bluuebunny/crossref_metadata_2025_split huggingface dataset:
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map
Authors: Hao Minsheng , Hua Kui , Zhang Xuegong 
Published: June 2021

Abstract

Motivation
Recent developments of spatial transcriptomic sequencing technologies provide powerful tools for understanding cells in the physical context of tissue microenvironments. A fundamental task in spatial gene expression analysis is to identify genes with spatially variable expression patterns, or spatially variable genes (SVgenes). Several computational methods have been developed for this task. Their high computational complexity limited their scalability to the latest and future large-scale spatial expression data.

Results
We present SOMDE, an efficient method for identifying SVgenes in large-scale spatial expression data. SOMDE uses self-organizing map to cluster neighboring cells into nodes, and then uses a Gaussian process to fit the node-level spatial gene expression to identify SVgenes. Experiments show that SOMDE is about 5–50 times faster than existing methods with comparable results. The adjustable resolution of SOMDE makes it the only method that can give results in ∼5 min in large datasets of more than 20 000 sequencing sites. SOMDE is available as a python package on PyPI at https://pypi.org/project/somde free for academic use.

Availability and implementation
SOMDE is available for download from PyPI, and the source code is openly available from the Github repository https://github.com/XuegongLab/somde.

Supplementary information
Supplementary data are available at Bioinformatics online.
State of assisted reproduction technology in the coronavirus disease 2019 era and consequences on human reproductive system
Authors: Chandi Anadeep , Jain Neelam 
Published: June 2021

AbstractThe outbreak of the coronavirus disease 2019 (COVID-19) has created havoc on the socio-economic aspect of the world. With billions of lives being affected by this wrecking pandemic, global fertility services were also not left untouched by its impact. The possibility of sexual transmission of SARS-CoV-2 virus, its impact on male and female fertility, pregnancy, its potential teratogenic effect, and handling of gametes in the clinical laboratories were major concerns among reproductive medicine specialists, which led down all the reproductive health services, including IUI, IVF/ICSI in most of the countries. Even the people did not intend to conceive during the pandemic crisis and were hesitant to avail such services. Discrete evidence regarding the pathophysiology of COVID-19 infection and its impact on the human reproductive system is not very clear. In this review article, we intend to incorporate all the evidence related to the COVID-19 infection and its impact on human reproduction available to date. It is our responsibility to provide rightful information and to keep our patients familiar with the existing lack of clear evidence. In this COVID-19 era, it is important that the fertility management be prioritized in sub-fertile couples with diminished fertility reserve and high-risk conditions, like malignancies, that may affect their long-term fertility prospects.
Testing for unit roots based on sample autocovariances
Authors: Chang Jinyuan , Cheng Guanghui , Yao Qiwei 
Published: June 2021

SummaryWe propose a new unit-root test for a stationary null hypothesis $H_0$ against a unit-root alternative $H_1$. Our approach is nonparametric as $H_0$ assumes only that the process concerned is $I(0)$, without specifying any parametric forms. The new test is based on the fact that the sample autocovariance function converges to the finite population autocovariance function for an $I(0)$ process, but diverges to infinity for a process with unit roots. Therefore, the new test rejects $H_0$ for large values of the sample autocovariance function. To address the technical question of how large is large, we split the sample and establish an appropriate normal approximation for the null distribution of the test statistic. The substantial discriminative power of the new test statistic is due to the fact that it takes finite values under $H_0$ and diverges to infinity under $H_1$. This property allows one to truncate the critical values of the test so that it has asymptotic power 1; it also alleviates the loss of power due to the sample-splitting. The test is implemented in $\texttt{R}$.
Inverse moment methods for sufficient forecasting using high-dimensional predictors
Authors: Luo Wei , Xue Lingzhou , Yao Jiawei , Yu Xiufan 
Published: June 2021

Summary
We consider forecasting a single time series using a large number of predictors in the presence of a possible nonlinear forecast function. Assuming that the predictors affect the response through the latent factors, we propose to first conduct factor analysis and then apply sufficient dimension reduction on the estimated factors to derive the reduced data for subsequent forecasting. Using directional regression and the inverse third-moment method in the stage of sufficient dimension reduction, the proposed methods can capture the nonmonotone effect of factors on the response. We also allow a diverging number of factors and only impose general regularity conditions on the distribution of factors, avoiding the undesired time reversibility of the factors by the latter. These make the proposed methods fundamentally more applicable than the sufficient forecasting method of Fan et al. (2017). The proposed methods are demonstrated both in simulation studies and an empirical study of forecasting monthly macroeconomic data from 1959 to 2016. Also, our theory contributes to the literature of sufficient dimension reduction, as it includes an invariance result, a path to perform sufficient dimension reduction under the high-dimensional setting without assuming sparsity, and the corresponding order-determination procedure.
Regression-Adjusted Real-Time Quality Control
Authors: Duan Xincen , Wang Beili , Zhu Jing , Zhang Chunyan , Jiang Wenhai , Zhou Jiaye , Shao Wenqi , Zhao Yin , Yu Qian , Lei Luo , Yiu Kwok Leung , Chin Kim Thiam , Pan Baishen , Guo Wei 
Published: June 2021

Abstract

Background
Patient-based real-time quality control (PBRTQC) has gained increasing attention in the field of clinical laboratory management in recent years. Despite the many upsides that PBRTQC brings to the laboratory management system, it has been questioned for its performance and practical applicability for some analytes. This study introduces an extended method, regression-adjusted real-time quality control (RARTQC), to improve the performance of real-time quality control protocols.

Methods
In contrast to the PBRTQC, RARTQC has an additional regression adjustment step before using a common statistical process control algorithm, such as the moving average, to decide whether an analytical error exists. We used all patient test results of 4 analytes in 2019 from Zhongshan Hospital, Fudan University, to compare the performance of the 2 frameworks. Three types of analytical error were added in the study to compare the performance of PBRTQC and RARTQC protocols: constant, random, and proportional errors. The false alarm rate and error detection charts were used to assess the protocols.

Results
The study showed that RARTQC outperformed PBRTQC. RARTQC, compared with the PBRTQC, improved the trimmed average number of patients affected before detection (tANPed) at total allowable error by about 50% for both constant and proportional errors.

Conclusions
The regression step in the RARTQC framework removes autocorrelation in the test results, allows researchers to add additional variables, and improves data transformation. RARTQC is a powerful framework for real-time quality control research.
Liquid Biopsy Hotspot Variant Assays: Analytical Validation for Application in Residual Disease Detection and Treatment Monitoring
Authors: Hallermayr Ariane , Benet-Pagès Anna , Steinke-Lange Verena , Mansmann Ulrich , Rentsch Markus , Holinski-Feder Elke , Pickl Julia M A 
Published: June 2021

Abstract

Background
Analysis of circulating tumor DNA (ctDNA) in plasma is a powerful approach to guide decisions in personalized cancer treatment. Given the low concentration of ctDNA in plasma, highly sensitive methods are required to reliably identify clinically relevant variants.

Methods
We evaluated the suitability of 5 droplet digital PCR (ddPCR) assays targeting KRAS, BRAF, and EGFR variants for ctDNA analysis in clinical use.

Results
We investigated assay performance characteristics for very low amounts of variants, showing that the assays had very low limits of blank (0% to 0.11% variant allele frequency, VAF) and limits of quantification (0.41% to 0.7% VAF). Nevertheless, striking differences in detection and quantification of low mutant VAFs between the 5 tested assays were observed, highlighting the need for assay-specific analytical validation. Besides in-depth evaluation, a guide for clinical interpretation of obtained VAFs in plasma was developed, depending on the limits of blank and limits of quantification values.

Conclusion
It is possible to provide comprehensive clinical reports on actionable variants, allowing minimal residual disease detection and treatment monitoring in liquid biopsy.
A Social Network Link Prediction Method Based on Stacked Generalization
Authors: Liu Xiaoyang , Li Xiang 
Published: June 2021

AbstractTraditional link prediction methods of social network are vulnerable to the influence of network structure and have poor generalization, and only on a small number of networks and evaluation indicators. To improve the stability and accuracy of link prediction, this paper assembles 15 similarity indexes, introduces the idea of stacking into the link prediction of complex networks, and presents a link prediction method (Logistic-regression LightGBM Stacking Link Prediction, LLSLP). Firstly, social network link prediction is regarded as a binary classification problem. Secondly, the hyper parameters of the basic model are determined by using cross-validation and grid searching; thirdly, Logistic-regression and LightGBM are integrated by stacked generalization; Finally, take 10 different networks as practical examples. The feasibility and effectiveness of the proposed method are verified by comparing 7 evaluation indicators. The experimental results show that: the proposed method is not only more than 98.71% higher than the traditional CN (Common Neighbor) and other models are 10.52% higher on average. In addition, compared with the traditional 15 link prediction algorithms, $F1- score$ value and $MCC$ (Matthews Correlation Coefficient) value is increased by 3.2% ~ 9.7% and 5.9% ~ 14% respectively. The proposed method has good accuracy and generalization. It can also be applied to recommendation system.
Conflicts and Tentative Solutions to Protecting Personal Data in Investment Arbitration
Authors: Huang Jie (Jeanne) 
Published: June 2021

Abstract
Personal data protection in investment arbitration is increasingly important as more and more countries enact mandatory personal data protection laws and the COVID-19 pandemic makes online hearings the new normal. Tribunals have to consider critical, yet unresolved, normative questions, such as (i) how data protection laws would influence the trend towards transparency in investment arbitrations brought pursuant to modern investment treaties; (ii) whether a party can invoke a data protection law to reject access to fundamental documents and completely shift the power in an arbitration proceeding; (iii) whether it is good to have multiple data protection laws directly applicable in an investment arbitration; and (iv) whether the so-called Brussels Effect may take hold of investment arbitration. These questions directly address the alleged legitimacy crisis of investment arbitration (for example, procedural transparency and efficiency) in the digital era. They also have a critical impact on the fairness of proceedings and are closely related to the protection of fundamental human rights and the concern of digital surveillance. This article comprehensively maps the consensual and mandatory applications of data protection laws in investment arbitration. Adopting comparative-law and conflict-of-laws methodologies, it intends to provide tentative solutions to the four questions mentioned above.
Technological Neutrality and Regulation of Digital Trade: How Far Can We Go?
Authors: Shadikhodjaev Sherzod 
Published: June 2021

Abstract
In this age of rapid digital transformations, the principle of technological neutrality can help the international economic community adapt dated rules to changing realities. While the acceptance of this principle would respond to the difficulty of timely norm making and norm updating in international relations, it could also cause legal uncertainty in the case of unforeseen technological developments in the future. Therefore, not every country today is willing to unconditionally acknowledge the applicability of ‘old’ rules for any emerging trading patterns enabled by, or based on, digital and other technological innovations. The World Trade Organization, the United Nations Commission on International Trade Law and several regional trade agreements have addressed technological neutrality in the context of electronic commerce and digital trade. This article examines this issue, focusing on such areas of trade regulation as services, intellectual property and paperless trading, and concludes that the principle of technological neutrality should be given universal recognition, supplemented by policy flexibilities where necessary.
Better data, higher impact: improving agricultural data systems for societal change
Authors: Carletto Calogero 
Published: June 2021

AbstractThe agricultural sector is undergoing a period of rapid transformation, driven by the powerful and interconnected impacts of climate change, demographic transitions and uneven economic growth around the world. For governments and the international community to navigate this period of upheaval to protect vulnerable populations and ensure positive societal change will require a similar degree of transformation within agricultural data systems. While technological innovation has resulted in substantive improvements in the availability, timeliness and overall quality of agricultural data, many technical and institutional challenges remain. This paper reviews recent developments in the agricultural data landscape, highlights existing constraints to further progress and argues for agricultural economists to take responsibility for building agricultural data systems equipped to respond to the diverse needs of a changing world.
Impact of the COVID-19 pandemic on in-hospital mortality in cardiovascular disease: a meta-analysis
Authors: Cannata Antonio , Watson Samuel A , Daniel Allen , Giacca Mauro , Shah Ajay M , McDonagh Theresa A , Scott Paul A , Bromage Daniel I 
Published: June 2021

AbstractAims The COVID-19 pandemic has resulted in excess mortality due to both COVID-19 directly and other conditions, including cardiovascular (CV) disease. We aimed to explore the excess in-hospital mortality, unrelated to COVID-19 infection, across a range of CV diseases.Methods and results A systematic search was performed for studies investigating in-hospital mortality among patients admitted with CV disease without SARS-CoV-2 infection compared with a period outside the COVID-19 pandemic. Fifteen studies on 27 421 patients with CV disease were included in the analysis. The average in-hospital mortality rate was 10.4% (n = 974) in the COVID-19 group and 5.7% (n = 1026) in the comparator group. Compared with periods outside the COVID-19 pandemic, the pooled risk ratio (RR) demonstrated increased in-hospital mortality by 62% during COVID-19 [95% confidence interval (CI) 1.20–2.20, P = 0.002]. Studies with a decline in admission rate &gt;50% during the COVID-19 pandemic observed the greatest increase in mortality compared with those with &lt;50% reduction [RR 2.74 (95% CI 2.43–3.10) vs. 1.21 (95% CI 1.07–1.37), P &lt; 0.001]. The observed increased mortality was consistent across different CV conditions (P = 0.74 for interaction).Conclusions In-hospital mortality among patients admitted with CV diseases was increased relative to periods outside the pandemic, independent of co-infection with COVID-19. This effect was larger in studies with the biggest decline in admission rates, suggesting a sicker cohort of patients in this period. However, studies were generally poorly conducted, and there is a need for further well-designed studies to establish the full extent of mortality not directly related to COVID-19 infection.
Paleomagnetism from multi-orogenic terranes is “not a simple game”: Pyrenees' Paleozoic warning
Authors: Pastor-Galán Daniel , Groenhof Oscar , Pueyo Emilio L , Izquierdo-Llavall Esther , Dinarès-Turell Jaume , Dekkers Mark J 
Published: June 2021

Summary
Paleomagnetism is a versatile tool in the Earth sciences: it provides critical input to geological time scales and plate tectonic reconstructions. Despite its undeniable perks, paleomagnetism is not without complications. Remagnetizations overprinting the original magnetic signature of rocks are frequent, especially in orogens which tend to be the areas with better rock exposure. Unraveling the magnetic history of the rocks is a complicated task, especially in areas that underwent several orogenic pulses. In turn, constraining the timing of remagnetization represents an opportunity to solve post-magnetization structural and tectonic kinematics. Here, we evaluate the magnetization history of Silurian-Devonian carbonates from the Axial Zone of the Pyrenees. The Pyrenees are a multi-orogenic mountain belt where Silurian-Devonian rocks have seen the Variscan collision (late Paleozoic), the opening of the Atlantic/Bay of Biscay (early Cretaceous) and the Alpine orogeny (late Cretaceous to Miocene). Our results show widespread remagnetization(s) carried by magnetite and pyrrhotite in the Silurian-Devonian series of the Pyrenees. The majority of the samples show a post-folding but pre-alpine tilting magnetization. Considering the equatorial inclinations found in such samples, we suggest that they likely acquired their magnetization during the late Carboniferous and early Permian times. Two of the studied sites (located at the western Axial Zone) were subsequently remagnetized at the end of the Alpine orogeny. The paleomagnetic results constrained that the Variscan orogeny was responsible for the main folding event affecting Paleozoic rocks in the Axial Zone, whereas the Alpine orogeny produced the large-scale thrusting and antiformal stacking of these units. In addition, we observed a general clockwise rotational pattern which could be related with the formation of the Cantabrian Orocline and/or rotations associated with the Alpine orogeny. The Silurian-Devonian carbonates are thus useful to understand the tectonic evolution of the Pyrenean mountain range after a systematic combination of paleomagnetism with structural and petrological observations. In contrast, the secondary character of magnetization and complications associated with the Variscan tectonics indicate that a reassessment of Siluro-Devonian poles from the Variscan elsewhere in Europe might be appropriate.
Grandmothers’ care practices in areas of high deprivation of Scotland: the potential for health promotion
Authors: Chambers Stephanie A , Dobbie Fiona , Radley Andrew , Rowa-Dewar Neneh 
Published: June 2021

SummaryIn many families grandparents play an essential role by providing secondary care for grandchildren. The family is a key setting for promoting children’s health; however, studies describing health initiatives with grandparents are rare. Grandparents could play an important role in promoting health for their grandchildren within their families and communities. The aim of this study was to examine the care practices of grandparents in families living in areas of high deprivation, and to consider the extent to which grandparents could be at the centre of health-promoting initiatives for children. A family practices approach was used to examine care practices within the framework of family resource (assets/capitals) use. In-depth interviews were carried out with grandmothers (n = 15) and mothers (n = 15) living in areas of high deprivation in Scotland. The results are presented as three economies of family living—political, moral and emotional. Grandparent care was described as a form of social capital, central to the wellbeing of the families, and enabled parents to access education and employment. Grandparent care was supported through families’ ability to access cultural amenities and green space (political). Grandparents’ care practices were described as either being responsible or fun (moral). Love appeared to be at the centre of grandparents’ care (emotional). The strengths and weaknesses of this framework were examined in relation to developing initiatives with grandparents. With further development work, grandparents could be the focus of health initiatives with their grandchildren with the support of appropriate policies and resources within their communities.
ZNF224 is a mediator of TGF-β pro-oncogenic function in melanoma
Authors: Cesaro Elena , Pastore Arianna , Polverino Alessia , Manna Lorenzo , Divisato Giuseppina , Quintavalle Cristina , Sanzo Maddalena Di , Faniello Maria Concetta , Grosso Michela , Costanzo Paola 
Published: June 2021

Abstract
The zinc finger protein ZNF224 plays a dual role in cancer, operating as both tumour suppressor and oncogenic factor depending on cellular and molecular partners.
In this research we investigated the role of ZNF224 in melanoma, a highly invasive and metastatic cancer, and provided evidence for the involvement of ZNF224 in the TGF-β signalling as a mediator of the TGF-β pro-oncogenic function.
Our results showed that ZNF224, whose expression increased in melanoma cell lines after TGF-β stimulation, potentiated the activation induced by TGF-β on its target genes involved in epithelial–mesenchymal transition (EMT). Accordingly, overexpression of ZNF224 enhanced the tumourigenic properties of melanoma cells, promoting cell proliferation and invasiveness, whereas ZNF224 knockdown had the opposite effect. Moreover, ZNF224 positively modulates the expression of TGF-β itself and its type 1 and 2 receptors (TβR1 and TβR2), thus highlighting a possible mechanism by which ZNF224 could enhance the endogenous TGFβ/Smad signalling.
Our findings unveil a positive regulatory loop between TGF-β and ZNF224 to promote EMT, consequently increasing the tumour metastatic potential.