bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Authors: Way Gregory P. , Zietz Michael , Rubinetti Vincent , Himmelstein Daniel S. , Greene Casey S. 
Published: May 2020

Abstract
Background
Unsupervised compression algorithms applied to gene expression data extract latent or hidden signals representing technical and biological sources of variation. However, these algorithms require a user to select a biologically appropriate latent space dimensionality. In practice, most researchers fit a single algorithm and latent dimensionality. We sought to determine the extent by which selecting only one fit limits the biological features captured in the latent representations and, consequently, limits what can be discovered with subsequent analyses.

Results
We compress gene expression data from three large datasets consisting of adult normal tissue, adult cancer tissue, and pediatric cancer tissue. We train many different models across a large range of latent space dimensionalities and observe various performance differences. We identify more curated pathway gene sets significantly associated with individual dimensions in denoising autoencoder and variational autoencoder models trained using an intermediate number of latent dimensionalities. Combining compressed features across algorithms and dimensionalities captures the most pathway-associated representations. When trained with different latent dimensionalities, models learn strongly associated and generalizable biological representations including sex, neuroblastoma MYCN amplification, and cell types. Stronger signals, such as tumor type, are best captured in models trained at lower dimensionalities, while more subtle signals such as pathway activity are best identified in models trained with more latent dimensionalities.

Conclusions
There is no single best latent dimensionality or compression algorithm for analyzing gene expression data. Instead, using features derived from different compression models across multiple latent space dimensionalities enhances biological representations.
Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia
Authors: Wang Ping , Tang Zhonghui , Lee Byoungkoo , Zhu Jacqueline Jufen , Cai Liuyang , Szalaj Przemyslaw , Tian Simon Zhongyuan , Zheng Meizhen , Plewczynski Dariusz , Ruan Xiaoan , Liu Edison T. , Wei Chia-Lin , Ruan Yijun 
Published: May 2020

Abstract
Background
Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML-RARα, a major etiological agent in APL. However, the molecular mechanisms underlying the role of PML-RARα in leukemogenesis remain largely unknown.

Results
Using an inducible system, we comprehensively analyze the 3D genome organization in myeloid cells and its reorganization after PML-RARα induction and perform additional analyses in patient-derived APL cells with native PML-RARα. We discover that PML-RARα mediates extensive chromatin interactions genome-wide. Globally, it redefines the chromatin topology of the myeloid genome toward a more condensed configuration in APL cells; locally, it intrudes RNAPII-associated interaction domains, interrupts myeloid-specific transcription factors binding at enhancers and super-enhancers, and leads to transcriptional repression of genes critical for myeloid differentiation and maturation.

Conclusions
Our results not only provide novel topological insights for the roles of PML-RARα in transforming myeloid cells into leukemia cells, but further uncover a topological framework of a molecular mechanism for oncogenic fusion proteins in cancers.
Retaining participants in community-based health research: a case example on standardized planning and reporting
Authors: Catherine Nicole L. A. , Lever Rosemary , Marcellus Lenora , Tallon Corinne , Sheehan Debbie , MacMillan Harriet , Gonzalez Andrea , Jack Susan M. , Waddell Charlotte 
Published: May 2020

Abstract
Background
Effective strategies for participant retention are critical in health research to ensure validity, generalizability and efficient use of resources. Yet standardized guidelines for planning and reporting on retention efforts have been lacking. As with randomized controlled trial (RCT) and systematic review (SR) protocols, retention protocols are an opportunity to improve transparency and rigor. An RCT being conducted in British Columbia (BC), Canada provides a case example for developing a priori retention frameworks for use in protocol planning and reporting.

Methods
The BC Healthy Connections Project RCT is examining the effectiveness of a nurse home-visiting program in improving child and maternal outcomes compared with existing services. Participants (N = 739) were girls and young women preparing to parent for the first time and experiencing socioeconomic disadvantage. Quantitative data were collected upon trial entry during pregnancy and during five follow-up interviews until participants’ children reached age 2 years. A framework was developed to guide retention of this study population throughout the RCT. We reviewed relevant literature and mapped essential retention activities across the study planning, recruitment and maintenance phases. Interview completion rates were tracked.

Results
Results from 3302 follow-up interviews (in-person/telephone) conducted over 4 years indicate high completion rates: 90% (n = 667) at 34 weeks gestation; and 91% (n = 676), 85% (n = 626), 80% (n = 594) and 83% (n = 613) at 2, 10, 18 and 24 months postpartum, respectively. Almost all participants (99%, n = 732) provided ongoing consent to access administrative health data. These results provide preliminary data on the success of the framework.

Conclusions
Our retention results are encouraging given that participants were experiencing considerable socioeconomic disadvantage. Standardized retention planning and reporting may therefore be feasible for health research in general, using the framework we have developed. Use of standardized retention protocols should be encouraged in research to promote consistency across diverse studies, as now happens with RCT and SR protocols. Beyond this, successful retention approaches may help inform health policy-makers and practitioners who also need to better reach, engage and retain underserved populations.

Trial registration
ClinicalTrials.gov, NCT01672060. Registered on 24 August 2012.
Spatial variation in the frequency of knockdown resistance genotypes in Florida Aedes aegypti populations
Authors: Mundis Stephanie J. , Estep Alden S. , Waits Christy M. , Ryan Sadie J. 
Published: May 2020

Abstract
Background
The development of insecticide resistance in disease-vectoring mosquito species can lead to vector control failure and disease resurgence. However, insecticide applications remain an essential public health intervention. In Florida, insecticide resistance in Aedes aegypti, an anthropophilic mosquito species capable of transmitting dengue, chikungunya, and Zika virus, is a major concern. Understanding the location, scale, and driving factors of insecticide resistance can enhance the ability of vector control organizations to target populations effectively.

Methods
We used previously collected data on frequencies of mutations that confer resistance to commonly used pyrethroid insecticides in Ae. aegypti specimens from 62 sites distributed across 18 counties in Florida. To determine the scale of clustering for the most resistant variant, we used a Ripley’s K function. We also used a spatial scanning statistic technique to identify locations of clusters where higher than expected frequencies of susceptible or resistant mosquitoes occurred. We then tested for associations between landscape, demographic, and insecticide-use factors using a beta regression modelling approach and evaluated the effect of spatial lag and spatial error terms on overall explanatory power of these models.

Results
The scale at which maximum clustering of the most resistant variant occurs is approximately 20 kilometers. We identified statistically significant clusters of genotypes associated with resistance in several coastal cities, although some of these clusters were near significant clusters of susceptible mosquitoes, indicating selection pressures vary at the local scale. Vegetation density, distance from roads, and pyrethroid-use by vector control districts were consistently significant predictors of knockdown resistance genotype frequency in the top-performing beta regression models, although pyrethroid use surprisingly had a negatively associated with resistance. The incorporation of spatial lags resulted in improvements to the fit and explanatory power of the models, indicating an underlying diffusion process likely explains some of the spatial patterns observed.

Conclusions
The genetic mutations that confer resistance to pyrethroids in Ae. aegypti mosquitoes in Florida exhibit spatial autocorrelation and patterns that can be partially explained by landscape and insecticide-use factors. Further work at local scales should be able to identify the mechanisms by which these variables influence selection for alleles associated with resistance.
Increased serum calpain activity is associated with HMGB1 levels in systemic sclerosis
Authors: Zheng Ji-Na , Li Yang , Yan Yue-Mei , Yu Yong , Shao Wen-Qi , Wang Qiang 
Published: May 2020

AbstractBackgroundSystemic sclerosis (SSc) or scleroderma is an intractable autoimmune disorder that affects multiple organs. The objectives were to investigate clinical correlations of serum calpain activity and high mobility group box 1 (HMGB1) levels with immunological and clinical traits.MethodsA total of 31 patients with SSc, 20 age- and gender-matched healthy control subjects (HC), and 10 patients with other connective tissue diseases (CTD) were recruited in the study. We measured serum calpain activity and HMGB1 levels and analyzed the datasets (GSE40839, GSE48149, GSE76808, GSE81292, GSE33463, and GSE58095) from Gene Expression Omnibus (GEO) database to explore the potential mechanism by which calpain exerts its function through bioinformatics methods.ResultsSerum calpain activity was significantly increased in patients with SSc compared with those in HC and in patients with CTD and was correlated with serum HMGB1 levels, modified Rodnan skin score, erythrocyte sedimentation rate, mean platelet volume, and plateletcrit. Notably, serum calpain activity and HMGB1 levels in SSc patients with interstitial lung disease (ILD) were significantly higher than those in SSc patients without ILD. Serum calpain activity and HMGB1 levels could be the independent risk factors for SSc-ILD and novel biomarkers in patients with SSc.ConclusionThis is the first study that reports increased serum calpain activity and the correlation between calpain and HMGB1 in patients with SSc or SSc-ILD. The serum calpain activity and HMGB1 levels may serve as measures of ILD in patients with SSc. Also, calpain and HMGB1 could be potential therapeutic targets for patients with SSc or SSc-ILD in the future.
Hypermethylation and decreased expression of TMEM240 are potential early-onset biomarkers for colorectal cancer detection, poor prognosis, and early recurrence prediction
Authors: Chang Shih-Ching , Liew Phui-Ly , Ansar Muhamad , Lin Shih-Yun , Wang Sheng-Chao , Hung Chin-Sheng , Chen Jian-Yu , Jain Shikha , Lin Ruo-Kai 
Published: May 2020

Abstract
Background
Gene silencing by aberrant DNA methylation of promoter regions remains the most dominant phenomenon occurring during tumorigenesis. Improving the early diagnosis, prognosis, and recurrence prediction of colorectal cancer using noninvasive aberrant DNA methylation biomarkers has encouraging potential. The aim of this study is to characterize the DNA methylation of the promoter region of TMEM240, as well as gene expression and its effect on cell biological functions and its applications in early detection and outcome prediction.

Results
Highly methylated CpG sites were identified in the TMEM240 gene by Illumina methylation 450K arrays in 26 Taiwanese patient paired samples and 38 paired samples from The Cancer Genome Atlas (TCGA) colorectal cancer dataset. Transient transfection and knockdown of TMEM240 were performed to demonstrate the role of TMEM240 in colorectal cancer cells. The data showed that TMEM240 could lead to G1 cell cycle arrest, repress cancer cell proliferation, and inhibit cancer cell migration. The quantitative methylation-specific real-time polymerase chain reaction (PCR) results revealed that 87.8% (480 of 547) of the colorectal cancer tumors had hypermethylated TMEM240, and this was also found in benign tubular adenomas (55.6%). Circulating cell-free methylated TMEM240 was detected in 13 of 25 (52.0%) Taiwanese colorectal cancer patients but in fewer (28.6%) healthy controls. In 72.0% (85/118) of tissue samples, TMEM240 mRNA expression was lower in Taiwanese CRC tumor tissues than in normal colorectal tissues according to real-time reverse transcription PCR results, and this was also found in benign tubular adenomas (44.4%). The TMEM240 protein was analyzed in South Korean and Chinese CRC patient samples using immunohistochemistry. The results exhibited low protein expression in 91.7% (100/109) of tumors and 75.0% (24/32) of metastatic tumors but exhibited high expression in 75.0% (6/8) of normal colon tissues. Multivariate Cox proportional hazards regression analysis found that mRNA expression of TMEM240 was significantly associated with overall, cancer-specific, and recurrence-free survival (p = 0.012, 0.007, and 0.022, respectively).

Conclusions
Alterations in TMEM240 are commonly found in Western and Asian populations and can potentially be used for early prediction and as poor prognosis and early-recurrence biomarkers in colorectal cancer.
Recruitability and effect of PEEP in SARS-Cov-2-associated acute respiratory distress syndrome
Authors: Beloncle François M. , Pavlovsky Bertrand , Desprez Christophe , Fage Nicolas , Olivier Pierre-Yves , Asfar Pierre , Richard Jean-Christophe , Mercat Alain 
Published: May 2020

Abstract
Background
A large proportion of patients with a SARS-Cov-2-associated respiratory failure develop an acute respiratory distress syndrome (ARDS). It has been recently suggested that SARS-Cov-2-associated ARDS may differ from usual non-SARS-Cov-2-associated ARDS by higher respiratory system compliance (CRS), lower potential for recruitment with positive end-expiratory pressure (PEEP) contrasting with severe shunt fraction. The purpose of the study was to systematically assess respiratory mechanics and recruitability in SARS-Cov-2-associated ARDS.

Methods
Gas exchanges, CRS and hemodynamics were assessed at 2 levels of PEEP (15 cmH2O and 5 cmH2O) within 36 h (day1) and from 4 to 6 days (day 5) after intubation. The recruited volume was computed as the difference between the volume expired from PEEP 15 to 5 cmH2O and the volume predicted by compliance at PEEP 5 cmH2O (or above airway opening pressure). The recruitment-to-inflation (R/I) ratio (i.e. the ratio between the recruited lung compliance and CRS at PEEP 5 cmH2O) was used to assess lung recruitability. A R/I ratio value higher than or equal to 0.5 was used to define highly recruitable patients.

Results
The R/I ratio was calculated in 25 of the 26 enrolled patients at day 1 and in 15 patients at day 5. At day 1, 16 (64%) were considered as highly recruitable (R/I ratio median [interquartile range] 0.7 [0.55–0.94]) and 9 (36%) were considered as poorly recruitable (R/I ratio 0.41 [0.31–0.48]). The PaO2/FiO2 ratio at PEEP 15 cmH2O was higher compared to PEEP 5 cmH2O only in highly recruitable patients (173 [139–236] vs 135 [89–167] mmHg; p < 0.01). Neither PaO2/FiO2 or CRS measured at PEEP 15 cmH2O or at PEEP 5 cmH2O nor changes in PaO2/FiO2 or CRS in response to PEEP changes allowed to identify highly or poorly recruitable patients.

Conclusion
In this series of 25 patients with SARS-Cov-2 associated ARDS, 64% were considered as highly recruitable and only 36% as poorly recruitable based on the R/I ratio performed on the day of intubation. This observation suggests that a systematic R/I ratio assessment may help to guide initial PEEP titration to limit harmful effect of unnecessary high PEEP in the context of Covid-19 crisis.
A deep learning-aided temporal spectral ChannelNet for IEEE 802.11p-based channel estimation in vehicular communications
Authors: Zhu Xuchen , Sheng Zhichao , Fang Yong , Guo Denghong 
Published: May 2020

AbstractIn vehicular communications using IEEE 802.11p, estimating channel frequency response (CFR) is a remarkably challenging task. The challenge for channel estimation (CE) lies in tracking variations of CFR due to the extremely fast time-varying characteristic of channel and low density pilot. To tackle such problem, inspired by image super-resolution (ISR) techniques, a deep learning-based temporal spectral channel network (TS-ChannelNet) is proposed. Following the process of ISR, an average decision-directed estimation with time truncation (ADD-TT) is first presented to extend pilot values into tentative CFR, thus tracking coarsely variations. Then, to make tentative CFR values accurate, a super resolution convolutional long short-term memory (SR-ConvLSTM) is utilized to track channel extreme variations by extracting sufficiently temporal spectral correlation of data symbols. Three representative vehicular environments are investigated to demonstrate the performance of our proposed TS-ChannelNet in terms of normalized mean square error (NMSE) and bit error rate (BER). The proposed method has an evident performance gain over existing methods, reaching about 84.5% improvements at some high signal-noise-ratio (SNR) regions.
A limited memory BFGS subspace algorithm for bound constrained nonsmooth problems
Authors: Li Xiangrong 
Published: May 2020

AbstractThe subspace technique has been widely used to solve unconstrained/constrained optimization problems and there exist many results that have been obtained. In this paper, a subspace algorithm combining with limited memory BFGS update is proposed for large-scale nonsmooth optimization problems with box-constrained conditions. This algorithm can ensure that all iteration points are feasible and the sequence of objective functions is decreasing. Moreover, rapid changes in the active set are allowed. The global convergence is established under some suitable conditions. Numerical results show that this method is very effective for large-scale nonsmooth box-constrained optimization, where the largest dimension of the test problems is 11,000 variables.
Global continuum and multiple positive solutions to one-dimensional p-Laplacian boundary value problem
Authors: Wei Liping , Ma Ruyun 
Published: May 2020

AbstractWe show the global structure of the set of positive solutions of a discrete Dirichlet problem involving the p-Laplacian difference operator suggesting suitable conditions on the weight function and nonlinearity. We obtain existence and multiplicity of positive solutions for λ lying in various intervals in $\mathbb {R}$R by using the directions of a bifurcation and the Picone-type identity for discrete p-Laplacian operators.
Social determinants of overweight and obesity in the mother-child binomial: evidences from Mexico
Authors: Arredondo Armando , Torres Christian , Orozco Emanuel , Resendiz Oscar 
Published: May 2020

Abstract
Background
To analyze the influence of socioeconomic determinants on the development of overweight and obesity in the mother-child binomial.

Methods
This is a study based on a prospective cohort of the mother-child binomial. Using STATA software, the association between the mothers’ body mass index and the nutritional status of minors was analyzed using a logistic regression model with socioeconomic and demographic variables.

Results
The combined prevalence of overweight and obesity in cohort mothers was 53.2%. A statistically significant association was found between the overweight mothers and minors with possible risk of overweight (p 0.001) and with overweight (p 0.001). The logistic regression model was adjusted by age and marital status and linked maternal overweight and obesity with the following variables: severe food insecurity (RR 1.17, CI 0.04–1.31), having a health problem (RR 1.5, CI 0.86–2.05), income (RR 0.79, CI .49–1.30), smoking (RR 1.1, CI 0.80–1.37) and dietary pattern (RR 1.5, CI 0.38–1.87).

Conclusions
The study highlights the importance of paying attention to risk factors starting at the gestational stage, since at this time the mother’s nutritional status has an influence on the offspring’s growth and development. Evidences exist of an association between intergenerational transmission of obesity and socioeconomic aspects of the mother. These evidences must be considered in the revision and adjustments to health system interventions for the prevention of obesity in the mother-child binomial.
Motivational climate of group exercise sessions in nursing homes
Authors: Charles Alexia , Buckinx Fanny , Mouton Alexandre , Reginster Jean-Yves , Bruyère Olivier 
Published: May 2020

Abstract
Background
Motivational climate in exercise group environments would have an impact on adherence, effort and enjoyment. We examined the motivational climate among nursing home residents who were involved in group exercise sessions.

Methods
This cross-sectional study was conducted in 10 nursing homes of Liège area that offer group exercise sessions. Sociodemographic data (age, sex, body mass index), cognitive status (by the Mini Mental State Examination) and independence in activities of daily living (by the Katz Scale) were retrieved in the medical records. The “Abbreviated-Perceived Motivational Climate in Exercise Questionnaire” was translated into French and then administered face to face with a clinical researcher. This is composed of 6 ego-involving climate items (corresponding to rivalry, comparison and favoritism) and 6 task-involving climate items (corresponding to valorization, individual efforts, self-improvement and cooperation). Each item is ranged on a 5-point Likert scale ranging from 1 (not at all focused on ego or task) to 5 (totally focused on ego or task). Each subscale has a total score expressed as an average.

Results
A total of 102 subjects of exercise group sessions were included (84.3 ± 7.7 years and 83 (81.4%) women). The mean score of task-involving and ego-evolving motivational climate was respectively 3.57 (SD = 0.67) and 1.52 (SD = 0.49), suggesting that the motivational climate was more focused on the task-involving climate than on ego-involving climate. Some items results were of particular interest: 55.9% of the respondents found that the instructor doesn’t remark/reward when they try hard, 63.7% said that the instructor doesn’t encourage mutual aid and 38.2% found that instructor doesn’t encourage to do new exercises.

Conclusions
Participants tended to perceive motivational climate as more task-involving than ego-involving. The absence of individual positive feedback, new exercises and mutual aid were also highlighted.