Development of a quantitative index system for evaluating the quality of electronic medical records in disease risk intelligent prediction.

OBJECTIVE: This study aimed to develop and validate a quantitative index system for evaluating the data quality of Electronic Medical Records (EMR) in disease risk prediction using Machine Learning (ML). MATERIALS AND METHODS: The index system was developed in four steps: (1) a preliminary index system was outlined based on literature review; (2) we utilized the Delphi method to structure the indicators at all levels; (3) the weights of these indicators were determined using the Analytic Hierarchy Process (AHP) method; and (4) the developed index system was empirically validated using real-world EMR data in a ML-based disease risk prediction task. RESULTS: The synthesis of review findings and the expert consultations led to the formulation of a three-level index system with four first-level, 11 second-level, and 33 third-level indicators. The weights of these indicators were obtained through the AHP method. Results from the empirical analysis illustrated a positive relationship between the scores assigned by the proposed index system and the predictive performances of the datasets. DISCUSSION: The proposed index system for evaluating EMR data quality is grounded in extensive literature analysis and expert consultation. Moreover, the system's high reliability and suitability has been affirmed through empirical validation. CONCLUSION: The novel index system offers a robust framework for assessing the quality and suitability of EMR data in ML-based disease risk predictions. It can serve as a guide in building EMR databases, improving EMR data quality control, and generating reliable real-world evidence.

Evolution and diversification of Mountain voles (Rodentia: Cricetidae).

The systematics of the Cricetid genus Neodon have long been fraught with uncertainty due to sampling issues and a lack of comprehensive datasets. To gain better insights into the phylogeny and evolution of Neodon, we systematically sampled Neodon across the Hengduan and Himalayan Mountains, which cover most of its range in China. Analyses of skulls, teeth, and bacular structures revealed 15 distinct patterns corresponding to 15 species of Neodon. In addition to morphological analyses, we generated a high-quality reference genome for the mountain vole and generated whole-genome sequencing data for 47 samples. Phylogenomic analyses supported the recognition of six new species, revealing a long-term underestimation of Neodon diversity. We further identified positively selected genes potentially related to high-elevation adaptation. Together, our results illuminate how climate change caused the plateau to become the centre of Neodon origin and diversification and how mountain voles have adapted to the hypoxic high-altitude plateau environment.

Phylogenomics reveals the evolution, biogeography, and diversification history of voles in the Hengduan Mountains.

The Hengduan Mountains (HDM) of China are a biodiversity hotspot whose temperate flora and fauna are among the world's richest. However, the origin and evolution of biodiversity in the HDM remain poorly understood, especially in mammals. Given that the HDM shows the highest richness of vole species in the world, we used whole-exome capture sequencing data from the currently most comprehensive sampling of HDM voles to investigate their evolutionary history and diversification patterns. We reconstructed a robust phylogeny and re-estimated divergence times of the HDM voles. We found that all HDM voles could be divided into a western lineage (Volemys, Proedromys, and Neodon) and an eastern lineage (Caryomys and Eothenomys), and the two lineages originated from two migration events from North Eurasia to the HDM approximately 9 Mya. Both vole lineages underwent a significant acceleration of net diversification from 8-5 Mya, which was temporally congruent with the orogeny of the HDM region. We also identified strong intertribal gene flow among the HDM voles and hypothesized that frequent gene flow might have facilitated the speciation burst of the HDM voles. Our study highlights the importance of both environmental and biotic factors in shaping the biodiversity of mammals in mountain ecosystems.

A new species of Tamiops (Rodentia, Sciuridae) from Sichuan, China.

During a small mammal survey in Wanglang National Natural Reserve, Sichuan, China in AugustOctober 2018, we collected four specimens of an Asiatic striped squirrel (genus Tamiops) that could not be assigned morphologically to any described species. Phylogenetic analyses of CYTB and nuDNA sequences strongly supported them in the genus Tamiops. The p-distances of CYTB between these individuals and other species of Tamiops ranged from 17.4 to 19.1%. Morphologically, they differed from their congeners, including T. maritimus, T. mcclellandii, T. rodolphii, and T. swinhoei by pelage, skull, and baculum characteristics. Based on the results of morphological comparisons and molecular analyses, we describe the four specimens as the new species Tamiops minshanica sp. nov.

Out of Tibet: Genomic Perspectives on the Evolutionary History of Extant Pikas.

Pikas are widely distributed in the Northern Hemisphere and are highly adapted to cold and alpine environments. They are one of the most complex and problematic groups in mammalian systematics, and the origin and evolutionary history of extant pikas remain controversial. In this study, we sequenced the whole coding sequences of 105 pika samples (29 named species and 1 putative new species) and obtained DNA data for more than 10,000 genes. Our phylogenomic analyses recognized four subgenera of extant pikas: Alienauroa, Conothoa, Ochotona, and Pika. The interrelationships between the four subgenera were strongly resolved as (Conothoa, (Alienauroa, (Ochotona, Pika))), with the mountain group Conothoa being the sister group of all other pikas. Our divergence time and phylogeographic analyses indicated that the last common ancestor of extant pikas first occurred on in the middle Miocene, ∼14 Ma. The emergence of opportunities related to the climate, food supply, and spreading paths in concert promoted the dispersal of pikas from the Qinghai-Tibetan Plateau (QTP) to other parts of Eurasia and North America. We found that the genes that were positively selected in the early evolution of pikas were most concentrated in functional categories related to cold tolerance. These results suggest that the QTP may have served as a training ground for cold tolerance in early pikas, which gives pikas a great advantage when the climate continued to cool after the middle Miocene. Our study highlights the importance of the QTP as a center of origin for many cold-adapted animals.

Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China.

BACKGROUND: Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS: We obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB, BRCA1, RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that the C. rapax rapax is embedded within C. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C. sp.1, C. sp.2 and C. sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China's Crocidura species began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene. CONCLUSIONS: The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China's Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of Chinese Crocidura species.

How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses.

Apodemus (mice) and Rattus (rats) are the top rodent reservoirs for zoonoses in China, yet little is known about their diversity. We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank. We also tested whether species could be identified using external and craniodental measurements exclusively. Measurements from 147 specimens of Apodemus and 236 specimens of Rattus were used for morphological comparisons. We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations. Results demonstrated that nine species of Apodemus and seven species of Rattus, plus a new subspecies of Rattus nitidus, are distributed in China. Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species. The occurrence of Rattus pyctoris in China remains uncertain.

Taxonomic position of Chinese voles of the tribe Arvicolini and the description of 2 new species from Xizang, China.

China has 26 species in the tribe Arvicolini. The taxonomic status of these voles remains controversial despite much effort. Herein, we evaluate the taxonomic position of 22 species plus 2 unidentified taxa using mitochondrial DNA gene sequences (cytb + CO1). We also evaluate 18 species and 2 unidentified taxa using morphological data. Phylogenetic analyses of cytb resolve monophyly for the genera Alexandromys, Lasiopodomys, Microtus, Neodon, Proedromys, and Volemys with strong support. Stenocranius clusters with Chionomys but with very weak support. Analyses of concatenated cytb + CO1 resolve the same genera with strong support, but the topology of the tree differs from that of cytb in that Chionomys roots at the base of the tree independent of Stenocranius, which forms the sister-group of Lasiopodomys in a more terminal position. The matrilineal genealogy excludes the type species Arvicola amphibius from the rest of the Arvicolini. This species forms the sister-group of Ondatra with high support. Neodon includes N. irene, N. linzhiensis, N. fuscus, N. leucurus, N. sikimensis, Microtus clarkei, and 2 unidentified specimens. Alexandromys includes the former species Microtus oeconomus, M. kikuchii, M. limnophilus, M. fortis, and M. maximowiczii. Finally, Microtus has the subgenera Blanfordimys, Microtus, Mynomes, Pedomys, Pitymys, and Terricola, which includes the Chinese species M. agrestis, M. arvalis, and Blanfordimys juldaschi. General mixed Yule-coalescent species delimitation modeling demarcates 6 currently recognized species and 2 new species of Neodon. A principal component analysis of the morphological data among 7 matrilines shows that all variables have positive loadings of high magnitude on the 1st component. Canonical discriminant analysis for Neodon (including M. clarkei and 2 unidentified species) correctly classifies 93.0% of specimens. Overall, our analyses support the recognition of Alexandromys, Lasiopodomys, Microtus, Neodon, Proedromys, and Volemys as genera. Stenocranius includes Microtus gregalis, and the genealogical position of Stenocranius remains uncertain. The status of Arvicola requires further study. We assign M. clarkei to Neodon and describe 2 new species of Neodon.