussed starting from the data about molecular and imaging endophenotypes of bipolar disorder.
An approximate point-based alternative for the estimation of variance under big BAF sampling
Authors: Lynch Thomas B. , Gove Jeffrey H. , Gregoire Timothy G. , Ducey Mark J. 
Published: May 2021

AbstractBackgroundA new variance estimator is derived and tested for big BAF (Basal Area Factor) sampling which is a forest inventory system that utilizes Bitterlich sampling (point sampling) with two BAF sizes, a small BAF for tree counts and a larger BAF on which tree measurements are made usually including DBHs and heights needed for volume estimation.MethodsThe new estimator is derived using the Delta method from an existing formulation of the big BAF estimator as consisting of three sample means. The new formula is compared to existing big BAF estimators including a popular estimator based on Bruce’s formula.ResultsSeveral computer simulation studies were conducted comparing the new variance estimator to all known variance estimators for big BAF currently in the forest inventory literature. In simulations the new estimator performed well and comparably to existing variance formulas.ConclusionsA possible advantage of the new estimator is that it does not require the assumption of negligible correlation between basal area counts on the small BAF factor and volume-basal area ratios based on the large BAF factor selection trees, an assumption required by all previous big BAF variance estimation formulas. Although this correlation was negligible on the simulation stands used in this study, it is conceivable that the correlation could be significant in some forest types, such as those in which the DBH-height relationship can be affected substantially by density perhaps through competition. We derived a formula that can be used to estimate the covariance between estimates of mean basal area and the ratio of estimates of mean volume and mean basal area. We also mathematically derived expressions for bias in the big BAF estimator that can be used to show the bias approaches zero in large samples on the order of$\frac {1}{n}$1nwherenis the number of sample points.
Socio-demographics and asthma prevalence, management, and outcomes among children 1–11 years of age in California
Authors: Banta Jim E. , Ramadan Majed , Alhusseini Noara , Aloraini Khaled , Modeste Naomi 
Published: May 2021

AbstractBackgroundAsthma disproportionately affects minority and low-income children. We examined asthma prevalence, management and outcomes, focusing on race/ethnicity and acculturation of parents (particularly English language proficiency).MethodsThis cross-sectional, correlational analysis used a de-identified population-based survey, the California Health Interview Survey, for years 2001–2015. Survey-weighted analysis with SAS 9.4 was used to determine asthma prevalence among children 1 to 11 years of age. Descriptive analysis was conducted, adjusting for survey design and combination of multiple years of data. The Pearson test, using design-based F values was used to determine statistically significant differences between those having/not having a doctor diagnosis of asthma. Multivariable logistic regression, with jackknife approach to obtain confidence intervals, was used to examine associations of child and parental characteristics with asthma prevalence, management, and outcomes.ResultsThe 61,625 completed surveys represented an estimated annual population of 5.7 million children, of which 12.9 % had asthma. There were significant (p < 0.001) differences by age, gender, race, and language proficiency, with higher asthma prevalence for children 6 to 11 years of age (15.5 %), males (15.3 %), African Americans (19.5 %), and parents speaking English very well (14.1 %). Compared to children whose parents spoke English very well, those whose parents spoke English not well or not at all were less likely to achieve optimal asthma management, i.e. to have received a management plan from doctor (OR 0.30; 95 % Confidence Interval 0.20–0.46)), to be currently taking medication to control asthma (OR 0.52; 95 % CI 0.36–0.74)), or to be not confident in ability to control asthma (OR 3.10; 95 % CI 1.49–6.42). Children whose parents spoke English fairly well rather than very well had worse outcomes, i.e. were more likely to have an emergency room visit in past 12 months (OR 1.92; 95 % CI 1.03–3.61) and were more likely to miss school due to asthma in past 12 months (OR 0.71; 1.01–2.94).ConclusionsSocio-demographics had a limited role in explaining differences across a handful of asthma management and outcome measures in California. Parental English language proficiency had the most consistent influence, underscoring the need for culturally and linguistically competent care.
High-speed Stokes vector receiver enabled by a spin-dependent optical grating
Authors: Xie Youpeng , Lei Ting , Wang Dawei , Ren Jianxin , Dai Yanmeng , Chen Yanjun , Du Luping , Liu Bo , Li Zhaohui , Yuan Xiaocong 
Published: May 2021

Stokes vector direct detection is a promising, cost-effective technology for short-distance communication applications. Here, we design and fabricate a spin-dependent liquid crystal grating to detect light polarization states. By separating the circular and linear components of incident light, the polarization states can be resolved with accuracy of up to 0.25°. We achieved Stokes vector direct detection of quadrature phase-shift keying (QPSK), 8PSK, and 16-ary quadrature amplitude modulation signals with 32, 16, and 16 GBd rates, respectively. We integrated the system, including the grating, photodetectors, and optical elements, on a miniaturized printed circuit board and demonstrated high-speed optical communications with 16 GBd rate QPSK signals.
“I want to perform and succeed more than those who are HIV-seronegative” Lived experiences of youth who acquired HIV perinetally and attend Zewditu Memorial Hospital ART clinic, Addis Ababa, Ethiopia
Authors: Solomon Nahom , Molla Mitike , Ketema Bezawit 
Published: May 2021

Background
In Ethiopian Human Immunodeficiency Virus (HIV) prevention program one of the focusing areas is prevention of mother-to-child transmission and decreasing morbidity and mortality among those who already acquired it. However, the needs and the sexual behavior of children who acquired HIV perinatally was not given due attention. Therefore, we conducted this study with the aim of exploring the lived experiences of youth who acquired HIV perinatally to contribute to HIV prevention and control program.

Methods
We conducted a qualitative study using a phenomenological approach from March to May 2018 among 16 purposively selected youth who were infected with HIV vertically and receive ART services at Zewditu Memorial Hospital, Addis Ababa, Ethiopia. They were recruited based on their willingness after obtaining written informed consent and assent. Data were audio taped, transcribed verbatim in Amharic and later translated to English, and coded using Open Code version 4.02 software. Findings were summarized under four themes by applying interpretative phenomenological analysis.

Findings
Seven males and nine females, aged 16 to 22 years have participated in the study. These youth reported as they had support from families and ART clinics, while pill-load, and fear of stigma are some of challenges they have faced, especially majorities don’t want to disclose their status because of fear of stigma and discrimination. Half of them have ever had sexual relations usually with a seronegative partner and most of these had their first sex in their17-18 years of age. Unsafe sex was common among them where four girls reported to have had unprotected sex with their seropositive or seronegative sexual partners. Most wish to have purposeful life and love mate of the same serostatus but also fear they may remain alone.

Conclusion
Youth who had acquired HIV from parents are challenged due to their serostatus and were not sure what type of life they may have in the future. They were also not comfortable in disclosing their serostatus and also engaged in unsafe sexual relation. This calls for an urgent intervention among HIV infected youth and their families; health care providers, and young people in general to halt HIV transmission. Special attention should be given on sexual behavior of all young people (10–24) and in disclosure of HIV status to children and life skills education to cop-up with stigma and discrimination.
A nitric oxide-releasing prodrug promotes apoptosis in human renal carcinoma cells: Involvement of reactive oxygen species
Authors: Xie Jindong , Chen Lieqian , Huang Dongqiang , Yue Weiwei , Chen Jingyu , Liu Chunxiao 
Published: May 2021

Abstract

Background
JS-K is a nitric oxide (NO)-releasing prodrug of the O2-arylated diazeniumdiolate group that shows pronounced cytotoxicity and antitumor properties in numerous cancer models, including in vitro as well as in vivo. Reactive oxygen species (ROS) induce carcinogenesis by altering the redox status, causing increment in vulnerability to oxidative stress.

Material and methods
To determine the effect of JS-K, a glutathione S-transferase (GST)-activated NO-donor prodrug, on the induction of ROS accumulation, proliferation, and apoptosis in human renal carcinoma cells, we measured the changes of cell proliferation, apoptosis, ROS growth, and initiation of the mitochondrial signaling pathway before and after JS-K treatment.

Results

In vitro, dose- and time-dependent development of renal carcinoma cells were controlled for JS-K, and JS-K also triggered ROS aggregation and cell apoptosis. Treatment with JS-K induces the levels of pro-apoptotic proteins (Bak and Bax) and decrease the number of anti-apoptotic protein (Bcl-2). In fact, JS-K-induced apoptosis was reversed by the antioxidant N-acetylcysteine, and oxidized glutathione, a pro-oxidant, improved JS-K-induced apoptosis. Finally, we demonstrated that in renal carcinoma cells, JS-K improved the chemosensitivity of doxorubicin.

Conclusion
Our data indicate that JS-K-released NO induce apoptosis of renal carcinoma cells by increasing ROS levels.
Influence of interbedded rock association and fracture characteristics on gas accumulation in the lower Silurian Shiniulan formation, Northern Guizhou Province
Authors: Guo Ruibo , Zhang Jinchuan , Zhao Panwang , Liu Ziyi 
Published: May 2021

Abstract
The northern Guizhou area, located near the southwestern margin of the Yangtze Block, is a promising area for shale gas exploration and development. The Lower Silurian Shiniulan Formation as a new discovery stratum of natural gas marks an exciting breakthrough in natural gas exploration in northern Guizhou area. Based on several field investigations and samples analyses, the lithology and fracture characteristics were systematically analyzed in the lower Shiniulan Formation, and the reservoir specificity and its influence on natural gas accumulation were determined. The characteristics of the relatively fractures and lithology assemblages were identified as key factors controlling the natural gas accumulation. The lower Shiniulan Formation is deposited as calcareous shale and marlstone with frequent centimeter-scale interlayers. This is reflective of a shallow sea shelf strata with decreasing sedimentary rhythm and gradual weakening of sedimentary changes and developed calcareous shale and marlstone with frequent centimeter scale interlayer changes. The gas reservoir is dominated by calcareous mudstone, controlled by the interbedded rock association (calcareous mudstone and limestone), characterized by the raw-storage and the accumulation-reservoir interbedded system. The reservoir is located in the central part of the syncline and is characterized by strong sealing of the stratum, large proportion of free gas, and high abnormal pressure. The Lower Shiniulan Formation is formed between the shale layer with horizontal fractures and dense limestone with underdeveloped fractures. Among them, the shale section generally develops diagenetic shrinkage fractures, which provide good storage space for natural gas and act as the main body of natural gas. The pore sizes in limestone (2.8 nm) are significantly smaller than those in mudstone (7.5 nm), which results in a good capping and preservation of shale gas. This paper reports on results that are of significance for supplementing the theory of unconventional natural gas accumulation and guiding shale gas exploration in similar areas.
Multi-input single-output (MISO) all optical logic (ALG) AND/NOR gate using FWM in dispersion compensation fibers in Mach-Zehnder configuration (DCF-MZI)
Authors: Sharma Deepti , Singh Charanjit , Kaur Rajbir 
Published: May 2021

Abstract
Ultrafast all optical computing is getting attention for future generation services and all optical logic gates are basic building block for the photonic circuits in processing units. In this work, a multi-input single-output all optical AND/NOR gates are proposed using dispersion compensation fibers in Mach-Zehnder configuration (DCFs-MZI). Four wave mixing effect emerges in DCF and due to Kerr’s effect, aforementioned gates are realized at 10.2 Gbps. A low power logic gates with >23 dB extinction ratio are achieved and performance analysis is performed in terms of Q factor.
Synchronization of Caputo fractional neural networks with bounded time variable delays
Authors: Almeida Ricardo , Hristova Snezhana , Tersian Stepan 
Published: May 2021

Abstract
One of the main problems connected with neural networks is synchronization. We examine a model of a neural network with time-varying delay and also the case when the connection weights (the influential strength of the

j

j

th neuron to the

i

i

th neuron) are variable in time and unbounded. The rate of change of the dynamics of all neurons is described by the Caputo fractional derivative. We apply Lyapunov functions and the Razumikhin method to obtain some sufficient conditions to ensure synchronization in the model. These sufficient conditions are explicitly expressed in terms of the parameters of the system, and hence, they are easily verifiable. We illustrate our theory with a particular nonlinear neural network.