cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6406052
title: Marginal Bayesian Semiparametric Modeling of Mismeasured Multivariate Interval-Censored Data

description: Motivated by data gathered in an oral health study, we propose a Bayesian nonparametric approach for population-averaged modeling of correlated time-to-event data, when the responses can only be determined to lie in an interval obtained from a sequence of examination times and the determination of the occurrence of the event is subject to misclassification. The joint model for the true, unobserved time-to-event data is defined semiparametrically; proportional hazards, proportional odds, and accelerated failure time (proportional quantiles) are all fit and compared. The baseline distribution is modeled as a flexible tailfree prior. The joint model is completed by considering a parametric copula function. A general misclassification model is discussed in detail, considering the possibility that different examiners were involved in the assessment of the occurrence of the events for a given subject across time. We provide empirical evidence that the model can be used to estimate the underlying time-to-event distribution and the misclassification parameters without any external information about the latter parameters. We also illustrate the effect on the statistical inferences of neglecting the presence of misclassification. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5358001
title: Late Ordovician high-Mg adakitic andesite in the western South China block: evidence of oceanic subduction

description: The Early Palaeozoic was an important period in the geologic evolution of the South China block (SCB), marking the intracontinental orogen in the Wuyi-Yunkai region. One salient feature of the western SCB is the absence of Early Palaeozoic oceanic subduction-related magmatism. Here, we report the first known occurrence of Late Ordovician andesites from the Shimian area, western SCB. Zircon SHRIMP U–Pb dating reveals that the andesites formed at ca. 451 Ma. They have geochemical features of high-Mg adakitic andesite (HMAA) and are characterized by low K<sub>2</sub>O (1.09–2.24 wt.%) and Th (2.50–5.65 ppm) and high MgO (4.02–6.91 wt.%) and Mg# (56–71). Furthermore, their zircon grains display positive <i>ε</i><sub>Hf</sub>(<i>t</i>) (+11.4 to +19.6) and low <i>δ</i><sup>18</sup>O (4.72–6.20‰) values. The andesites are interpreted to have been derived from partial melting of a peridotitic mantle wedge in an oceanic subduction setting and subsequent fractional crystallization. Integrating previous studies of the Qinling-Dabie orogenic belt with the data presented in this contribution, we suggest that the SCB was probably involved in the Early Palaeozoic Andean-type orogeny along the Gondwanan proto-Tethyan margin.
DOI: 10.6084/m9.figshare.14270420
title: Geochronological systematics of the Huayna Potosí, Zongo and Taquesi plutons, Cordillera Real of Bolivia, by the K/Ar, Rb/Sr and U/Pb methods

description: Abstract The Huayna Potosi, Zongo and Taquesi are Triassic plutons located at the core of the Real Cordillera of Bolivia. In this paper, several Rb-Sr and K-Ar ages obtained in the past at the São Paulo Geochronology Laboratory, yet unpublished, will be presented, along with newer U-Pb Sensitive High-Resolution Ion Microprobe (SHRIMP) determinations made in the same laboratory, allowing us to redefine the geologic history of this part of the Central Andes. Rb/Sr analyses of some low grade metapelitic country rocks of the early Paleozoic (Amutara and Cancañiri Formations) yielded a Rb-Sr isochron age of 344 ± 38 Ma, indicating the action of an early Gondwanide regional event. A five-point Rb-Sr isochron from a granite outcrop of the Huayna Potosi pluton yielded an age of 224 ± 28 Ma. In addition, an important Ar loss in micas was detected in the Zongo granitoids and their country rocks, recording a thermal event that opened this isotopic system in the Oligocene. Newer U-Pb SHRIMP zircon ages of ca. 221 Ma were obtained in two other granitic outcrops of the Huayna Potosi granite. They confirmed its Triassic crystallization age, and a similar U-Pb SHRIMP age of 221.9 ± 1.5 Ma was obtained for one sample of the Taquesi pluton. For the Zongo pluton, many of the zircon grains obtained from one sample of its Kuticucho facies yielded extremely high uranium content, which produced reverse discordant apparent ages. However, due to the fair alignment of the analytical points in the Concordia diagram, possibly corresponding to a linear correlation, we made a regression calculation and the interception of the Concordia curve resulted in a rather imprecise age of 220 ± 20 Ma. Our conclusion was that the final magmatic crystallization and the intrusion of plutons in the central part of the Cordillera Real of Bolivia have occurred close to 221.5 ± 2.0 Ma, in late Triassic times. Finally, the U-Pb SHRIMP ages obtained in inherited zircon xenocrysts from the four available granitic rocks yielded very different ages, and many of them are related to previous magmatic episodes of the Andean Tectonic System. A few other age measurements indicated sources related to much older Proterozoic magmatic events associated with rocks from the Andean basement.
DOI: 10.5281/zenodo.10638774
title: Deep Learning-based Simulations of Boundary Layer Clouds over the SGP
DOI: 10.5281/zenodo.10638775
title: Deep Learning-based Simulations of Boundary Layer Clouds over the SGP
DOI: 10.6084/m9.figshare.22141127
title: Adaptive Endpoints Selection with Application in Rare Disease

description: In rare diseases, there are many unanswered questions that are critical to clinical development. Among them, one important question is how to choose primary endpoints that translate into meaningful improvement of health outcomes for patients while maximizing trial probability of success at the same time. A natural history study is often recommended by regulatory agencies. Following this traditional approach has dampened enthusiasm for many drug developers because it entails much higher cost and longer timeline. We propose to use an innovative design that allows adaptation on primary endpoint(s) so that learning about disease endpoints can be done within the pivotal trial itself through a subset of patients (i.e., informational cohort). The overall Family Wise Error Rate (FWER) will be controlled through the use of combination test following partition testing principle. A case example in patients with Pompe disease is used to show that the proposed innovative design maintains robust power across treatment effect scenarios while traditional fixed design bears the high risk of failure due to incorrect endpoint selection. Even if multiple endpoints can be included as primary, the proposed innovative design can still improve power over traditional designs by optimizing alpha allocations in cases with differential treatment effects.
DOI: 10.6084/m9.figshare.22141127.v2
title: Adaptive Endpoints Selection with Application in Rare Disease

description: In rare diseases, there are many unanswered questions that are critical to clinical development. Among them, one important question is how to choose primary endpoints that translate into meaningful improvement of health outcomes for patients while maximizing trial probability of success at the same time. A natural history study is often recommended by regulatory agencies. Following this traditional approach has dampened enthusiasm for many drug developers because it entails much higher cost and longer timeline. We propose to use an innovative design that allows adaptation on primary endpoint(s) so that learning about disease endpoints can be done within the pivotal trial itself through a subset of patients (i.e., informational cohort). The overall Family Wise Error Rate (FWER) will be controlled through the use of combination test following partition testing principle. A case example in patients with Pompe disease is used to show that the proposed innovative design maintains robust power across treatment effect scenarios while traditional fixed design bears the high risk of failure due to incorrect endpoint selection. Even if multiple endpoints can be included as primary, the proposed innovative design can still improve power over traditional designs by optimizing alpha allocations in cases with differential treatment effects.
DOI: 10.6084/m9.figshare.20038201.v1
title: Differential transformation efficiency of Japonicarice varieties developed in northern China

description: The production of japonica rice in northern China plays an important role in food security for the world. Agrobacterium-mediated gene transfer is becoming a powerful approach to generate germplasm and develop varieties. However, the transgenic efficiency of the japonica rice varieties in northern China has been completely unknown, which obstructs the development of transgenic breeding and the exploration of gene functions. In this study, the transgenic efficiencies of six japonica rice varieties developed in northern China are evaluated. The rates of primary and secondary callus induction of the varieties are similar. However, transgenic efficiency and the regeneration ability of the varieties are greatly different. The results have established a platform for transformation of the rice varieties and proposed a suitable variety, SN9816, for gene transfer. SN9816 can be applied as an elite germplasm for transgenic breeding and basic research of molecular biology in northern China or an area in the same latitude.
DOI: 10.6084/m9.figshare.16367910
title: High performance of a novel point-of-care blood test for <i>Toxoplasma</i> infection in women from diverse regions of Morocco

description: Point-of-care (POC) testing for <i>Toxoplasma</i> infection has the potential to revolutionize diagnosis and management of toxoplasmosis, especially in high-risk populations in areas with significant environmental contamination and poor health infrastructure precluding appropriate follow-up and preventing access to medical care. Toxoplasmosis is a significant public health challenge in Morocco, with a relatively heavy burden of infection and, to this point, minimal investment nationally to address this infection. Herein, we analyse the performance of a novel, low-cost rapid test using fingerstick-derived whole blood from 632 women (82 of whom were pregnant) from slums, educational centres, and from nomad groups across different geographical regions (i.e. oceanic, mountainous) of Morocco. The POC test was highly sensitive and specific from all settings. In the first group of 283 women, sera were tested by Platelia ELISA IgG and IgM along with fingerstick whole blood test. Then a matrix study with 349 women was performed in which fingerstick – POC test results and serum obtained by venipuncture contemporaneously were compared. These results show high POC test performance (Sensitivity: 96.4% [IC95 90.6–98.9%]; Specificity: 99.6% [IC95 97.3–99.9%]) and high prevalence of <i>Toxoplasma</i> infection among women living in rural and mountainous areas, and in urban areas with lower educational levels. The high performance of POC test confirms that it can reduce the need for venipuncture and clinical infrastructure in a low-resource setting. It can be used to efficiently perform seroprevalence determinations in large group settings across a range of demographics, and potentially expands healthcare access, thereby preventing human suffering.
DOI: 10.6084/m9.figshare.12173985.v1
title: A hybrid transfer learning framework for in-plane freeform shape accuracy control in additive manufacturing

description: Shape accuracy control is one of the quality issues of greatest concern in Additive Manufacturing (AM). An efficient approach to improving the shape accuracy of a fabricated product is to compensate the fabrication errors of AM systems by modifying the input shape defined by a digital design model. In contrast with mass production, AM processes typically fabricate customized products with extremely low volume and huge shape varieties, which makes shape accuracy control in AM a challenging problem. In this article, we propose a hybrid transfer learning framework to predict and compensate the in-plane shape deviations of new and untried freeform products based on a small number of previously fabricated products. Within this framework, the shape deviation is decomposed into a shape-independent error and a shape-specific error. A parameter-based transfer learning approach is used to facilitate a sharing of parameters for modeling the shape-independent error, whereas a feature-based transfer learning approach is taken to promote the learning of a common representation of local shape features for modeling the shape-specific error. Experimental studies of a fused filament fabrication process demonstrate the effectiveness of our proposed framework in predicting the shape deviation and improving the shape accuracy of new products with freeform shapes.
DOI: 10.6084/m9.figshare.12173997
title: Online contextual learning with perishable resources allocation

description: We formulate a novel class of online matching problems with learning. In these problems, randomly arriving customers must be matched to perishable resources so as to maximize a total expected reward. The matching accounts for variations in rewards among different customer–resource pairings. It also accounts for the perishability of the resources. Our work is motivated by a healthcare application, but it can be easily extended to other service applications. Our work belongs to the online resource allocation streams in service systems. We propose the first online algorithm for contextual learning and resource allocation with perishable resources. Our algorithm explores and exploits in distinct interweaving phases. We prove that our algorithm achieves an expected regret per period that increases sub-linearly with the number of planning cycles.
DOI: 10.6084/m9.figshare.4834025
title: Late Mesozoic high-K calc-alkaline magmatism in Southeast China: the Tongling example

description: We report new zircon U–Pb ages, Hf isotopic and geochemical results for the Tongling granitic plutons of Southeast China. SHRIMP U–Pb ages for the Miaojia quartz monzodiorite porphyrite，the Tianebaodan and Tongguanshan quartz monzodiorites, the Xinqiaotou granodiorite porphyry, and the Shatanjiao and Nanhongchong granodiorite are 143 ± 2, 141 ± 1 and 142 ± 1, 147 ± 1, and 145 ± 1 and 139 ± 1 Ma, respectively. Combined with previous geochronological data, our results indicate that the porphyritic rocks are older than rocks of the same type lacking porphyritic texture. Geochemically, these high-K calc-alkaline intrusive rocks are characterized by arc-like trace element distribution patterns, with significant enrichment in LILE and LREE but depletion in HFSE. Lu–Hf isotopic compositions of zircons from the high-K calc-alkaline (HKCA) rocks have <i>ε</i><sub>Hf</sub>(<i>t</i>) values of magmatic 139–147 Ma zircons from −8.1 to −25.6, with two-stage model ages (<i>t</i><sub>DM2</sub>) of 1.71–2.67 Ga, whereas <i>ε</i><sub>Hf</sub>(<i>t</i>) values of inherited 582–844 Ma zircons range from 5.4 to −9.5, with <i>t</i><sub>DM2</sub> of 1.39–2.22 Ma, younger than <i>t</i><sub>DM2</sub> values of igneous zircon, indicating that newly formed mantle material was added to the continental crust of the Yangtze Block. Moreover, <i>ε</i><sub>Hf</sub>(<i>t</i>) values of inherited zircon cores older than 1000 Ma are from −7.8 to −26, similar to magmatic zircons, and the <i>t</i><sub>DM2</sub> values are all greater than 3.0 Ga (3.16–3.75 Ga), reflecting partial melting of ancient sialic material. We conclude that the plutonic melts were derived from both the enriched mantle and the ancient crust. The HKCA Tongling intrusions coincide temporally with the J<sub>3</sub>–K<sub>1</sub> magmatic event that was widespread in Southeast China. This igneous activity may have accompanied sinistral slip along the Tan-Lu fault due to oblique subduction of the Palaeo-Pacific plate.
DOI: 10.6084/m9.figshare.20038222
title: Construction and characterization of a bacterial artiﬁcial chromosome library of the maize inbred line Qi319

description: Abstract Zea mays L. has been the most cultivated crop and the crop with the largest yield in China since 2012. We constructed a bacterial artificial chromosome (BAC) library for the maize inbred line Qi319, which may be used as a key source for disease-resistant maize breeding in China. The BAC contains 270,720 clones, with an average insert size of 90 kb. The coverage of the library is about 10.43 genome equivalents when considering a haploid genome size of 2300 Mb, providing a 99.99% likelihood of isolating any maize gene or sequence in the library. An average of 12 clones were obtained by polymerase chain reaction screening by using primer pairs linked to the genes for resistance to maize southern rust and rough dwarf. The results indicate that the library can satisfy the requirements for recovering specific sequences. The library is available to researchers to whom it may be of interest.
DOI: 10.6084/m9.figshare.5358001.v1
title: Late Ordovician high-Mg adakitic andesite in the western South China block: evidence of oceanic subduction

description: The Early Palaeozoic was an important period in the geologic evolution of the South China block (SCB), marking the intracontinental orogen in the Wuyi-Yunkai region. One salient feature of the western SCB is the absence of Early Palaeozoic oceanic subduction-related magmatism. Here, we report the first known occurrence of Late Ordovician andesites from the Shimian area, western SCB. Zircon SHRIMP U–Pb dating reveals that the andesites formed at ca. 451 Ma. They have geochemical features of high-Mg adakitic andesite (HMAA) and are characterized by low K<sub>2</sub>O (1.09–2.24 wt.%) and Th (2.50–5.65 ppm) and high MgO (4.02–6.91 wt.%) and Mg# (56–71). Furthermore, their zircon grains display positive <i>ε</i><sub>Hf</sub>(<i>t</i>) (+11.4 to +19.6) and low <i>δ</i><sup>18</sup>O (4.72–6.20‰) values. The andesites are interpreted to have been derived from partial melting of a peridotitic mantle wedge in an oceanic subduction setting and subsequent fractional crystallization. Integrating previous studies of the Qinling-Dabie orogenic belt with the data presented in this contribution, we suggest that the SCB was probably involved in the Early Palaeozoic Andean-type orogeny along the Gondwanan proto-Tethyan margin.
DOI: 10.6084/m9.figshare.22141184
title: Factor Modeling for Clustering High-Dimensional Time Series

description: We propose a new unsupervised learning method for clustering a large number of time series based on a latent factor structure. Each cluster is characterized by its own cluster-specific factors in addition to some common factors which impact on all the time series concerned. Our setting also offers the flexibility that some time series may not belong to any clusters. The consistency with explicit convergence rates is established for the estimation of the common factors, the cluster-specific factors, and the latent clusters. Numerical illustration with both simulated data as well as a real data example is also reported. As a spin-off, the proposed new approach also advances significantly the statistical inference for the factor model of Lam and Yao. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.22141184.v4
title: Factor Modeling for Clustering High-Dimensional Time Series

description: We propose a new unsupervised learning method for clustering a large number of time series based on a latent factor structure. Each cluster is characterized by its own cluster-specific factors in addition to some common factors which impact on all the time series concerned. Our setting also offers the flexibility that some time series may not belong to any clusters. The consistency with explicit convergence rates is established for the estimation of the common factors, the cluster-specific factors, and the latent clusters. Numerical illustration with both simulated data as well as a real data example is also reported. As a spin-off, the proposed new approach also advances significantly the statistical inference for the factor model of Lam and Yao. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.14270955
title: Network Characteristics Analysis of Air Traffic Management Technical Support System Based on Multi-source Weighting

description: ABSTRACT In order to make reasonable suggestions for the expansion of the Air Traffic Management Technical Support System (ATMTSS), it is necessary to conduct a comprehensive analysis of the ATMTSS network. This paper constructs a multi-source weighted ATMTSS network which considers the working characteristics and geographical locations of the facilities. The complex network metrics, such as degree, node strength, clustering coefficient, average path length, diameter, and the improved Fast-Newman (FN) algorithm, are used in the analysis of the network. The results show that the ATMTSS network is a complex network with small-world characteristics and random characteristics, and that the distribution of ATMTSS network support capability is not the same as the topology network structure. The weighted network is looser than the non-weighted network. The air traffic management in remote areas is less affected by facilities than that in developed areas.
DOI: 10.6084/m9.figshare.20038201
title: Differential transformation efficiency of Japonicarice varieties developed in northern China

description: The production of japonica rice in northern China plays an important role in food security for the world. Agrobacterium-mediated gene transfer is becoming a powerful approach to generate germplasm and develop varieties. However, the transgenic efficiency of the japonica rice varieties in northern China has been completely unknown, which obstructs the development of transgenic breeding and the exploration of gene functions. In this study, the transgenic efficiencies of six japonica rice varieties developed in northern China are evaluated. The rates of primary and secondary callus induction of the varieties are similar. However, transgenic efficiency and the regeneration ability of the varieties are greatly different. The results have established a platform for transformation of the rice varieties and proposed a suitable variety, SN9816, for gene transfer. SN9816 can be applied as an elite germplasm for transgenic breeding and basic research of molecular biology in northern China or an area in the same latitude.
DOI: 10.6084/m9.figshare.14270955.v1
title: Network Characteristics Analysis of Air Traffic Management Technical Support System Based on Multi-source Weighting

description: ABSTRACT In order to make reasonable suggestions for the expansion of the Air Traffic Management Technical Support System (ATMTSS), it is necessary to conduct a comprehensive analysis of the ATMTSS network. This paper constructs a multi-source weighted ATMTSS network which considers the working characteristics and geographical locations of the facilities. The complex network metrics, such as degree, node strength, clustering coefficient, average path length, diameter, and the improved Fast-Newman (FN) algorithm, are used in the analysis of the network. The results show that the ATMTSS network is a complex network with small-world characteristics and random characteristics, and that the distribution of ATMTSS network support capability is not the same as the topology network structure. The weighted network is looser than the non-weighted network. The air traffic management in remote areas is less affected by facilities than that in developed areas.
DOI: 10.6084/m9.figshare.14795141.v1
title: Additional file 2 of Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

description: Additional file 2: Table S2. Summary of hypomethylation regions in CHP vs. YP.