102 Works

Unravelling the identity of the platanistoid Notocetus vanbenedeni Moreno, 1892 (Cetacea, Odontoceti) from the early Miocene of Patagonia (Argentina)

Mariana Viglino, Mónica Romina Buono, Yoshihiro Tanaka, José Ignacio Cuitiño & Robert Ewan Fordyce
Platanistoidea remains one of the most evolutionarily intriguing lineages of toothed whales (Odontoceti). The clade comprises mostly extinct species from the late Oligocene–early Miocene onward and a single extant riverine genus (Platanista). There is an ongoing debate as to the membership of Platanistoidea and the causes of their near extinction. In Patagonia (Argentina), the most abundant platanistoid recorded in the lower Miocene Gaiman Formation is Notocetus vanbenedeni, first described by Moreno in 1892 based on...

The Cauchy Combination Test under Arbitrary Dependence Structures

Mingya Long, Zhengbang Li, Wei Zhang & Qizhai Li
Combining individual p-values to perform an overall test is often encountered in statistical applications. The Cauchy combination test (CCT) (Journal of the American Statistical Association, 2020, 115, 393–402) is a powerful and computationally efficient approach to integrate individual p-values under arbitrary dependence structures for sparse signals. We revisit this test to additionally show that (i) the tail probability of the CCT can be approximated just as well when more relaxed assumptions are imposed on individual...

Additional file 2 of A genetic map of the chromatin regulators to drug response in cancer cells

Bo Chen, Pengfei Li, Mingyue Liu, Kaidong Liu, Min Zou, Yiding Geng, Shuping Zhuang, Huanhuan Xu, Linzhu Wang, Tingting Chen, Yawei Li, Zhangxiang Zhao, Lishuang Qi & Yunyan Gu
Additional file 2: Table S3. CRs genetic interactions related to drug response in cancers.

Additional file 4 of MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer

Natsumi Tsuboyama, Aileen Patricia Szczepanski, Zibo Zhao & Lu Wang
Additional file 4: Table S3. Mass spectrometry results for GFP-tagged SBA-MBD purification from drosophila S2 cells.

Local field potentials reflect cortical population dynamics in a region-specific and frequency-dependent manner

Cecilia Gallego-Carracedo, Matthew G. Perich, Raeed H. Chowdhury, Lee E. Miller & Juan A. Gallego
The spiking activity of populations of cortical neurons is well described by a small number of population-wide covariance patterns, the “latent dynamics”. These latent dynamics are largely driven by the same correlated synaptic currents across the circuit that determine the generation of local field potentials (LFP). Yet, the relationship between latent dynamics and LFPs remains largely unexplored. Here, we characterised this relationship for three different regions of primate sensorimotor cortex during reaching. The correlation between...

CCNE1 is a potential target of Metformin for tumor suppression of ovarian high-grade serous carcinoma

Jie Mei, Huixiang Tian, Hsuan-Shun Huang, Nayiyuan Wu, Yu-Ligh Liou, Tang-Yuan Chu, Jing Wang & Wei Zhang
High-grade serous ovarian cancer (HGSOC) is the most common and malignant type of ovarian cancer, accounting for 70%–80% of mortality. However, the treatment of HGSOC has improved little in the past few decades. Metformin is the first-line medication for the treatment of type 2 diabetes and has now gained more attention in cancer treatment. In this study, we sought to identify potential hub genes that metformin could target in the treatment of HGSOC. We downloaded...

Additional file 3 of Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma

Guisheng Zhao, Patrick Newbury, Yukitomo Ishi, Eugene Chekalin, Billy Zeng, Benjamin S. Glicksberg, Anita Wen, Shreya Paithankar, Takahiro Sasaki, Amreena Suri, Javad Nazarian, Michael E. Pacold, Daniel J. Brat, Theodore Nicolaides, Bin Chen & Rintaro Hashizume
Additional file 3: Table S3. Meta-signature derived from the two bulk RNAseq datasets.

Sprouty4 is epigenetically upregulated in human colorectal cancer

Alexei J. Stuckel, Shuai Zeng, Zhen Lyu, Wei Zhang, Xu Zhang, Urszula Dougherty, Reba Mustafi, Tripti Khare, Qiong Zhang, Trupti Joshi, Marc Bissonnette & Sharad Khare
Sprouty4 (SPRY4) has been frequently reported as a tumor suppressor and is therefore downregulated in various cancers. For the first time, we report that SPRY4 is epigenetically upregulated in colorectal cancer (CRC). In this study, we explored DNA methylation and hydroxymethylation levels of SPRY4 in CRC cells and patient samples and correlated these findings with mRNA and protein expression levels. Three loci within the promoter region of SPRY4 were evaluated for 5mC levels in CRC...

Additional file 2 of Molecular, cellular and neurological consequences of infection by the neglected human pathogen Nocardia

Xingzhao Ji, Lichao Han, Weiying Zhang, Lina Sun, Shuai Xu, Xiaotong Qiu, Shihong Fan & Zhenjun Li
Additional file 2. DEGs of N. farcinica at 3 and 6 phi.

Additional file 3 of Molecular, cellular and neurological consequences of infection by the neglected human pathogen Nocardia

Xingzhao Ji, Lichao Han, Weiying Zhang, Lina Sun, Shuai Xu, Xiaotong Qiu, Shihong Fan & Zhenjun Li
Additional file 3. DEGs of A549 cells at 3 and 6 phi.

Additional file 3 of Molecular, cellular and neurological consequences of infection by the neglected human pathogen Nocardia

Xingzhao Ji, Lichao Han, Weiying Zhang, Lina Sun, Shuai Xu, Xiaotong Qiu, Shihong Fan & Zhenjun Li
Additional file 3. DEGs of A549 cells at 3 and 6 phi.

Additional file 4 of Molecular, cellular and neurological consequences of infection by the neglected human pathogen Nocardia

Xingzhao Ji, Lichao Han, Weiying Zhang, Lina Sun, Shuai Xu, Xiaotong Qiu, Shihong Fan & Zhenjun Li
Additional file 4: Video 1. [head falling on one side, body quiescent tremor and rhythmical and vertical head movements]. Video 2. [a tendency to turn in the same direction when lifted by the tail]. Video 3. [stagnation and turning backward in the same direction in unfamiliar environments, with the hind limbs open and stride length altered]. Video 4. [mice circling after infection].

The Upper Extremity Functional Scale for Prosthesis Users (UEFS-P): subscales for one and two-handed tasks

Linda Resnik, Matthew Borgia, Allen W. Heinemann, Phillip Stevens, Melissa A. Clark & Pengsheng Ni
To develop a self-report measure of activity performance for upper limb prosthesis users that quantifies outcomes by level of amputation and prosthesis type. Telephone survey of 423 adults with major upper limb amputation (ULA) who used a prosthesis. Item generation, cognitive, and pilot testing were followed by field testing. Items were categorized as one- or two-handed. Factor and Rasch analyses evaluated unidimensionality, monotonicity, item fit, differential item functioning (DIF), and reliability. Test–retest reliability was evaluated...

Additional file 2 of Association of body mass index and inflammatory dietary pattern with breast cancer pathologic and genomic immunophenotype in the nurses’ health study

Sarah Asad, Adrienne Damicis, Yujing J. Heng, Kathryn Kananen, Katharine A. Collier, Elizabeth J. Adams, Kevin H. Kensler, Gabrielle M. Baker, Robert Wesolowski, Sagar Sardesai, Margaret Gatti-Mays, Bhuvaneswari Ramaswamy, A. Heather Eliassen, Susan E. Hankinson, Fred K. Tabung, Rulla M. Tamimi & Daniel G. Stover
Additional file 2: Supplementary Table S2. Immune Gene Expression Scores. Gene expression scores for all samples used in analyses.

Mechanical nanolattices printed using nanocluster-based photoresists

John Kulikowski, David Doan, Qi Li, Ottman Tertuliano, Charles Zeman, Melody Wang, George Schatz & Wendy Gu
Natural materials exhibit emergent mechanical properties due to their nanoarchitected, nanocomposite structures with optimized hierarchy, anisotropy and nanoporosity. Fabrication of such complex systems is currently challenging because high-quality 3D nanoprinting is mostly limited to simple, homogenous materials. We report a strategy for the rapid nanoprinting of complex structural nanocomposites using metal nanoclusters. These ultrasmall, quantum-confined nanoclusters function as highly sensitive two-photon activators, and simultaneously serve as precursors for mechanical reinforcements and nanoscale porogens. Nanocomposites with...

Additional file 4 of Accuracy of next-generation sequencing for molecular profiling of small specimen of lung cancer: a prospective pilot study of side-by-side comparison

Xiaosong Ben, Dan Tian, Weitao Zhuang, Rixin Chen, Sichao Wang, Zihao Zhou, Cheng Deng, Ruiqing Shi, Songlin Liu, Dongkun Zhang, Jiming Tang, Liang Xie, Haiyu Zhou, Zhou Zhang, Min Li, Xuanye Zhang & Guibin Qiao
Additional file 4.

Additional file 11 of Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions

Kristin Johnson, Simon Freedman, Rosemary Braun & Carole LaBonne
Additional file 11. Supplemental Table 2. Gene Lists from all Overlapping Categories from UpSet Plots of all Transcription Factors expressed >10 TPM corresponding with Supplemental Figure 2.

Additional file 21 of Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions

Kristin Johnson, Simon Freedman, Rosemary Braun & Carole LaBonne
Additional file 21. Supplemental Table 12. Lists of epidermal and mesoderm GO Terms and their over represented p value in genes differentially expressed between the epidermal and mesoderm lineages corresponding with supplemental figure 7B.

Additional file 15 of Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions

Kristin Johnson, Simon Freedman, Rosemary Braun & Carole LaBonne
Additional file 15. Supplemental Table 6. Temporal DESeq Epi Neur Venn Diagram Gene Lists corresponding with Figure 3B.

Additional file 20 of Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions

Kristin Johnson, Simon Freedman, Rosemary Braun & Carole LaBonne
Additional file 20. Supplemental Table 11. List of Genes from Venn Diagrams of Genes Temporally Differentially Expressed in mesoderm and epidermal lineages corresponding with Fig. 7C.

Additional file 20 of Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions

Kristin Johnson, Simon Freedman, Rosemary Braun & Carole LaBonne
Additional file 20. Supplemental Table 11. List of Genes from Venn Diagrams of Genes Temporally Differentially Expressed in mesoderm and epidermal lineages corresponding with Fig. 7C.

DiffExpAnalysis

Xuebin Fu, Rachana Mishra, ling chen, mir arfat, Sudhish Sharma, Tami Kingsbury, Charles Hong, Peixin Yang, Deqiang Li & Sunjay Kaushal
The exosomal microRNAs were screened in dilated cardiomyopathy patients' derived cardiomyocytes.

Long non-coding RNA-PCGEM1 contributes to prostate cancer progression by sponging microRNA miR-129-5p to enhance chromatin licensing and DNA replication factor 1 expression

Qiao Fu, Fangfang Wang, Jun Yang, Wei Sun, Zhi Hu, Lv Xu, Hao Chu, Xiao Wang & Wei Zhang
PCGEM1 facilitates prostate cancer (PCa) progression. This study aimed to elucidate the mechanism of action of PCGEM1 in PCa. The expression of PCGEM1, microRNA miR-129-5p, chromatin licensing, and DNA replication factor 1 (CDT1) was detected by quantitative reverse transcription-PCR (qRT-PCR). A series of function experiments including cell counting kit-8 (CCK-8), caspase-3 activity, and cell cycle assays were performed to evaluate the influence of PCGEM1, miR-129-5p, and CDT1 on the biological processes of PCa cells. CyclinD1,...

The Cauchy Combination Test under Arbitrary Dependence Structures

Mingya Long, Zhengbang Li, Wei Zhang & Qizhai Li
Combining individual p-values to perform an overall test is often encountered in statistical applications. The Cauchy combination test (CCT) (Journal of the American Statistical Association, 2020, 115, 393–402) is a powerful and computationally efficient approach to integrate individual p-values under arbitrary dependence structures for sparse signals. We revisit this test to additionally show that (i) the tail probability of the CCT can be approximated just as well when more relaxed assumptions are imposed on individual...

Additional file 2 of A genetic map of the chromatin regulators to drug response in cancer cells

Bo Chen, Pengfei Li, Mingyue Liu, Kaidong Liu, Min Zou, Yiding Geng, Shuping Zhuang, Huanhuan Xu, Linzhu Wang, Tingting Chen, Yawei Li, Zhangxiang Zhao, Lishuang Qi & Yunyan Gu
Additional file 2: Table S3. CRs genetic interactions related to drug response in cancers.

Registration Year

  • 2022
    102

Resource Types

  • Dataset
    102

Affiliations

  • Northwestern University
    102
  • Shanghai Jiao Tong University
    34
  • Southern Medical University
    32
  • Peking University People's Hospital
    28
  • Sun Yat-sen University
    24
  • University of Chinese Academy of Sciences
    23
  • Sichuan University
    20
  • First Affiliated Hospital of Soochow University
    20
  • West China Hospital of Sichuan University
    17
  • Zhejiang University
    17