bluuebunny/crossref_metadata_2025_split huggingface dataset:
A network regularized linear model to infer spatial expression pattern for single cells
Authors: Gu Chaohao , Liu Zhandong 
Published: March 2021

Abstract
Spatial gene-expression is a crucial determinant of cell fate and behavior. Recent imaging and sequencing-technology advancements have enabled scientists to develop new tools that use spatial information to measure gene-expression at close to single-cell levels. Yet, while Fluorescence In-situ Hybridization (FISH) can quantify transcript numbers at single-cell resolution, it is limited to a small number of genes. Similarly, slide-seq was designed to measure spatial-expression profiles at the single-cell level but has a relatively low gene-capture rate. And although single-cell RNA-seq enables deep cellular gene-expression profiling, it loses spatial information during sample-collection. These major limitations have stymied these methods’ broader application in the field. To overcome spatio-omics technology’s limitations and better understand spatial patterns at single-cell resolution, we designed a computation algorithm that uses glmSMA to predict cell locations by integrating scRNA-seq data with a spatial-omics reference atlas. We treated cell-mapping as a convex optimization problem by minimizing the differences between cellular-expression profiles and location-expression profiles with an L1 regularization and graph Laplacian based L2 regularization to ensure a sparse and smooth mapping. We validated the mapping results by reconstructing spatial- expression patterns of well-known marker genes in complex tissues, like the mouse cerebellum and hippocampus. We used the biological literature to verify that the reconstructed patterns can recapitulate cell-type and anatomy structures. Our work thus far shows that, together, we can use glmSMA to accurately assign single cells to their original reference-atlas locations.
Interfacial interactions between urea formaldehyde and cellulose nanofibrils (CNFs) of varying chemical composition and their impact on particle boards manufacture (PBs)
Authors: Iglesias Maria C. , McMichael Philip S. , Asafu-Adjaye Osei A. , Via Brian K. , Peresin Maria S. 
Published: March 2021

Abstract
Wood-based panels are commonly used as building materials for interior and exterior purposes. Their production and utilization have increased over the past decades due to the useful properties they present. Adhesive-bonded products make up to 80% of the wood alternatives on the global market, and of that, urea-formaldehyde (UF) makes up approximately 81% of the resins used. Formaldehyde-based resins are used due to their effectiveness and low cost, as well as their ease of application and lack of color. Nevertheless, their main disadvantages are the lack of tackiness and the emission of formaldehyde over time. To improve UF performance, the utilization of microfibrillated cellulose, has been demonstrated to be effective. However, more understanding on the mechanisms of the interactions is of relevant importance. In this work, we studied interfacial interactions between UF with bleached (BCNF) and unbleached (LCNF) cellulose nanofibrils using Quartz Crystal Microbalance with dissipation monitoring (QCM-D) technique observing the superior performance of lignin-containing CNF. Additionally, the surface free energies were investigated using Contact Angle Measurements (CA) showing a decrease of the values mainly when utilizing LCNF, which was later correlated with the wettability properties of the particle boards (PBs). PBs with different adhesive/CNF formulations were produced showing larger improvements when adding LCNF in terms of modulus of elasticity (MOE), modulus of rupture (MOR), and internal bonding (IB). To gain a better understanding on the interactions between CNF and UF, CNF was fully characterized in terms of morphology, chemical composition, charge density, as well as thermal and colloidal stability.
Evaluation of the Combined Effect of Mobility and Seasonality on the COVID-19 Pandemic: A Lombardy-Based Study
Authors: Falzone Yuri , Bosco Luca , Sferruzza Giacomo , Russo Tommaso , Vabanesi Marco , Filippi Massimo 
Published: March 2021

Abstract
Restrictions to human mobility had a significant role in limiting SARS-CoV-2 spread. It has been suggested that seasonality might affect viral transmissibility. Our study retrospectively investigates the combined effect that seasonal environmental factors and human mobility played on transmissibility of SARS-CoV-2 in Lombardy, Italy, in 2020.Environmental data were collected from accredited open-source web services. Aggregated mobility data for different points of interests were collected from Google Community Reports. The Reproduction number (Rt), based on the weekly counts of confirmed symptomatic COVID-19, non-imported cases, was used as a proxy for SARS-CoV-2 transmissibility. Assuming a non-linear correlation between selected variables, we used a Generalized Additive Model (GAM) to investigate with univariate and multivariate analyses the association between seasonal environmental factors (UV-index, temperature, humidity, and atmospheric pressure), location-specific mobility indices, and Rt. UV-index was the most effective environmental variable in predicting Rt. An optimal two-week lag-effect between changes in explanatory variables and Rt was selected. The association between Rt variations and individually taken mobility indices differed: Grocery & Pharmacy, Transit Station and Workplaces displayed the best performances in predicting Rt when individually added to the multivariate model together with UV-index, accounting for 85.0%, 85.5% and 82.6% of Rt variance, respectively. According to our results, both seasonality and social interaction policies played a significant role in curbing the pandemic. Non-linear models including UV-index and location-specific mobility indices can predict a considerable amount of SARS-CoV-2 transmissibility in Lombardy during 2020, emphasizing the importance of social distancing policies to keep viral transmissibility under control, especially during colder months.
Saliva as a testing sample for SARS-CoV-2 detection by RT-PCR in low prevalence community settings
Authors: Gavars Didzis , Gavars Mikus , Perminov Dmitrij , Stasulans Janis , Stana Justine , Metla Zane , Pavare Jana , Tauckels Eriks , Gulbis Egils , Dumpis Uga 
Published: March 2021

Abstract
There is an urgency for the rapid and simple SARS-CoV-2 detection method. Our study aimed to demonstrate that saliva can be used as a specimen for SARS-CoV-2 detection notably for the screening of extensive population groups via pooling. We collected paired nasopharyngeal/oropharyngeal swabs (NPS) and saliva and performed 36 serial measurements of 8 SARS-CoV-2 positive saliva samples to confirm the stability of the specimen. We also completed 37 pools by adding one positive saliva specimen per pool. A field study including 3,660 participants was performed between September 29 and October 1, 2020. Saliva specimens were stable for testing for up to 24 hours. Overall, 1.2% of the saliva samples tested positive for SARS-CoV-2. The results of saliva samples were consistent with those obtained from NPS with 90% sensitivity (95% CI 68.3%-98.7%) and 100% specificity during the first two weeks after the onset of symptoms. All pools showed 100% positivity in different pooling proportions. Our findings demonstrate that saliva is an appropriate specimen for pooling and SARS-CoV-2 screening with accurate diagnostic performance. Patient-performed specimen collection allows testing an extensive number of people rapidly, obtaining results of the spread of SARS-CoV-2 and allowing authorities to take timely measures.
Salinity Sensor Based on 1-D Photonic Crystals by Tamm Resonance With Different Geometrical Shapes
Authors: Sayed Hassan , Aly Arafa hussien 
Published: March 2021

Abstract
In this paper, we demonstrate a novel Salinity sensor based on Tamm-Plasmon-polariton (TPP), comprising of different shapes of Bragg reflector (ordinary, texturing, and Sawtooth) and metallic layer, is proposed. The finite element method is used to study the considered structure and sensing performance by using the COMSOL multiphysics simulation procedure. Here, we study the effect of surface morphology on the sensitivity; firstly, in the case of one-dimensional photonic crystals centered defect, it has a negative effect on the sensitivity, secondly, texturing and sawtooth in the case of Tamm resonance is increase the sensitivity as For texturing the surface, the sensitivity (S) = 569nm/RIU, quality factor (Q) =236, and figure of merit (FOM)= 170 RIU-1. While, for Sawtooth surface, S = 612.29nm/RIU, Q = 272.4, and FOM = 199RIU-1. The consequences of structural parameters on the efficiency of sensing are studied and new procedures are proposed to enhance TPP-based sensors. A simple and functional alternative to conventional salinity sensors may be the proposed solution.
Fungal Sticky Porous Cell Wall Evolved for Efficient Uptake and Export
Authors: Ebrahimi Hoda , Siavoshi Farideh , Jazayeri Mir Hadi , Sarrafnejad Abdolfattah , Saniee Parastoo , Mobini Maryam 
Published: March 2021

Abstract
Observing release of large extracellular vesicles (EVs) from yeast cell raised the question about size and flexibility of cell wall pores. To estimate the approximate size of pores, internalization of nanoparticles (NPs) with different sizes, into the intact yeast cell was examined. Candida tropicalis was cultured in N-acetylglucoseamine-yeast extract broth (NYB) and examined every 12 hr by light microscopy for observing release of EVs. Yeast culture in NYB was treated with Fluorescein isothiocyanate (FITC) -labelled NPs; gold (45, 70 and 100 nm), albumin (100 nm) and Fluospheres (1000 and 2000 nm). Fluorescence microscope was used for recording internalization of NPs with different concentrations (0.1-10%) after few seconds to 120 min of treatment. Release of EVs with different size and morphology from yeast mostly occurred at 36 hr. Best NPs’ concentration was 0.1% and internalization occurred within few seconds after treatment. Positively charged 45 nm gold NPs internalized into yeast cell and accumulated in the vacuole and 100 nm gold NPs destroyed the yeast cell. Gold NPs with 70 nm size and 100 nm negatively charged albumin NPs were internalized into the vacuole of a few yeast cells. Inert Fluospheres were first degraded outside the yeast’s cell and then absorbed into yeast’s cell and finally reached the vacuole. Release of large EVs from yeast indicated flexibility of cell wall pores and EVs for remodelling. Furthermore, physicochemical properties of internalizing NPs and those of cell wall determined uptake of NPs by yeast cell.
High prevalence of vitamin D deficiency among the South Asian adults: A systematic review and meta-analysis
Authors: Siddiqee Mahbubul H. , Bhattacharjee Badhan , Siddiqi Umme Ruman , Rahman Mohammad Meshbahur 
Published: March 2021

Abstract
Background: Vitamin D deficiency is linked to a wide range of chronic and infectious diseases. Body of literature suggested that the prevalence of this deficiency can have geographical variation. Although, vitamin D deficiency is frequently reported in the South Asian population, the scarcity of systematic reviews and meta-analyses means the true extent of the disease and the underlying factors causing it are poorly characterized.Methods: A systematic search was performed using databases (PubMed, Scopus and Google Scholar) for original studies on the South Asian population (published from January 1, 2001 to December 31, 2019). Following the search, a random effect meta-analyses was performed to calculate population level weighted average, pooled prevalence of deficiency, and heterogeneity of vitamin D among different countries and genders; in addition to South Asia as a whole.Results: Our study, based on our selection criteria was narrowed down to a total of 44,717 participants; that spanned over 65 studies from five South Asian countries. Overall, the pooled prevalence of deficiency was 68% [95% CI: 64% to 72%] with significant heterogeneity (I2 = 98%; p = 0.00). Average level of vitamin D ranged from 4.7 to 32 ng/mL, with a weighted mean of 19.15 ng/mL (weighted standard deviation 11.59 ng/mL). The highest prevalence of vitamin D deficiency was found in Pakistan (73%; 95% CI: 63% to 83%) followed by Bangladesh (67%; 95% CI: 50% to 83%), India (67%; 95% CI: 61% to 73%), Nepal (57%; 95% CI: 53% to 60%) and Sri Lanka (48%; 95% CI: 41% to 55%), respectively. This finding indicated a high degree of heterogeneity among the population. (I2 = 98.76%), Furthermore, a gender wise analysis suggested that in South Asia, the prevalence of vitamin D deficiency was higher in females than males. Conclusion: Our findings reveal highly prevalent and variable vitamin D deficiency among the adults of different South Asian countries. Findings from this review would be helpful to generate hypotheses and explore the factors affecting the inter-country variability, alongside strengthening evidence for governments to prioritize mitigation strategies in this region.
Suppression of &nbsp;lncRNA&nbsp;LINC00472&nbsp;Prevents Amyloid-β-induced Neurotoxicity in PC12&nbsp;Cells via Regulating miR-141-3p/Foxo3&nbsp;Axis&nbsp;
Authors: Guo Min , Li Jilai , Wang Peifu , Jin Di 
Published: March 2021

Abstract
Alzheimer's Disease (AD) is characterized by the accumulations of amyloid-β (Aβ) plaques and neurofibrillary tangles in brain, dysfunctions and loss of synaptic connections, exaggerated inflammation, and eventually neuronal death. Oxidative damage may explain the key features and suggest the therapeutic potential to prevent AD progression, yet it remains largely elusive the occurrence and thus the interventions of oxidative damage. Besides, miRNA dysregulation is tightly associated with AD progression. By recruiting 30 AD patients and 30 age-matched control, we demonstrated the upregulations of LINC00472, pro-inflammatory cytokines and ROS in the serum of AD subjects. Similar results were reproduced in Aβ treated SH-SY5Y cells. In addition, through luciferase reporter and RNA pull-down assays, we revealed direct interactions between LINC00472 and miR-141-3p, and between miR-141-3p and FOXO3 and the signalling loop LINC00472/miR-141-3p/FOXO3 loop is involved in Aβ administration induced oxidative stress. Moreover, we raised evidence that knocking down LINC00472 in SH-SY5Y cells ameliorated the Aβ administration induced oxidative stress. Thus, normalization of LINC00472 may be therapeutic to retard AD progression via ameliorating oxidative stress. Future works may further strengthen the pharmacological potentials of interventions for AD progression by targeting LINC00472/ miR-141-3p/ FOXO3 loop.
Profiles of ferroptosis-related genes and their prognostic values in patients with breast cancer brain metastasis
Authors: Zhu Lei , Chen Mu , Huang Bingsong , Liu Min , Zhong Chunlong , Li Qinchuan 
Published: March 2021

Abstract
Background Ferroptosis is involved in various cancers. The role of ferroptosis in breast cancer brain metastasis (BCBM) is unclear. This study aimed to explore the ferroptosis-related genes (FRG) expression profiles in BCBM, as well as evaluate the FRG prognostic values in breast cancer patients.Methods Genes expression and clinical data were downloaded from Gene Expression Omnibus (GEO). Functional enrichment analysis was used to investigate the FRG bioinformatics functions. Univariate and multivariate cox regression analysis were performed to explore the independent prognostic factors. The correlation between ferroptosis and immunity was also evaluated. Finally, the FRG and their prognostic values were validated in external cohorts.Results Fourteen significantly different FRG were screened between breast cancer and BCBM tissues. GO and KEGG results showed FRG were enriched in the ferroptosis-related activities. Protein‑protein interaction (PPI) network analysis showed the HMOX1 and TFRC were hub genes. Survival analysis demonstrated HMOX1 and PEBP1 were significantly associated with overall survival (OS) (HR=2.100, P=0.035; HR=0.421, P=0.017 respectively). The KEAP1 and LPCAT3 had prognostic values for relapse-free survival (RFS) (HR=0.745, P=0.002; HR=2.536, P=0.008 respectively). Patients in high-risk group have worse OS and RFS compared with those in low-risk group (P=0.004, 0.021 respectively). Clinical correlation analysis revealed FRG were significantly associated with estrogen receptor (ER) status, progesterone receptor (PgR) status, HER2 and pathological grade in breast cancer patients (all P<0.05). In addition, we also found that immune-related pathways and immune status were different between high and low-risk groups. External cohort results showed FRG were significantly different between breast cancer and BCBM tissues. Survival validation demonstrated ALOX5 and CS were associated with prognosis in breast cancer patients (P=0.044, 0.032 respectively). Conclusions Our study identified the ferroptosis-related genes that may be involved in biology of BCBM, and FRG could serve as prognostic biomarkers in breast cancer patients. New therapy targeting ferroptosis holds probabilities for effective treatment in BCBM patients.
Comparing Fertility Rates of Fresh Versus Frozen Embryo Transfer in Antagonist IVF Cycles
Authors: Seyedoshohadaei Fariba , Honarbakhsh Yasamin , Allahveisi Azra , Rezaei Masoumeh , Rezaie Mohammad Jafar , Zandvakili Farnaz , Soufizadeh Nasrin , Tahmasebi Fatemeh , Rahmani Khaled 
Published: March 2021

Abstract
The authors have requested that this preprint be removed from Research Square.
Learn, Engage, Act, Dedicate (LEAD): Development and feasibility testing of a task-shifted intervention to improve alcohol use, depression and family engagement for fathers
Authors: Giusto Ali , Ayuku David , Puffer Eve 
Published: March 2021

Abstract
Men’s depression, alcohol use, and family problems commonly co-occur to create of cluster of mental health problems. Yet, few treatments exist to address these problems, especially in low and middle-income countries (LMICs). This paper describes the development and initial feasibility and acceptability of a novel task-shifted intervention to address this cluster of men’s mental health problems with a focus on engaging and retaining men in treatment. The intervention, Learn, Engage, Act, Dedicate (LEAD), is based in behavioral activation blended with motivational interviewing and was pilot tested in Kenya. To develop LEAD, we engaged in a community-engaged multi-step, collaborative process with local Kenyan stakeholders. LEAD was piloted with nine fathers reporting problem drinking. To assess initial feasibility and acceptability, recruitment and participation were tracked and descriptive statistics were generated given engagement of men was key for proof of concept. Semi-structured interviews were conducted with participants and analyzed using thematic content analysis. The development process resulted in a weekly 5-session intervention rooted in behavioral activation, motivational interviewing, and masculinity discussion strategies. These approaches were combined and adapted to fit contextually salient constructs, such as the importance of the man as provider, and streamlined for lay providers. Feasibility and acceptability results were promising with high attendance, acceptability of delivery and intervention content, and perceived intervention helpfulness. Results describe an acceptable task-shifted treatment that may engage men in care and addresses a cluster of common mental health problems among men. Findings set the stage for a larger trial. Trial registration: ISRCTN, ISRCTN130380278. Registered 7 October 2019 - Retrospectively registered, http://www.isrctn.com/ISRCTN13038027
Study on Mining Pressure Control of Deep Coal Seam——Based on Artificial Fault Technology
Authors: Xu Xiaoding , Gao Yubing , He Manchao , Fu Qiang , Wei Xingjian 
Published: March 2021

Abstract
Based on the pressure transfer principle and stress distribution characteristics around a fault, introducing artificial fault technology to control the propagation of abutment pressure, and a mechanical model of abutment pressure under the influence of artificial fault was established. This new mechanical model can well fit the distribution law of mining stress after roof cutting. The pressure transfer mechanism of prefabrication support of rock blasting was analyzed, and the transfer trend of pressure and the mining stress of rock top was determined. It is of great significance to guide the implementation of the pressure relief work at the top of the stope. The study shows that the total energy of the system is conserved, the integrity of rock layer is destroyed by blasting, and the deformation and damage of pressure relief zone absorb a large amount of energy. Thus, the accumulated strain energy of abutment pressure region is released, and the influencing range of abutment pressure is reduced. As the horizontal distance from the cutting surface is farther away from the working surface, the smaller the stress difference on both sides of the cutting top, the less obvious the blocking effect of mining pressure. When the cutting point is closer to the working surface, the higher the peak value of abutment pressure due to the superposition of peripheral stress concentration caused by the cutting and peak of abutment pressure caused by mining. Then, the numerical simulation analysis was carried out, the results show that the technology of forming artificial fault by cutting the top can cut off the influence range of the mining pressure. It can effectively control the deformation of dynamic pressure tunnl. Finally, a practice of rock blasting pressure relief engineering was carried out, and the influencing range of abutment pressure of working face before blasting pressure reduction was reduced by 1/3 compared with that before the pressure relief.
Reading on smartphone causes sigh inhibition with brain overactivity and comprehension decline
Authors: Honma Motoyasu , Masaoka Yuri , Iizuka Natsuko , Wada Sayaka , Kamimura Sawa , Yoshikawa Akira , Moriya Rika , Kamijo Shotaro , Izumizaki Masahiko 
Published: March 2021

Abstract
Electronic devices have become an indispensable part of our lives, while negative aspects have been reported. One downside is that reading comprehension is reduced when reading from electronic device, but the cause of this is unclear. In this study, we investigated a cause for the decline in comprehension by simultaneously measuring respiration and brain activity during reading from a smartphone medium, on thirty-four healthy individuals. Here we found that, compared to a paper medium, reading from the smartphone elicits a suppression of sigh, brain overactivity in prefrontal cortex, and decline in reading comprehension. Furthermore, a path analysis suggests that interactive relationship between sigh inhibition and overactivity in prefrontal cortex causes the comprehension decline. These findings provide new insight into a respiration-mediated mechanism of cognitive function.