bluuebunny/crossref_metadata_2025_split huggingface dataset:
GraphAligner: rapid and versatile sequence-to-graph alignment
Authors: Rautiainen Mikko , Marschall Tobias 
Published: September 2020

AbstractGenome graphscan represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph. Yet, so far, this step is often prohibitively slow. We present GraphAligner, a tool for aligning long reads to genome graphs. Compared to the state-of-the-art tools, GraphAligner is 13x faster and uses 3x less memory. When employing GraphAligner for error correction, we find it to be more than twice as accurate and over 12x faster than extant tools.Availability: Package manager:https://anaconda.org/bioconda/graphalignerand source code:https://github.com/maickrau/GraphAligner
Effects of butaphosphan and cyanocobalamin mixture on immunity and stress in olive flounder, Paralichthys olivaceus
Authors: Kim Seung Min , Kim You Jeong , Lee Da Won , Jun Lyu Jin , Jeong Joon Bum , Park Hyun Kyung , Jeong You Young , Lee Sung Ho , Kwon Mun-Gyeong , Lee Soon Jeong 
Published: September 2020

Abstract

Background
The study evaluated the effects of a butaphosphan and cyanocobalamin mixture on the immune system and stress in olive flounders, Paralichthys olivaceus.

Methods
The mixture was intramuscularly injected into olive flounders at the current recommended dose. Furthermore, to determine the toxicity of overdose, a histological examination was performed after injection of 1-, 2-, and 4-fold higher than the recommended dose.

Results
Immunity parameters were altered during the first 2 weeks after a single intramuscular injection of the mixture in olive flounders (average weight 20.5 ± 1.1 g). The levels of all tested items, except glutathione and anti-protease, were higher in the treated group than in the control group in the first week; the levels of all tested items were even higher in the second week in the treated group than in the control group. The level of nitro-blue tetrazolium, myeloperoxidase, and superoxide dismutase between the two groups differed significantly. Changes in the stress response to different seawater temperatures (increase or decrease in seawater temperature by 3–5 °C using 50 L heated or cooled seawater tanks) were studied by determining the changes in cortisol and glucose levels on days 1 and 7. Both cortisol and glucose levels were significantly lower in the treated group than in the control group. Histological analysis did not reveal any abnormalities after intramuscular injection of the mixture at doses that were 1-, 2-, and 4-fold higher than the recommended dose.

Conclusions
Intramuscular injection of a butaphosphan and cyanocobalamin mixture is safe and effective in reducing stress and improving immunity in olive flounders.
Effect of diode laser potentiality on proliferation of dental pulp stem cells (in vitro study)
Authors: Abo El-Dahab Mohamed M. , Gheith Mostafa , Soliman Nadia Lashin , Aly Riham Mohamed 
Published: September 2020

Abstract
Background
The field of laser-based photochemical reactions receives a great promising for additional applications especially for targeting cells, pathogens, or molecules. Limited studies have investigated the impact of light-emitting diode on stem cell behavior. Thus, the aim of the present study was to assess the effect of diode laser irradiations on the proliferation of stem cells isolated from the human dental pulp. Isolation procedures were according to previously developed protocols for dental pulp stem cells (DPSCs). Low-level laser therapy irradiation (LLLT) was applied in two doses (0.5 J/cm2 and 1 J/cm2 for 20 s) into 96-well plates by the diode laser device (970 nm) through the fiber optic (SiroLaser fibers 320) at a distance from the opening of the wells to be accurate for equal distribution of the laser irradiation. To assess the proliferation capacity of the isolated stem cells, MTT assay was performed 24 h, 48 h, and 72 h.

Results
There was no significant difference among the different groups (gp 1 control, gp II dose 0.5 J/cm2, gp III dose 1 J/cm2) on day 1. While on day 2, the optical density of DPSCs subjected to dose 1 was found to be significantly higher than that of those subjected to dose 2. This was also demonstrated on day 3. It was also demonstrated that the proliferation of DPSCs subjected to dose 1 increased compared to that of DPSCs subjected to dose 2 from day 1 to day 2. There was a significant decrease in the cell number in both groups by 72 h.

Conclusion
In conclusion, the use of LLLT as a stimulatory factor for enhancing and proliferation of the stem cells is very promising.
A comparison of two modalities of stereotactic body radiation therapy for peripheral early-stage non-small cell lung cancer: results of a prospective French study
Authors: Claude Line , Morelle Magali , Mahé Marc-André , Pasquier David , Boisselier Pierre , Bondiau Pierre Yves , Touboul Emmanuel , Peignaux-Casasnovas Karine , Martel-Lafay Isabelle , Gassa Frederic , Perrier Lionel , Dussart Sophie , Beckendorf Veronique 
Published: September 2020

Objectives: This prospective, observational, non-randomized multicentric study was conducted to compare efficiency and toxicity using different modalities of stereotactic body radiation therapy (SBRT) in early-stage peripheral non-small cell lung cancer (NSCLC). Methods: From 9 April to 11 December, 106 patients were treated according to the local equipment availability for peripheral NSCLC with SBRT: 68 by linear accelerator equipped for SBRT and 38 by Cyberknife®. Multivariate analysis and propensity score analysis using Inverse Probability Treatment Weighting (IPTW) were undertaken in an effort to adjust for potential bias due to non-randomization. Results: 2-year local control rates were 97.0% (95% CI: [90.6%; 99.4%]) with SBRT by Linac vs 100% (95% CI: ([100%; 100%]) with Cyberknife® (p = 0.2839). 2-year PFS and 2-year OS rates were 52.7% (95% CI [39.9%;64.0%]) versus 54.1% (95% CI [36.8; 68.6%]) (p = 0.8582) and 65.1% (95% CI: [51.9%; 75.5%] versus 83.9% (95% CI: [67.5%; 92.4%] (p = 0.0831) using Linac and Cyberknife® respectively. Multivariate regression analysis indicates no significant effect of SBRT treatment type on PFS or OS. Local relapse could not be modeled due to the small number of events (n = 2). Acute and late toxicity rates were not significantly different. After IPTW adjustment, results were unchanged. Conclusions: No difference in efficiency or toxicity was shown after SBRT of peripheral NSCLC treatment using Linac or Cyberknife®. Advances in knowledge: This is the first large prospective non-randomized study focusing on peripheral localized NSCLC comparing SBRT using an appropriately equipped linac with Cyberknife®. No significant difference in efficiency or toxicity was shown in this situation.
Perceptions of Surrogacy Within the Socio-Cultural Context of Nigeria
Authors: Alabi Oluwatobi Joseph 
Published: September 2020

Background: Surrogacy might be a reproductive process that brings joy and fulfilment to many, but it also brings with it numerous ethical and legal concerns; it raises questions about the fundamental human rights, welfare and wellbeing of women and infants, especially within a context where it is barely regulated. This article examines the perception of surrogacy within the socio-cultural context of Nigeria. It brings to the fore various socio-cultural concerns that question the influence of surrogacy as a reproductive process on womanhood, motherhood and parenthood. It discusses, by analysing the narratives of the participants, how the surrogacy process is a dereliction of the sacredness and cultural sanctity of the family system, most especially in an African context. Methods: Fifteen (15) stakeholders (traditional birth attendants, medical gynaecologists and legal professionals within the social, medico-legal framework of reproductive health) in Nigeria were engaged in in-depth interviews to unravel the challenges which surrogacy might be facing or encountering as an ART in Nigeria. Results: There are various social, traditional, cultural, and religious beliefs that police the reproductive sphere of Nigeria, which have grave implications on fertility treatment. These socio-cultural and religious factors do not provide a fertile ground for surrogacy to thrive in Nigeria. Hence, it is important that the socio-cultural framing of reproducing in Nigeria become receptive to modern medical reproductive alternatives and innovations. Conclusions: For surrogacy to permeate the reproductive terrain of the country there is a need to jettison several socio-cultural and religious sentimental beliefs policing reproduction in Nigeria.
Interventions to improve birth outcomes of pregnant women living in low- and middle-income countries: a systematic review and network meta-analysis
Authors: Park Jay J. H. , Harari Ofir , Siden Ellie , Zoratti Michael , Dron Louis , Zannat Noor-E , Lester Richard T. , Thorlund Kristian , Mills Edward J. 
Published: September 2020

Background: Improving the health of pregnant women is important to prevent adverse birth outcomes, such as preterm birth and low birthweight. We evaluated the comparative effectiveness of interventions under the domains of micronutrient, balanced energy protein, deworming, maternal education, and water sanitation and hygiene (WASH) for their effects on these adverse birth outcomes. Methods: For this network meta-analysis, we searched for randomized clinical trials (RCTs) of interventions provided to pregnant women in low- and middle-income countries (LMICs). We searched for reports published until September 17, 2019 and hand-searched bibliographies of existing reviews. We extracted data from eligible studies for study characteristics, interventions, participants’ characteristics at baseline, and birth outcomes. We compared effects on preterm birth (<37 gestational week), low birthweight (LBW; <2500 g), and birthweight (continuous) using studies conducted in LMICs. Results: Our network meta-analyses were based on 101 RCTs (132 papers) pertaining to 206,531 participants. Several micronutrients and balanced energy food supplement interventions demonstrated effectiveness over standard-of-care. For instance, versus standard-of-care, micronutrient supplements for pregnant women, such as iron and calcium, decreased risks of preterm birth (iron: RR=0.70, 95% credible interval [Crl] 0.47, 1.01; calcium: RR=0.76, 95%Crl 0.56, 0.99). Daily intake of 1500kcal of local food decreased the risks of preterm birth (RR=0.36, 95%Crl 0.16, 0.77) and LBW (RR=0.17, 95%Crl 0.09, 0.29), respectively when compared to standard-of-care. Educational and deworming interventions did not show improvements in birth outcomes, and no WASH intervention trials reported on these adverse birth outcomes. Conclusion: We found several pregnancy interventions that improve birth outcomes. However, most clinical trials have only evaluated interventions under a single domain (e.g. micronutrients) even though the causes of adverse birth outcomes are multi-faceted. There is a need to combine interventions that of different domains as packages and test for their effectiveness. Registration: PROSPERO CRD42018110446; registered on 17 October 2018.
Interventions to improve linear growth during complementary feeding period for children aged 6-24 months living in low- and middle-income countries: a systematic review and network meta-analysis
Authors: Park Jay J. H. , Harari Ofir , Siden Ellie , Dron Louis , Zannat Noor-E , Singer Joel , Lester Richard T. , Thorlund Kristian , Mills Edward J. 
Published: September 2020

Background:Optimizing linear growth in children during complementary feeding period (CFP) (6-24 months) is critical for their development. Several interventions, such as micronutrient and food supplements, deworming, maternal education, and water, sanitation and hygiene (WASH), could potentially be provided to prevent stunting, but their comparative effectiveness are currently unclear. In this study, we evaluated comparative effectiveness of interventions under these domains on child linear growth outcomes of height-for-age z-score (HAZ) and stunting (HAZ <-2SD)Methods:For this study, we searched for low- and middle-income country (LMIC)-based randomized clinical trials (RCTs) of aforementioned interventions provided to children during CFP. We searched for reports published until September 17, 2019 and hand-searched bibliographies of existing reviews. We performed random-effects network meta-analysis (NMA) for HAZ and stunting.Results:The evidence base for our NMA was based on 79 RCTs (96 papers) involving 81,786 children. Among the micronutrients, compared to standard-of-care, iron + folic acid (IFA) (mean difference =0.08; 95% credible interval [CrI]: 0.01, 0.15) and multiple micronutrients (MMN) (mean difference =0.06; 95%CrI: 0.01, 0.11) showed improvements for HAZ; MMN also reduced the risks for stunting (RR=0.86; 95%Crl: 0.73, 0.98), whereas IFA did not (RR=0.92; 95%Crl: 0.64, 1.23). For food supplements, flour in the caloric range of 270-340 kcal (RR=0.73; 95%Crl: 0.51, 1.00) and fortified lipid-based nutrient supplements (LNS) containing 220-285 kcal (RR=0.80; 95%Crl: 0.66, 0.97) decreased the risk of stunting compared to standard-of-care, but these interventions and other food supplements did not show improvements for HAZ. Deworming, maternal education, and WASH interventions did not show improvements for HAZ nor stunting.Conclusion:While we found micronutrient and food supplements to be effective for HAZ and/or stunting, the evidence base for other domains in this life stage was limited, highlighting the need for more investigation.Registration:PROSPEROCRD42018110449; registered on 17 October 2018.
Applying the Fogg Behavior Model to improve contraceptive social marketing during the COVID-19 lockdown in Nigeria: a case study
Authors: Meekers Dominique , Onuoha Chidinma , Olutola Olaniyi 
Published: September 2020

The coronavirus pandemic may have harmful effects on use of family planning services. Lockdown regulations make it more difficult for people to visit health providers to obtain information about family planning, to discuss side-effects or problems they are experiencing with their current method, and go out to obtain new family planning supplies (e.g., to renew their contraceptive injection). The inability to earn income during the lockdown may also make family planning products and services unaffordable. As a result, efforts to curb the pandemic may cause unintended interruptions in contraceptive use and may prevent non-users from adopting a contraceptive method. Given these rapidly changing circumstances, it is important that family planning implementers make program adjustments without delay. When a timely programmatic response is of the essence, program implementers need simple behavior change models that can be used to inform programmatic decisions. This paper presents a case study of how DKT/Nigeria applied a behavior change model from persuasive design - the Fogg Behavior Model – to make timely adjustments to their contraceptive social marketing program during the course of the COVID-19 lockdown. Other public health programs, including programs that target health areas other than family planning, may be able to use similar approaches to guide the design of timely and responsive program adjustments.
Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project
Authors: Achtman Mark , Zhou Zhemin , Alikhan Nabil-Fareed , Tyne William , Parkhill Julian , Cormican Martin , Chiou Chien-Shun , Torpdahl Mia , Litrup Eva , Prendergast Deirdre M. , Moore John E. , Strain Sam , Kornschober Christian , Meinersmann Richard , Uesbeck Alexandra , Weill François-Xavier , Coffey Aidan , Andrews-Polymenis Helene , Curtiss rd Roy , Fanning Séamus 
Published: September 2020

Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.
Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study
Authors: Eyre Max T. , Burns Rachel , Kirkby Victoria , Smith Catherine , Denaxas Spiros , Nguyen Vincent , Hayward Andrew , Shallcross Laura , Fragaszy Ellen , Aldridge Robert W. 
Published: September 2020

Background: Diagnostic testing forms a major part of the UK’s response to the current coronavirus disease 2019 (COVID-19) pandemic with tests offered to anyone with a continuous cough, high temperature or anosmia. Testing capacity must be sufficient during the winter respiratory season when levels of cough and fever are high due to non-COVID-19 causes. This study aims to make predictions about the contribution of baseline cough or fever to future testing demand in the UK. Methods: In this analysis of the Bug Watch prospective community cohort study, we estimated the incidence of cough or fever in England in 2018-2019. We then estimated the COVID-19 diagnostic testing rates required in the UK for baseline cough or fever cases for the period July 2020-June 2021. This was explored for different rates of the population requesting tests and four COVID-19 second wave scenarios. Estimates were then compared to current national capacity. Results: The baseline incidence of cough or fever in the UK is expected to rise rapidly from 154,554 (95%CI 103,083 - 231,725) cases per day in August 2020 to 250,708 (95%CI 181,095 - 347,080) in September, peaking at 444,660 (95%CI 353,084 - 559,988) in December. If 80% of baseline cough or fever cases request tests, average daily UK testing demand would exceed current capacity for five consecutive months (October 2020 to February 2021), with a peak demand of 147,240 (95%CI 73,978 - 239,502) tests per day above capacity in December 2020. Conclusions: Our results show that current national COVID-19 testing capacity is likely to be exceeded by demand due to baseline cough and fever alone. This study highlights that the UK’s response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is immediately scaled up to meet this high predicted demand.
Symptomatic hepatothorax presenting 25 years after penetrating thoracoabdominal injury
Authors: Variawa S , Marais R , Buitendag JJP , Edge J , Steyn E 
Published: September 2020

Hepatic herniation through the diaphragm is a rare finding. It generally occurs due to a congenital diaphragmatic abnormality or blunt trauma resulting in a diaphragmatic defect. Making the diagnosis is difficult, as there are few definitive clinical signs and chest radiograph (CXR) findings may be non-specific. To our knowledge, only a single case report exists of penetrating right diaphragm injury leading to hepatic herniation. A 42-year-old man presented to the emergency department of a regional hospital with hyperglycaemia and exertional dyspnoea. He was diagnosed with diabetes mellitus type 2. He gave a history of smoking for 15 pack-years, was negative for retroviral disease and had no history of pulmonary tuberculosis. He had no significant surgical history but reported being stabbed with a knife in 1995. The point of entry was below the level of the nipple in the right anterior axillary line. At the time, he was treated with an intercostal drain and discharged home. CXR showed a right-sided chest mass. We considered a differential diagnosis of pulmonary consolidation, diaphragm eventration or hepatothorax. Computerized tomography of the chest and abdomen demonstrated apparent intrathoracic extension of the right liver lobe and partial attenuation of the superior vena cava and right atrium due to a mass effect. The upper border of the liver abutted the aortic arch. Surgical treatment options were discussed. The patient declined surgery and will be followed up as an outpatient.
Veil and Hijab: Twitter Sentiment Analysis Perspective
Authors: Lestari Lusiana , R Wahyudi M Didik , Kiftiyani Usfita 
Published: September 2020

Controversies about veil and hijab are often occur in society. Especially in today’s digital era, public opinion expressed through social media can greatly influence the others opinions, regardless of whether it is positive or negative. Therefore, this research was aiming to conduct an approach through analysis sentiment of public opinion about the veil and hijab to know how much accurate the sentiment analysis predict the positive, negative, or other sentiments with using Twitter data as the research object. The algorithm used in this study is Support Vector Machine (SVM) because of its fairly good classification model though it trained using small set of data. The SVM on this research was combined with Radial Base Function (RBF) kernel because of its numerical difficulties that are fewer than linear and polynomial kernel and also because this research doesn’t have a large feature. The amount of data used is 3556 tweets data. Tweets data, which is numbered 1056, is classified manually for the learning process. The remaining 2500 data will be classified automatically with the classifier model that has been created. A total of 1056 tweets data that have been classified manually is separated into training and testing data with a ratio of 8: 2. The result of the sentiment analysis process using Support Vector Machine algorithm RBF kernel with C=1 and γ=1 has an accuracy score of 73.6% with precision to negative opinions are 62%, positive opinions are 83%, neutral opinions reach 53% and irrelevant opinions that talk about hijab and veil reach 98%. It shows that sentiment analysis can be used for predicting the negative, positive or other sentiments of a sentence based on a certain topic, in this case veil and hijab.