bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive Assessment of Smoking and Sex Related Effects in Publicly Available Gene Expression Data
Authors: Flynn Emily , Chang Annie , Nugent Bridget M. , Altman Russ 
Published: September 2021

ABSTRACTSmoking greatly reduces life expectancy in both men and women, but with different patterns of morbidity. After adjusting for smoking history, women have higher risk of respiratory effects and diabetes from smoking, while men show greater mortality from smoking-related cancers. While many smoking-related sex differences have been documented, the underlying molecular mechanisms are not well understood. To date, identification of sex differences in response to smoking has been limited to a small number of studies and the resulting smoking-related effects require further validation. Publicly available gene expression data present a unique opportunity to examine molecular-level sex and smoking effects across many tissues and studies. We performed a systematic search to identify smoking-related studies from healthy tissue samples and found 31 separate studies as well as an additional group of overlapping studies that in total span 2,177 samples and 12 tissues. These samples and studies were overall male-biased. In smoking, while effects appeared to be somewhat tissue-specific and largely autosomal, we identified a small number of genes that were consistently differentially expressed across tissues, including AHRR and GZMH. We also identified one gene, AKR1C3, encoding an aldo-keto reductase, which showed strong opposite direction, smoking-related effects in blood and airway epithelium, with higher expression in airway epithelium and lower expression in blood of smokers versus non-smokers. By contrast, at similar significance thresholds, sex-related effects were entirely sex chromosomal and consistent across tissues, providing evidence of stronger effects of smoking than sex on autosomal expression. Due to sample size limitations, we only examined interaction effects in the largest study, where we identified 30 genes with sex differential effects in response to smoking, only one of which, CAPN9, replicated in a held-out analysis. Overall these results present a comprehensive analysis of smoking-related effects across tissues and an initial examination of sex differential smoking effects in public gene expression data.
Results from a conservation initiative for parrotfishes in the Colombian Caribbean
Authors: López-Angarita Juliana , Restrepo Orjuela María del Pilar , Peña Katherine Guzmán , Escobar Dairo 
Published: September 2021

AbstractParrotfish (Family Scaridae) are a family of herbivorous fishes crucial to coral reef health, particularly for Caribbean reefs due to their declining coral cover. However, despite parrotfish are fully protected in some countries, they are still heavy fished in most of their Caribbean range. The consequences of this targeted fishery in the Colombian Caribbean are not fully understood due to a lack of local conservation and management resources. This research aimed to evaluate and enhance the conservation status and protection of parrotfish among local communities in the National Natural Park Corales del Rosario and San Bernardo. Underwater visual census surveys (UVC) were undertaken to evaluate reef fish community structure, and participatory education campaigns and activities were carried out with local communities to raise awareness about parrotfish ecology and their functional role in conserving Caribbean coral reef ecosystems of Colombia. UVC showed parrotfish to be dominant in the fish community, yet there was evidence of exploitation of large adults by selective fishing. Conflicts exist between the community and environmental authorities because fishing regulations are not clear, and the level of enforcement is insufficient. Parrotfish are sold to tourists, as ‘red snapper’ to fulfil high seafood demand since commercially valuable fish are now scarce. However, following intensive awareness-raising activities developed as part of this study, the community has started to recognize the vital ecological role of parrotfish in coral reef systems, and are suggesting a redrafting of fishing legislation by the environmental authorities, in order to recognise and incorporate the traditional fishing rights of human communities living within the MPA. Lobbying for the protection of parrotfish and inclusion of local communities in decision-making will take time, but this research represents the crucial first steps towards sustainable practice and cooperative alliances in the Colombian Caribbean.
3D U-Net improves automatic brain extraction for isotropic rat brain MRI data
Authors: Hsu Li-Ming , Wang Shuai , Walton Lindsay , Wang Tzu-Wen Winnie , Lee Sung-Ho , Shih Yen-Yu Ian 
Published: September 2021

AbstractBrain extraction is a critical pre-processing step in brain magnetic resonance imaging (MRI) analytical pipelines. In rodents, this is often achieved by manually editing brain masks slice-by-slice, a time-consuming task where workloads increase with higher spatial resolution datasets. We recently demonstrated successful automatic brain extraction via a deep-learning-based framework, U-Net, using 2D convolutions. However, such an approach cannot make use of the rich 3D spatial-context information from volumetric MRI data. In this study, we advanced our previously proposed U-Net architecture by replacing all 2D operations with their 3D counterparts and created a 3D U-Net framework. We trained and validated our model using a recently released CAMRI rat brain database acquired at isotropic spatial resolution, including T2-weighted turbo-spin-echo structural MRI and T2*-weighted echo-planar-imaging functional MRI. The performance of our 3D U-Net model was compared with existing rodent brain extraction tools, including Rapid Automatic Tissue Segmentation (RATS), Pulse-Coupled Neural Network (PCNN), SHape descriptor selected External Regions after Morphologically filtering (SHERM), and our previously proposed 2D U-Net model. 3D U-Net demonstrated superior performance in Dice, Jaccard, Hausdorff distance, and sensitivity. Additionally, we demonstrated the reliability of 3D U-Net under various noise levels, evaluated the optimal training sample sizes, and disseminated all source codes publicly, with a hope that this approach will benefit rodent MRI research community.Significant methodological contributionWe proposed a deep-learning-based framework to automatically identify the rodent brain boundaries in MRI. With a fully 3D convolutional network model, 3D U-Net, our proposed method demonstrated improved performance compared to current automatic brain extraction methods, as shown in several qualitative metrics (Dice, Jaccard, PPV, SEN, and Hausdorff). We trust that this tool will avoid human bias and streamline pre-processing steps during 3D high resolution rodent brain MRI data analysis. The software developed herein has been disseminated freely to the community.
TT-Mars: Structural Variants Assessment Based on Haplotype-resolved Assemblies
Authors: Yang Jianzhi , Chaisson Mark 
Published: September 2021

AbstractVariant benchmarking is a critical component of method development and evaluating the accuracy of studies of genetic variation. Currently, the best approach to evaluate the accuracy of a callset is the comparison against a well curated gold standard. In repetitive regions of the genome it may be difficult to establish what is the truth for a call, for example when different alignment scoring metrics provide equally supported but different variant calls in on the same data. Here we provide an alternative approach, TT-Mars, that takes advantage of the recent production of high-quality haplotype-resolved genome assemblies by evaluating variant calls based on how well their call reflects the content of the assembly, rather than comparing calls themselves. We used TT-Mars to assess callsets from different SV discovery methods on multiple human genome samples and demonstrated that it is capable at accurately classifying true positive and false positive SVs. On the HG002 personal genome, TT-Mars recapitulates 96.0%-99.6% of the validations made using the Genome in a Bottle gold standard callset evaluated by truvari, and evaluates an additional 121-10,966 variants across different callsets. Furthermore, with a group of high-quality assemblies, TT-Mars can evaluate performance of SV calling algorithms as a distribution rather than a point estimate. We also compare TT-Mars against the long-read based validation tool, VaPoR, and when assembly-based variant calls produced by dipcall are used as a gold standard. Compared with VaPoR, TT-Mars analyzes more calls on a long read callset by assessing more short variant calls (< 100 bases), while requiring smaller input. Compared with validation using dipcall variants, TT-Mars analyzes 1,497-2,229 more calls on long read callsets and has favorable results when candidate calls are fragmented into multiple calls in alignments. TT-Mars is available at https://github.com/ChaissonLab/TT-Mars.git with accompanying assembly data and corresponding liftover files.
MARS: a tool for haplotype-resolved population-based structural variation detection
Authors: Zhang Lu , Sidow Arend , Zhou Xin 
Published: September 2021

AbstractMotivationLinked-reads enables genome-wide phased diploid assemblies. These haplotype-resolved assemblies allow us to genotype structural variants (SVs) with a high sensitivity and be able to further phase them. Yet, existing SV callers are designed for haploid genome assemblies only, and there is no tool to call SV from a large population of diploid assemblies which can define and refine SVs from a global view.ResultsWe introduce MARS (Multiple Alignment-based Refinement of Svs) in linked-reads for the detection of the most common SV types - indels from diploid genome assemblies of a large population. We evaluated SVs from MARS based on Mendelian law of inheritance and PacBio HiFi reads and it achieved a high validation rate around 73%-87% for indels that we have selected from 34 assembled samples.AvailabilitySource code and documentation are available on https://github.com/maiziex/MARS.Contactmaizie.zhou@vanderbilt.eduSupplementary informationSupplementary data are available at Bioinformatics online.
Overall vertical transmission of HCV, transmission net of clearance, and timing of transmission
Authors: Ades A E , Gordon Fabiana , Scott Karen , Collins Jeannie , Thorne Claire , Pembrey Lucy , Chappell Elizabeth , Mariné-Barjoan Eugènia , Butler Karina , Indolfi Giuseppe , Gibb Diana M , Judd Ali 
Published: September 2021

AbstractBackgroundIt is widely accepted that the risk of HCV vertical transmission (VT) is 5-6% in mono-infected women, and that 25-40% of HCV infection clears spontaneously within 5 years. However, VT and clearance rates have not been estimated from the same datasets, and there is a lack of information on VT rates “net” of clearance.MethodsWe re-analysed data on 1749 children in 3 prospective cohorts to obtain coherent estimates of overall VT rate and VT rates “net” of clearance at different ages. Clearance rates were used to impute the proportion of uninfected children who had been infected and then cleared before testing negative. The proportion of transmission early in utero, late in utero and at delivery was estimated from data on the proportion of RNA positives in samples tested within three days of birth, and differences between elective caesarean and non-elective caesarean deliveries.FindingsOverall VT rates were 7.2% (95% credible interval 5.6-8.9) in mothers who were HIV negative and 12.1% (8.6-16.8) in HIV-co-infected women. The corresponding rates net of clearance at 5 years were 2.4% (1.1-4.1) and 4.1% (1.7-7.3). We estimated that 24.8% (12.1-40.8) of infections occur early in utero, 66.0% (42.5-83.3) later in utero, and 9.3% (0.5-30.6) during delivery.ConclusionOverall VT rates are about 24% higher than previously assumed, but the risk of infection persisting beyond age 5 years is about 38% lower. The results can inform design of trials of to prevent or treat pediatric HCV infection, and strategies to manage children exposed in utero.Key pointsTaking account of infections that would have cleared spontaneously before detection, the rate of HCV vertical transmission is 7.2% (95%CrI 5.6-8.9) in mono-infected women, but transmission “net” of clearance is 3.1% (1.8-4.4) at 3 years, and 2.4% (1.1-4.1) at 5.
Is there an association between daytime napping, cognitive function and brain volume? A Mendelian randomisation study in the UK Biobank
Authors: Paz Valentina , Dashti Hassan S. , Garfield Victoria 
Published: September 2021

AbstractDaytime napping has been associated with cognitive function and brain health in observational studies. However, it remains elusive whether these associations are causal. Using Mendelian randomisation (MR), we studied the relationship between habitual daytime napping and cognitive/structural brain outcomes. Data were from UK Biobank (UKB) (maximum n= 378 932; mean age= 57 years). Our exposure (daytime napping) was instrumented using 92 previously identified genome-wide, independent genetic variants (single-nucleotide polymorphisms, SNPs). Our cognitive outcomes were reaction time and visual memory; our neuroimaging outcomes were total brain volume and hippocampal volume (cm3). Inverse-variance weighted (IVW) MR was implemented, with sensitivity analyses including MR-Egger and the Weighted Median Estimator for horizontal pleiotropy. We also tested different daytime napping instruments (47 SNPs, 86 SNPs and 17 SNPs) to ensure the robustness of our results. Our main MR analysis (IVW) showed an association between genetic liability to habitual daytime napping and larger total brain volume (unstandardised ß=15.80 cm3, 95% confidence interval (CI)=0.25; 31.34), but not hippocampal volume (ß=-0.03 cm3, 95%CI=-0.13; 0.06). No associations were found between daytime napping and reaction time (expß=1.01, 95%CI=1.00; 1.03), or visual memory (expß=0.99, 95%CI=0.94; 1.05). Additional analyses with 47 SNPs (adjusted for excessive daytime sleepiness), 86 SNPs (excluding sleep apnoea) and 17 SNPs (no sample overlap with UKB) were largely consistent with our main findings. MR-Egger and Weighted Median Estimator approaches showed no evidence of horizontal pleiotropy. Overall, we observed evidence of an association between genetically-instrumented daytime napping and larger total brain volume, but no evidence of an association between habitual daytime napping and hippocampal volume, reaction time or visual memory. Future studies could focus on the associations between napping and other cognitive/brain outcomes, as well as replication of these findings using other datasets and methods.Key MessagesDaytime napping has been linked with cognitive function and brain health in observational studies, but whether these links are causal remains elusive.Using Mendelian randomisation, we investigated the potential causal role of habitual daytime napping on cognitive and neuroimaging outcomes.We observed evidence of a modest causal association between habitual daytime napping and larger total brain volume, but not enough evidence to support associations with hippocampal volume, reaction time or visual memory.
A brief analysis of the COVID-19 death data in Malaysia
Authors: Arifin Wan Nor , Musa Kamarul Imran , Hanis Tengku Muhammad , Rodzlan Hasani Wan Shakira , Che Nawi Che Muhammad Nur Hidayat , Ershad Ahmad Khan Erwan , Suliman Mohd Azmi , Termizi Sahrol Azmi , Ab Aziz Wira Alfatah 
Published: September 2021

AbstractIn December 2019, the first cases of Coronavirus Disease 2019 (COVID-19) were detected in Wuhan, China. Since then, COVID-19 begun to spread rapidly all over the world. On March 11, 2020, the World Health Organisation declared COVID-19 a pandemic. As of September 7, 2021, there were over 220 million confirmed COVID-19 cases globally, with more than 4.6 million deaths. Malaysia reported 2,067,327 confirmed cases with 22,743 deaths. Given the severity of the pandemic, the Ministry of Health Malaysia has stepped up in its efforts in handling the pandemic locally by sharing the COVID-19 related data on the GitHub, enabling transparent data sharing. This enables timely data analysis and quick decision to better understand the COVID-19 situation in this country. This article aims to provide a quick analysis of the death and vaccination data provided by the Malaysian Ministry of Health and to provide useful insight into the analysis.
SARS-CoV-2 nucleocapsid antigen in urine of hospitalized patients with Covid-19
Authors: Veyrenche N , Pisoni A , Debiesse S , Bollore K , Bedin AS , Makinson A , Niel C , Alcocer-Cordellat C , Mondain AM , Le Moing V , Van de Perre P , Tuaillon E 
Published: September 2021

ABSTRACTIntroductionSARS-CoV-2 nucleocapsid antigen (N-Ag) can be detected in the blood of patients with Covid-19. In this study, we used a highly sensitive and specific nucleocapsid-Ag assay to explore the presence of N-Ag in urine during the course of Covid-19, and explore its relationship with the severity of the disease.Material and MethodsUrine and blood samples were collected from 82 patients with a SARS-CoV-2 infection proven by PCR and included in the COVIDotheque. We explored the presence of N-Ag in urine and blood using the AAZ N-Ag test, studied the kinetics of the marker according to the time since the onset of symptoms and evaluated the association between N-Ag levels, clinical severity and inflammation.ResultsIn the first and second weeks of Covid-19, hospitalized patients tested positive for urinary N-Ag (81.25% and 71.79%, respectively) and blood N-Ag (93.75% and 94.87%, respectively). N-Ag levels in urine and blood were moderately correlated with the number of days after the onset of symptoms (r=-0.43, p<0.0001; r=-0.55 p<0.0001, respectively). The follow up of seven SARS-CoV-2 infected patients confirmed the waning of N-Ag in urine and blood over the course of the disease. High urinary N-Ag levels were associated with the absence of SARS-CoV-2 nucleocapsid-IgG (N-IgG), admission in intensive care units, high C-reactive protein levels, lymphopenia, eosinopenia, and high lactate dehydrogenase (LDH).ConclusionOur study demonstrate that N-Ag is present in the urine of patients hospitalized in the early phase of Covid-19. As a direct marker of SARS-CoV-2, urinary N-Ag reflects the dissemination of viral compounds in the body. Urine N-Ag is a promising marker to predict adverse evolution of SARS-CoV-2 infections.
Initial Analysis of Viral Dynamics and Circulating Viral Variants During the mRNA-1273 Phase 3 COVE Trial
Authors: Pajon Rolando , Paila Yamuna D. , Girard Bethany , Dixon Groves , Kacena Katherine , Baden Lindsey R. , Sahly Hana M. El , Essink Brandon , Mullane Kathleen M , Frank Ian , Denhan Douglas , Kerwin Edward , Zhao Xiaoping , Ding Baoyu , Deng Weiping , Tomassini Joanne E , Zhou Honghong , Leav Brett , Schödel Florian 
Published: September 2021

AbstractThis analysis assessed the impact of mRNA-1273 vaccination on the viral dynamics of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in the ongoing Coronavirus Efficacy (COVE) trial. mRNA-1273 vaccination significantly reduced SARS-CoV-2 viral copy number (95% confidence interval [CI]) by 100-fold on the day of diagnosis (4.1 [3.4-4.8] versus placebo (6.2 [6.0-6.4] log10 copies/ml). Median times to undetectable viral copies were 4 days for mRNA-1273 and 7 for placebo. Vaccination also reduced the burden of disease and infection scores. Vaccine efficacies (95% CI) during the trial against SARS-CoV-2 variants circulating in the US were 82.4% (40.4%-94.8%) for Epsilon and Gamma, and 81.2% (36.1%-94.5%) for the Epsilon variants. The detection of other respiratory viruses during the trial was similar between groups. In those who became SARS-CoV-2 infected, the reduction of viral load after mRNA-1273 vaccination is potentially correlated to the risk of transmission, which has not been assessed in this study.
How a Positive COVID-19 diagnosis affects the physical, social and psychological wellbeing of people in the United Arab Emirates? An Explorative Qualitative Study
Authors: AlKuwaiti Mouza , Hamada Bayan Abu , AlJeneibi Noof , Paulo Marília Silva , Elbarazi Iffat 
Published: September 2021

AbstractPurposeExploring the effect of COVID-19 diagnosis on the individual has not been explored through an exploratory qualitative approach. This study aims to explore the physical, social, and psychological impact of the diagnosis on the individual through online interviews.MethodA qualitative study approach using online interviews was conducted. A sample of 30 participants of different age groups, gender, and nationalities were interviewed to explore the impact of a positive COVID-19 diagnosis on their physical, mental, social, psychological health, and lifestyle practices. An interview guide was created based on coping strategy model and conceptual framework of coping strategies. All interviews were recorded then transcribed after obtaining written consent from participants. Ethics approval was obtained from the United Arab Emirates Social Science Ethics Committee. NVIVO software was used for thematic analysis based on both identified coping models to highlight the most important feelings and emotions, family support, and changes in lifestyle that may impact the COVID-19 patient and family. Researchers identified the themes separately and then verified themes in one meeting.ResultsMajor themes include the physical effects, social effects, psychological effects, spiritual effects, and lifestyle effects. Emerging themes include coping mechanisms, trust in authorities and health care system, appreciation of the role of the government, conspiracy theories, and media roles. Those who had a positive infection towards the end of 2020 and in 2021 described having fewer negative emotions and better psychological resilience.ConclusionThe findings of this study indicate that people diagnosed with COVID-19 have perceived a very good support in terms of their physical health from the government and health authorities, but require social, psychological, and educational support during the infection period and post-recovery.