bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maintenance of Correction of the Modified Lapidus Procedure With a First Metatarsal to Intermediate Cuneiform Cross-Screw Technique
Authors: Langan Travis M. , Greschner Joseph M. , Brandão Roberto A. , Goss David A. , Smith Clair N. , Hyer Christopher F. 
Published: December 2019

Background: Recurrence of deformity remains a concern when fusing the first tarsometatarsal joint for correction of hallux valgus (HV). A recently described construct adds an additional point of fixation from the plantar medial first metatarsal to the intermediate cuneiform. The purpose of this study was to determine the maintenance of correction of the first and second intermetatarsal angle, hallux valgus angle, and tibial sesamoid position after undergoing a first tarsometatarsal joint arthrodesis using the proposed construct. Methods: A radiographic review was performed of patients with HV treated with a first tarsometatarsal joint arthrodesis with the addition of a cross-screw intermediate cuneiform construct. Three observers reviewed radiographic data, including preoperative weightbearing, first weightbearing, and final weightbearing plain-film radiographs. Initial improvement and maintenance of intermetatarsal angle, hallux valgus angle (HVA), and tibial sesamoid position were evaluated radiographically. A total of 62 patients met inclusion criteria and were included in the study. Mean follow-up time was 9.3 months (SD 6.7). Results: Bony union was achieved in 60 of 62 patients (96.7%). Two of 62 patients required revision surgery as a result of recurrence (3.3%). Final mean improvement of the intermetatarsal angle (IMA) was 6.8 degrees (±2.9 degrees), HVA was 14.8 degrees (±7.5 degrees), and tibial sesamoid position was 2.4 (±1.4) positions. Mean loss of IMA correction was 1.5 degrees (±1.6), HVA was 2.9 degrees (±4.8 degrees), and tibial sesamoid position was 0.8 (±0.8). Conclusion: This study showed that the cross-screw intermediate cuneiform construct for first tarsometatarsal joint arthrodesis had a good union rate, a low complication rate, and maintained radiographic correction. Level of Evidence: Level IV, retrospective case series.
Identifying miRNA synergism using multiple-intervention causal inference
Authors: Zhang Junpeng , Pham Vu Viet Hoang , Liu Lin , Xu Taosheng , Truong Buu , Li Jiuyong , Rao Nini , Le Thuc Duy 
Published: December 2019

Abstract
Background
Studying multiple microRNAs (miRNAs) synergism in gene regulation could help to understand the regulatory mechanisms of complicated human diseases caused by miRNAs. Several existing methods have been presented to infer miRNA synergism. Most of the current methods assume that miRNAs with shared targets at the sequence level are working synergistically. However, it is unclear if miRNAs with shared targets are working in concert to regulate the targets or they individually regulate the targets at different time points or different biological processes. A standard method to test the synergistic activities is to knock-down multiple miRNAs at the same time and measure the changes in the target genes. However, this approach may not be practical as we would have too many sets of miRNAs to test.

Results
n this paper, we present a novel framework called miRsyn for inferring miRNA synergism by using a causal inference method that mimics the multiple-intervention experiments, e.g. knocking-down multiple miRNAs, with observational data. Our results show that several miRNA-miRNA pairs that have shared targets at the sequence level are not working synergistically at the expression level. Moreover, the identified miRNA synergistic network is small-world and biologically meaningful, and a number of miRNA synergistic modules are significantly enriched in breast cancer. Our further analyses also reveal that most of synergistic miRNA-miRNA pairs show the same expression patterns. The comparison results indicate that the proposed multiple-intervention causal inference method performs better than the single-intervention causal inference method in identifying miRNA synergistic network.

Conclusions
Taken together, the results imply that miRsyn is a promising framework for identifying miRNA synergism, and it could enhance the understanding of miRNA synergism in breast cancer.
DeepMF: deciphering the latent patterns in omics profiles with a deep learning method
Authors: Chen Lingxi , Xu Jiao , Li Shuai Cheng 
Published: December 2019

Abstract
Background
With recent advances in high-throughput technologies, matrix factorization techniques are increasingly being utilized for mapping quantitative omics profiling matrix data into low-dimensional embedding space, in the hope of uncovering insights in the underlying biological processes. Nevertheless, current matrix factorization tools fall short in handling noisy data and missing entries, both deficiencies that are often found in real-life data.

Results
Here, we propose DeepMF, a deep neural network-based factorization model. DeepMF disentangles the association between molecular feature-associated and sample-associated latent matrices, and is tolerant to noisy and missing values. It exhibited feasible cancer subtype discovery efficacy on mRNA, miRNA, and protein profiles of medulloblastoma cancer, leukemia cancer, breast cancer, and small-blue-round-cell cancer, achieving the highest clustering accuracy of 76%, 100%, 92%, and 100% respectively. When analyzing data sets with 70% missing entries, DeepMF gave the best recovery capacity with silhouette values of 0.47, 0.6, 0.28, and 0.44, outperforming other state-of-the-art MF tools on the cancer data sets Medulloblastoma, Leukemia, TCGA BRCA, and SRBCT. Its embedding strength as measured by clustering accuracy is 88%, 100%, 84%, and 96% on these data sets, which improves on the current best methods 76%, 100%, 78%, and 87%.

Conclusion
DeepMF demonstrated robust denoising, imputation, and embedding ability. It offers insights to uncover the underlying biological processes such as cancer subtype discovery. Our implementation of DeepMF can be found at https://github.com/paprikachan/DeepMF.
LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics
Authors: Li Chen , Jiang Yiqi , Li Shuaicheng 
Published: December 2019

Abstract
Background
Horizontal Gene Transfer (HGT) refers to the transfer of genetic materials between organisms through mechanisms other than parent-offspring inheritance. HGTs may affect human health through a large number of microorganisms, especially the gut microbiomes which the human body harbors. The transferred segments may lead to complicated local genome structural variations. Details of the local genome structure can elucidate the effects of the HGTs.

Results
In this work, we propose a graph-based method to reconstruct the local strains from the gut metagenomics data at the HGT sites. The method is implemented in a package named LEMON. The simulated results indicate that the method can identify transferred segments accurately on reference sequences of the microbiome. Simulation results illustrate that LEMON could recover local strains with complicated structure variation. Furthermore, the gene fusion points detected in real data near HGT breakpoints validate the accuracy of LEMON. Some strains reconstructed by LEMON have a replication time profile with lower standard error, which demonstrates HGT events recovered by LEMON is reliable.

Conclusions
Through LEMON we could reconstruct the sequence structure of bacteria, which harbors HGT events. This helps us to study gene flow among different microbial species.
Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments
Authors: Hur Benjamin , Kang Dongwon , Lee Sangseon , Moon Ji Hwan , Lee Gung , Kim Sun 
Published: December 2019

Abstract
Background
The main research topic in this paper is how to compare multiple biological experiments using transcriptome data, where each experiment is measured and designed to compare control and treated samples. Comparison of multiple biological experiments is usually performed in terms of the number of DEGs in an arbitrary combination of biological experiments. This process is usually facilitated with Venn diagram but there are several issues when Venn diagram is used to compare and analyze multiple experiments in terms of DEGs. First, current Venn diagram tools do not provide systematic analysis to prioritize genes. Because that current tools generally do not fully focus to prioritize genes, genes that are located in the segments in the Venn diagram (especially, intersection) is usually difficult to rank. Second, elucidating the phenotypic difference only with the lists of DEGs and expression values is challenging when the experimental designs have the combination of treatments. Experiment designs that aim to find the synergistic effect of the combination of treatments are very difficult to find without an informative system.

Results
We introduce Venn-diaNet, a Venn diagram based analysis framework that uses network propagation upon protein-protein interaction network to prioritizes genes from experiments that have multiple DEG lists. We suggest that the two issues can be effectively handled by ranking or prioritizing genes with segments of a Venn diagram. The user can easily compare multiple DEG lists with gene rankings, which is easy to understand and also can be coupled with additional analysis for their purposes. Our system provides a web-based interface to select seed genes in any of areas in a Venn diagram and then perform network propagation analysis to measure the influence of the selected seed genes in terms of ranked list of DEGs.

Conclusions
We suggest that our system can logically guide to select seed genes without additional prior knowledge that makes us free from the seed selection of network propagation issues. We showed that Venn-diaNet can reproduce the research findings reported in the original papers that have experiments that compare two, three and eight experiments. Venn-diaNet is freely available at: http://biohealth.snu.ac.kr/software/venndianet
RETRACTED ARTICLE: Evaluation of PAX8 expression promotes the proliferation of stomach Cancer cells
Authors: Bie Liang-Yu , Li Ning , Deng Wen-Ying , Lu Xiao-Yu , Guo Ping , Luo Su-Xia 
Published: December 2019

Abstract
Background
PAX8 was not only a mitotic factor, but identified as a transcription factor involved in the prognosis of human tumor patients. Elucidating the function of PAX8 on the pathology of stomach cancer was meaningful.

Results
PAX8 was found to be upregulated in primary stomach cancer tissue and the TCGA stomach cancer dataset. Interestingly, SOX13 and PAX8 showed consistent expression patterns, and the combined high PAX8 and SOX18 expression induced a worse prognosis of stomach cancer patients. SOX13 was further identified as a transcription factor of PAX8, and further affect Aurora B and Cyclin B1 expression, two cell cycle related factors of the downstream of PAX8, including. Furthermore, PAX8 depletion inducted G1-phase arrest and the decrease of EdU incorporation, cell viability and colony formation can be rescued by SOX13 overexpression.

Conclusions
SOX13 participated in the elevated expression of PAX8, which promote the proliferation of stomach cancer cells. Therefore, SOX13 mediated PAX8 expression was recognized as a tumor-promoting role in stomach cancer.
A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information
Authors: Gan Wei , Luo Juan , Li Yi Zhou , Guo Jia Li , Zhu Min , Li Meng Long 
Published: December 2019

Abstract
Background
The three-dimensional (3D) structure of chromatins plays significant roles during cell differentiation and development. Hi-C and other 3C-based technologies allow us to look deep into the chromatin architectures. Many studies have suggested that topologically associating domains (TAD), as the structure and functional unit, are conserved across different organs. However, our understanding about the underlying mechanism of the TAD boundary formation is still limited.

Results
We developed a computational method, TAD–Lactuca, to infer this structure by taking the contextual information of the epigenetic modification signals and the primary DNA sequence information on the genome. TAD–Lactuca is found stable in the case of multi-resolutions and different datasets. It could achieve high accuracy and even outperforms the state-of-art methods when the sequence patterns were incorporated. Moreover, several transcript factor binding motifs, besides the well-known CCCTC-binding factor (CTCF) motif, were found significantly enriched on the boundaries.

Conclusions
We provided a low cost, effective method to predict TAD boundaries. Above results suggested the incorporation of sequence features could significantly improve the performance. The sequence motif enrichment analysis indicates several gene regulation motifs around the boundaries, which is consistent with TADs may serve as the functional units of gene regulation and implies the sequence patterns would be important in chromatin folding.
Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line
Authors: Zhou Shenghui , Zhang Jinpeng , Han Haiming , Zhang Jing , Ma Huihui , Zhang Zhi , Lu Yuqing , Liu Weihua , Yang Xinming , Li Xiuquan , Li Lihui 
Published: December 2019

Abstract
Background
Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies.

Results
Single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies. By analyzing RNA-Seq data, we identified tissue-enriched transcripts and assessed their GO term enrichment; the results indicated that tissue-enriched transcripts were enriched for particular molecular functions that varied by tissue. We identified 3398 novel and 1352 A. cristatum-specific transcripts compared with the wheat gene model set. To better apply this A. cristatum transcriptome, the A. cristatum transcripts were integrated with the wheat genome as a reference sequence to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line, Pubing 3035.

Conclusions
Full-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.
Lipopolysaccharide worsens the prognosis of experimental cerebral ischemia via interferon gamma-induced protein 10 recruit in the acute stage
Authors: Wang Ping , Zhang Jiaqi , Guo Feifei , Wang Shuang , Zhang Yi , Li Defeng , Xu Haiyu , Yang Hongjun 
Published: December 2019

Abstract
Background
Infection is an important clinical complication facing stroke-patients and triples the risk of death within 30 days post-stroke via mechanisms which are poorly understood.

Aims
We tried to explore the mechanisms that inflammation caused by infections aggravated the ischemic brain injury after middle cerebral artery occlusion (MCAO).

Methods
We used lipopolysaccharide (LPS) as systemic inflammatory stimuli to explore the mechanisms of aggravated ischemic brain injury after Sprague-Dawley male rats subjected to MCAO. Brain damage was evaluated by cerebral blood perfusion, Longa-5 scores, infarct volume and edema degree. Systemic cytokine responses and inflammatory changes in the plasma and brain were analyzed by ELISA kit, RT2 Profiler™ PCR array, and quantitative real-time PCR. The differential genes were subjected to Gene Ontology enrichment analysis and protein–protein interaction (PPI) network construction.

Results
Lipopolysaccharide profoundly aggravated the brain damage after 24 h post-MCAO. At the acute stage (ischemia/reperfusion 90 min/3 h), the brain homogenate gene expression of interleukin 6 (IL-6), tumor necrosis factor α (TNF-α), interleukin 1β (IL-1β) and Interferon gamma-induced protein 10 (IP-10) was significantly up-regulated and the contents in plasma and brain homogenate were significantly increased in MCAO and MCAO + LPS group. IP-10 was the only gene with significant difference between MCAO and MCAO + LPS group, which was also in an important position with degrees of ≥ 14 in PPI network.

Conclusions
It was possible that trace LPS aggravated the ischemic brain injury by induction of excessive IP-10 secretion in the acute stage, leading to excessive inflammatory response, which consequently increased the infarct volume and edema degree 24 h post-MCAO.
Maize brachytic2 (br2) suppresses the elongation of lower internodes for excessive auxin accumulation in the intercalary meristem region
Authors: Zhang Xiangge , Hou Xianbin , Liu Yinghong , Zheng Lanjie , Yi Qiang , Zhang Haojun , Huang Xinrong , Zhang Junjie , Hu Yufeng , Yu Guowu , Liu Hanmei , Li Yangping , Huang Huanhuan , Zhan Feilong , Chen Lin , Tang Jihua , Huang Yubi 
Published: December 2019

AbstractBackgroundShort internodes contribute to plant dwarfism, which is exceedingly beneficial for crop production. However, the underlying mechanisms of internode elongation are complicated and have been not fully understood.ResultsHere, we report a maize dwarf mutant,dwarf2014(d2014), which displays shortened lower internodes. Map-based cloning revealed that thed2014gene is a novelbr2allele with a splicing variation, resulting in a higher expression ofBR2-T02instead of normalBR2-T01. Then, we found that the internode elongation ind2014/br2exhibited a pattern of inhibition-normality-inhibition (transient for the ear-internode), correspondingly, at the 6-leaf, 12-leaf and 14-leaf stages. Indeed,BR2encodes a P-glycoprotein1 (PGP1) protein that functions in auxin efflux, and our in situ hybridization assay showed thatBR2was mainly expressed in vascular bundles of the node and internode. Furthermore, significantly higher auxin concentration was detected in the stem apex ofd2014at the 6-leaf stage and strictly in the node region for the ear-internode at the 14-leaf stage. In such context, we propose that BR2/PGP1 transports auxin from node to internode through the vascular bundles, and excessive auxin accumulation in the node (immediately next to the intercalary meristem) region suppresses internode elongation ofd2014.ConclusionsThese findings suggest that low auxin levels mediated by BR2/PGP1 in the intercalary meristem region are crucial for internode elongation.
Identifying subgroups of persons with multimorbidity based on their needs for care and support
Authors: Rijken Mieke , van der Heide Iris 
Published: December 2019

Abstract
Background
There is broad consensus that countries need to develop and implement person-centred integrated care to better meet the needs of their growing populations with multimorbidity. To develop appropriate care, it is essential to know the needs for care and support among these populations. For this purpose, we examined whether subgroups of people with multimorbidity could be distinguished based on their needs, and profiled these subgroups according to medical complexity and the availability of personal resources.

Methods
Persons diagnosed with two or more somatic chronic diseases (N = 613) were selected from 38 general practices throughout the Netherlands. We conducted a cluster analysis of their scores on the RAND-36 questionnaire of health-related quality of life (QoL), to gain insight in their needs for care and support. Differences in demographics, medical characteristics and personal resources between the identified clusters were tested using analysis of variance and chi-square tests.

Results
The cluster analysis revealed three subgroups: 1. a group with a relatively good QoL (48% of the sample), 2. a group with a poor physical QoL (28%), and 3. a group with a poor QoL in all domains assessed by the RAND-36 (24%). The group with a relatively good QoL had more favourable medical characteristics than the other groups, i.e., less chronic diseases, shorter illness duration, more stable course of illness, better controllable conditions, less polypharmacy. The group with a poor QoL in all domains could rely on less personal resources (education, income, social support, health literacy, self-management capabilities) than the other groups.

Conclusions
Different subgroups of people with multimorbidity can be distinguished based on their needs for care and support. These needs are not only determined by demographic and medical characteristics, but also by the personal resources people have available to manage their health and care. Patient profiles combining medical complexity and personal resources could guide the development of integrated care for specific target groups of persons with multimorbidity.