bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subfamily-specific differential contribution of individual monomers and the tether sequence to mouse L1 promoter activity
Authors: Kong Lingqi , Saha Karabi , Hu Yuchi , Tschetter Jada N. , Habben Chase E. , Whitmore Leanne S. , Yao Changfeng , Ge Xijin , Ye Ping , Newkirk Simon J. , An Wenfeng 
Published: April 2022

Abstract
Background
The internal promoter in L1 5’UTR is critical for autonomous L1 transcription and initiating retrotransposition. Unlike the human genome, which features one contemporarily active subfamily, four subfamilies (A_I, Gf_I and Tf_I/II) have been amplifying in the mouse genome in the last one million years. Moreover, mouse L1 5’UTRs are organized into tandem repeats called monomers, which are separated from ORF1 by a tether domain. In this study, we aim to compare promoter activities across young mouse L1 subfamilies and investigate the contribution of individual monomers and the tether sequence.

Results
We observed an inverse relationship between subfamily age and the average number of monomers among evolutionarily young mouse L1 subfamilies. The youngest subgroup (A_I and Tf_I/II) on average carry 3–4 monomers in the 5’UTR. Using a single-vector dual-luciferase reporter assay, we compared promoter activities across six L1 subfamilies (A_I/II, Gf_I and Tf_I/II/III) and established their antisense promoter activities in a mouse embryonic fibroblast cell line and a mouse embryonal carcinoma cell line. Using consensus promoter sequences for three subfamilies (A_I, Gf_I and Tf_I), we dissected the differential roles of individual monomers and the tether domain in L1 promoter activity. We validated that, across multiple subfamilies, the second monomer consistently enhances the overall promoter activity. For individual promoter components, monomer 2 is consistently more active than the corresponding monomer 1 and/or the tether for each subfamily. Importantly, we revealed intricate interactions between monomer 2, monomer 1 and tether domains in a subfamily-specific manner. Furthermore, using three-monomer 5’UTRs, we established a complex nonlinear relationship between the length of the outmost monomer and the overall promoter activity.

Conclusions
The laboratory mouse is an important mammalian model system for human diseases as well as L1 biology. Our study extends previous findings and represents an important step toward a better understanding of the molecular mechanism controlling mouse L1 transcription as well as L1’s impact on development and disease.
Comparison and aggregation of event sequences across ten cohorts to describe the consensus biomarker evolution in Alzheimer’s disease
Authors: Golriz Khatami Sepehr , Salimi Yasamin , Hofmann-Apitius Martin , Oxtoby Neil P. , Birkenbihl Colin ,   for the Alzheimer’s Disease Neuroimaging Initiative,   the Japanese Alzheimer’s Disease Neuroimaging Initiative,   the Alzheimer’s Disease Repository Without Borders Investigators
Published: April 2022

Abstract
Background
Previous models of Alzheimer’s disease (AD) progression were primarily hypothetical or based on data originating from single cohort studies. However, cohort datasets are subject to specific inclusion and exclusion criteria that influence the signals observed in their collected data. Furthermore, each study measures only a subset of AD-relevant variables. To gain a comprehensive understanding of AD progression, the heterogeneity and robustness of estimated progression patterns must be understood, and complementary information contained in cohort datasets be leveraged.

Methods
We compared ten event-based models that we fit to ten independent AD cohort datasets. Additionally, we designed and applied a novel rank aggregation algorithm that combines partially overlapping, individual event sequences into a meta-sequence containing the complementary information from each cohort.

Results
We observed overall consistency across the ten event-based model sequences (average pairwise Kendall’s tau correlation coefficient of 0.69 ± 0.28), despite variance in the positioning of mainly imaging variables. The changes described in the aggregated meta-sequence are broadly consistent with the current understanding of AD progression, starting with cerebrospinal fluid amyloid beta, followed by tauopathy, memory impairment, FDG-PET, and ultimately brain deterioration and impairment of visual memory.

Conclusion
Overall, the event-based models demonstrated similar and robust disease cascades across independent AD cohorts. Aggregation of data-driven results can combine complementary strengths and information of patient-level datasets. Accordingly, the derived meta-sequence draws a more complete picture of AD pathology compared to models relying on single cohorts.
The role of statisticians in the response to COVID-19 in Israel: a holistic point of view
Authors: Dattner Itai , Gal Reuven , Goldberg Yair , Goldshtein Inbal , Huppert Amit , Kenett Ron S. , Manor Orly , Pfeffermann Danny , Schechtman Edna , di Serio Clelia , Steinberg David M. 
Published: April 2022

AbstractThe COVID-19 pandemic cast a dramatic spotlight on the use of data as a fundamental component of good decision-making. Evaluating and comparing alternative policies required information on concurrent infection rates and insightful analysis to project them into the future. Statisticians in Israel were involved in these processes early in the pandemic in some silos as an ad-hoc unorganized effort. Informal discussions within the statistical community culminated in a roundtable, organized by three past presidents of the Israel Statistical Association, and hosted by the Samuel Neaman Institute in April 2021. The meeting was designed to provide a forum for exchange of views on the profession’s role during the COVID-19 pandemic, and more generally, on its influence in promoting evidence-based public policy. This paper builds on the insights and discussions that emerged during the roundtable meeting and presents a general framework, with recommendations, for involving statisticians and statistics in decision-making.
Intimate partner violence and timely antenatal care visits in sub-Saharan Africa
Authors: Aboagye Richard Gyan , Seidu Abdul-Aziz , Asare Bernard Yeboah-Asiamah , Adu Collins , Ahinkorah Bright Opoku 
Published: April 2022

Abstract
Background
Intimate partner violence (IPV) during pregnancy has negative physical and psychological health consequences on the pregnant women. As such, women who experience IPV during pregnancy are likely to have challenges accessing maternal healthcare services. In this study, we examined the influence of exposure to IPV on timely antenatal care (ANC) visits in sub-Saharan Africa.

Methods
Cross-sectional data from the most recent Demographic and Health Survey of twenty-two countries in sub-Saharan Africa between 2012 and 2020 were analysed. Data were obtained from 61,282 women with birth history in the five years prior to the survey. A multilevel logistic regression was used to determine the association between IPV and timely ANC visits while controlling for significant covariates. Adjusted odds ratios (aOR) with 95% Confidence Intervals (CI) were used to present results from the multilevel logistic regression analysis.

Results
The prevalence of timely ANC visit and IPV were 38.1% and 34.9% respectively. The highest and lowest prevalence of IPV were found in Sierra Leone (52.9%) and Comoros (8.1%), respectively. Timely ANC attendance among pregnant women was more prevalent in Liberia (74.9%) and lowest in DR Congo (19.0%). Women who experienced IPV during pregnancy were less likely to utilize timely ANC (aOR = 0.89, 95% CI = 0.86–0.92) compared to those who did not experience IPV. In terms of the covariates, the odds of timely ANC were higher among women aged 40–44 compared to those aged 15–19 (aOR = 1.35, 95% CI = 1.21–1.51). Higher odds of timely ANC was found among women who were cohabiting (aOR = 1.15, 95% CI = 1.10–1.20), those from the richest wealth quintile (aOR = 1.38, 95% CI = 1.28–1.48), those exposed to watching television (aOR = 1.24, 95% CI = 1.18–1.30), and those with health insurance (aOR = 1.46, 95% CI = 1.37–1.56).

Conclusion
Findings from the study indicate the role of IPV in timely ANC visit in sub-Saharan Africa. To enhance timely ANC visits, there is the need for policy makers to strengthen and enforce the implementation of policies that alleviate IPV during pregnancy. Education and sensitization of married and cohabiting women and men on the negative effects of IPV on timely ANC should be done using media sources such as television. Inequalities in timely ANC can be eliminated through the provision and strengthening of existing maternal health policies such as health insurance.
Social and housing indicators of dengue and chikungunya in Indian adults aged 45 and above: Analysis of a nationally representative survey (2017-18)
Authors: Paulson Winnie , Kodali Naveen Kumar , Balasubramani Karuppusamy , Dixit Rashi , Chellappan Savitha , Behera Sujit Kumar , Balabaskaran Nina Praveen 
Published: April 2022

Abstract
Background
Dengue and chikungunya (CHIKV) are the two major vector-borne diseases of serious public health concern in India. Studies on socioeconomic and housing determinants of dengue and CHIKV at a pan-India level are lacking. Here, we took advantage of the recently carried out Longitudinal Ageing Study in India (LASI) carried out across all the states and Union Territories of India to study the social indicators of dengue and CHIKV in India.

Methods
LASI-1 (2017-2018) data on the self-reported period prevalence of dengue and CHIKV from 70,932 respondents aged ≥45 years were used for this analysis. The state-wise distribution of dengue and CHIKV was mapped. Prevalence was estimated for each study variable, and the difference was compared using the χ2 test. The adjusted odds ratios (AOR) of the socioeconomic and housing variables for dengue and CHIKV were estimated using the multiple logistic regression model.

Results
Urban residence is the major socio-economic indicator of dengue and CHIKV (dengue AOR: 1.57, 95% CI: 1.18-2.11; CHIKV AOR: 1.84, 95% CI: 1.36-2.49). The other notable indicator is wealth; rich respondents have higher odds of dengue and CHIKV. Adults older than 54 years and those with high school education and above are associated with a lower likelihood of dengue and CHIKV. In addition, CHIKV is associated with scheduled and forward castes, households with improper toilet facilities, open defecation, and kutcha house type.

Conclusions
Despite the limitation that the data is only from adults ≥ 45, this analysis provides important insights into the socioeconomic and housing variables associated with higher odds of dengue and CHIKV in India. Understanding these determinants may assist in the national planning of prevention and control strategies for dengue and CHIKV.
Priorities of China’s participation in global malaria elimination: the perspective of malaria endemic countries
Authors: Xie Yan , Wang Jie , Sun Yinuo , Ke Xuedan , Xie Zheng , Cao Jun , Huang Yangmu 
Published: April 2022

Abstract
Background
Malaria is one of the major diseases affecting global health, while progress in malaria control and elimination has stagnated in some endemic countries. China has been certificated malaria free by World Health Organization in 2021, and will get more involved on global malaria elimination. Further discussion is needed on how to collaborate with the malaria endemic countries and provide effective help. This study was to investigate the perceptions of malaria endemic countries on China’s contribution to global malaria elimination and to lay a foundation for further action.

Methods
Semi-structured interviews were conducted with key informants including national malaria project managers and technicians from malaria endemic countries. Thematic framework approach was used to analyze the data.

Results
Malaria endemic countries now face challenges in insufficient funds, technique, products, public health systems and inadequacy of international assistance. They hold a positive attitude towards cooperation with China and identified experience and technique exchange, personnel training, system building and scientific research cooperation as prioritized areas.

Conclusions
China could make full use of its own advantages in technique transfer, health system improvement, information system construction, and health human resource training and take an active part in global malaria elimination.
Morphology of sporadic E layers derived from Fengyun-3C GPS radio occultation measurements
Authors: Xu Xiaohua , Luo Jia , Wang Han , Liu Haifeng , Hu Tianyang 
Published: April 2022

AbstractThe Global Positioning System (GPS) radio occultation (RO) data provided by the Fengyun-3C (FY-3C) mission during January 2015 to December 2019 are used to detect the existence of sporadic E (Es) layers over the globe, based on which the spatial and temporal distributions of the Es occurrence rates (ORs) are presented and analyzed. The results are compared with the Es morphology obtained using the RO data from the Constellation Observing System for the Meteorology, Ionosphere, and Climate (COSMIC) mission. It is found that the seasonal variation patterns of the spatial distributions of Es ORs derived from the FY-3C RO data, which show clearly the effects of wind shear mechanism and the Earth’s magnetic field on the formation of Es layers, are basically consistent with those derived from the COSMIC RO data. While the limited local time distribution of the FY-3C RO-detected Es occurrences makes it impossible to resolve the complete diurnal variations of Es layers. Detailed comparisons of the Es morphologies derived from the two different RO missions reveal that the magnitudes of the Es ORs derived by FY-3C data are slightly smaller than those derived by COSMIC data in the middle and low latitudes, which is due to that the top heights of the 50 Hz RO data of FY-3C mission are generally lower than those of the COSMIC mission. In the polar regions, the distinctly low ratio of the FY-3C RO 50 Hz measurements which reach the height of 90 km reduces the capability of these observations for Es-layer detections.
Graphical Abstract
Registration of immigrants’ educational attainment in Sweden: an analysis of sources and time to registration
Authors: Khaef Samaneh 
Published: April 2022

AbstractSwedish register data include a number of variables related to individuals’ educational level. In contrast to many other countries, the registers even include information on the education obtained by immigrants outside Sweden. For studies on immigrants’ labour market integration, this is an important asset. However, the quality of data in terms of the source and extent of data coverage for different migrant groups is less well-known. This explorative paper investigates the sources of information for immigrants’ educational levels, and examines the time taken until their education is registered for different migrant groups. Employing register data on immigrants who arrived in Sweden in the period 2000–2016, the methods include a descriptive analysis of the main sources of educational attainment, and event history analysis to estimate survival rates for not being in the educational registers. The results indicate that the ‘survey of foreign-born’ and the Swedish Public Employment Service are the two major sources of information regarding immigrants’ educational attainment in their year of arrival. However, the survey’s non-response rate is high. Results from the event history analysis show that as the length of stay in the country increases, the share of immigrants with missing educational information decreases substantially, especially after 2 years, with rather large differences for groups of immigrants. For the majority of refugees and family migrants, 2 years after arrival their educational levels are registered, while the educational levels of many Nordic migrants remained unregistered even after 10 years. In addition, attained education of women and younger immigrants is more often registered. Measuring the educational level of refugees and family migrants from 2 years after arrival can provide a reasonable representation of their educational characteristics at the time of migration, while it is questionable to use Nordic migrants’ educational level at any time.
Acute Leukemia Classification Using Transcriptional Profiles From Low-Cost Nanopore mRNA Sequencing
Authors: Wang Jeremy , Bhakta Nickhill , Ayer Miller Vanessa , Revsine Mahler , Litzow Mark R. , Paietta Elisabeth , Fedoriw Yuri , Roberts Kathryn G. , Gu Zhaohui , Mullighan Charles G. , Jones Corbin D. , Alexander Thomas B. 
Published: April 2022

PURPOSE Most cases of pediatric acute leukemia occur in low- and middle-income countries, where health centers lack the tools required for accurate diagnosis and disease classification. Recent research shows the robustness of using unbiased short-read RNA sequencing to classify genomic subtypes of acute leukemia. Compared with short-read sequencing, nanopore sequencing has low capital and consumable costs, making it suitable for use in locations with limited health infrastructure. MATERIALS AND METHODS We show the feasibility of nanopore mRNA sequencing on 134 cryopreserved acute leukemia specimens (26 acute myeloid leukemia [AML], 73 B-lineage acute lymphoblastic leukemia [B-ALL], 34 T-lineage acute lymphoblastic leukemia, and one acute undifferentiated leukemia). Using multiple library preparation approaches, we generated long-read transcripts for each sample. We developed a novel composite classification approach to predict acute leukemia lineage and major B-ALL and AML molecular subtypes directly from gene expression profiles. RESULTS We demonstrate accurate classification of acute leukemia samples into AML, B-ALL, or T-lineage acute lymphoblastic leukemia (96.2% of cases are classifiable with a probability of > 0.8, with 100% accuracy) and further classification into clinically actionable genomic subtypes using shallow RNA nanopore sequencing, with 96.2% accuracy for major AML subtypes and 94.1% accuracy for major B-lineage acute lymphoblastic leukemia subtypes. CONCLUSION Transcriptional profiling of acute leukemia samples using nanopore technology for diagnostic classification is feasible and accurate, which has the potential to improve the accuracy of cancer diagnosis in low-resource settings.
Genomic profiles of Indonesian colorectal cancer patients
Authors: Abdullah Murdani , Meilany Sofy , Trimarsanto Hidayat , Malik Safarina G. , Sukartini Ninik , Idrus Firhat , Nursyirwan Saskia A. , Muzellina Virly N. , Pribadi Rabbinu R. , Utari Amanda P. , Maulahela Hasan , Syam Ari F. 
Published: April 2022

Background: Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide and genetic mutation plays a vital role in CRC development. A previous study has suggested that genetic alterations among Indonesian patients with CRC might differ from those known in developed countries. This study aimed to describe the genomic profiles of Indonesian patients with CRC. Methods: A total of 13 patients were recruited for this study from May to July 2019. Tissue samples were collected, and genomic DNA was extracted from the samples. AmpliSeq for Illumina Cancer HotSpot Panel v2 Next-generation sequencing was used for DNA sequencing and a genome analysis toolkit was used for local realignment around the discovered variants. Results: A total of 45 genes comprising 391 single nucleotide variants (SNVs) with a depth >10 were observed. The genes with the most variants were STK11, SMAD4, EGFR, and ERBB4 and the genes with the most non-synonymous variants were SMAD4, TP53, FGFR3, CDKN2A, and STK11. Genes and SNVs in at least 90% of all samples consisted of 43 genes comprising 286 variants. Genes with the most non-synonymous SNVs were EGFR, SMO, FGFR3, TP53, STK11, CDKN2A. Genes related to the chromosomal instability pathway, such as TP53, SMAD4, KRAS, and APC, are also found in the analysis. Conclusions: Our findings showed that all patients with CRC in this study had genetic mutations in the chromosomal instability pathway. Analysis of genetic mutation of Indonesian patients with CRC might be crucial for advanced targeted therapy and for better clinical outcomes.
Application of the Lecture As an Interactive Method of Teaching the Theory of Life Safety
Authors: Romanchenko L. 
Published: April 2022

The article analyzes the prevailing opinion of modern scientists about the loss of effectiveness and justification for maintaining the status of the leading form of education for the lecture, in particular for the basic discipline "Life Safety". This is especially connected with the recent tragic events in the educational institutions of Russia. The widespread opinion that a lecture is not an effective form of education that does not arouse interest among most students and, when interactive forms and types of education are introduced, is moribund and basically useless, has no evidence base and is not always objective.
The author has drawn conclusions and expresses a firm conviction that the lecture remains the main and so far indispensable form of cognition for reproduction, even in the online learning format. The article provides justifications for this paradigm. Modern technology and digitalization of the education system using interactive forms and methods, allows, through reading and practical demonstration of actions of a different nature, to intelligibly convey to first-year students complex forms of legislative and legal principles and theoretical aspects of life safety to protect the population and economic facilities in various emergency situations.
Load Balancing Under Strict Compatibility Constraints
Authors: Rutten Daan , Mukherjee Debankur 
Published: April 2022

Consider a system with N identical single-server queues and a number of task types, where each server is able to process only a small subset of possible task types. Arriving tasks select [Formula: see text] random compatible servers and join the shortest queue among them. The compatibility constraints are captured by a fixed bipartite graph between the servers and the task types. When the graph is complete bipartite, the mean-field approximation is accurate. However, such dense compatibility graphs are infeasible for large-scale implementation. We characterize a class of sparse compatibility graphs for which the mean-field approximation remains valid. For this, we introduce a novel notion, called proportional sparsity, and establish that systems with proportionally sparse compatibility graphs asymptotically match the performance of a fully flexible system. Furthermore, we show that proportionally sparse random compatibility graphs can be constructed, which reduce the server degree almost by a factor [Formula: see text] compared with the complete bipartite compatibility graph. Funding: This work was supported by the National Science Foundation [Grant CCF-2113027].