134 Works

Gibbon genome (Nleu3.0) custom gene annotation file

Mariam Okhovat, Kimberly A. Nevonen, Brett A. Davis, Pryce Michener, Samantha Ward, Mark Milhaven, Lana Harshman, Ajuni Sohota, Jason D. Fernandes, Sofie R. Salama, Rachel J. O'Neill, Nadav Ahituv, Krishna R. Veeramah & Lucia Carbone
Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA, which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of...

Finding Grey Literature Evidence and Assessing for Outcome and Analysis Reporting Biases When Comparing Medical Interventions: AHRQ and the Effective Health Care Program

Howard Balshem & et al
The information in this report is intended to help health care decisionmakers—patients and clinicians, health system leaders, and policymakers, among others—make well informed decisions and thereby improve the quality of health care services.

Additional file 1 of Characterization of placental and decidual cell development in early pregnancy loss by single-cell RNA sequencing

Yuhua Zheng, Jing Pan, Chenglai Xia, Haiying Chen, Huadong Zhou, Weina Ju, Jerzy Wegiel, Leslie Myatt, James M. Roberts, Xiaoling Guo & Nanbert Zhong
Additional file 1: Figure S1. Heatmap of marker genes in cell clusters of early pregnancy loss. Heatmap of marker genes in cell clusters of different groups of early pregnancy loss. The numbers of clusters in groups A, B, C, and D were 16, 15, 16, and 18, respectively. Figure S2. Dot plot of top-10 marker genes (X axis) in trophoblast cell clusters VCT1 (upper), STB1 (middle), and EVT3 (lower), respectively, among early groups A_SM, B_SM,...

Dissection of a sensorimotor circuit underlying pathogen aversion in C. elegans

Adam Filipowicz, Jonathan Lalsiamthara & Alejandro Aballay
Abstract Background Altering animal behavior to reduce pathogen exposure is a key line of defense against pathogen attack. In Caenorhabditis elegans, alterations in intestinal physiology caused by pathogen colonization and sensation of microbial metabolites may lead to activation of pathogen aversive behaviors ranging from aversive reflexes to learned avoidance. However, the neural circuitry between chemosensory neurons that sense pathogenic bacterial cues and the motor neurons responsible for avoidance-associated locomotion remains unknown. Results Using C. elegans,...

Additional file 1 of Gray matter reduction in bilateral insula mediating adverse psychiatric effects of body mass index in schizophrenia

Hui Wu, Guochao Dai, Muyeseer Aizezi, Juan Tang, Ke Zou, Yuhua Wu & Xiaoli Wu
Additional file 1: Fig. S1. Partial correlation analysis between BMI and bilateral insula in SZ group, controlling for sex, age and education. Fig. S2. Partial correction analysis between negative symptom and bilateral insula in SZ group, controlling for sex, age and education. Fig. S3. Results of bilateral insula in the whole-brain VBM analyses. Red indicates the bilateral insula in the main effects of diagnosis (SZ

Gray matter reduction in bilateral insula mediating adverse psychiatric effects of body mass index in schizophrenia

Hui Wu, Guochao Dai, Muyeseer Aizezi, Juan Tang, Ke Zou, Yuhua Wu & Xiaoli Wu
Abstract Background Both schizophrenia (SZ) and overweight/obesity (OWB) have shown some structural alterations in similar brain regions. As higher body mass index (BMI) often contributes to worse psychiatric outcomes in SZ, this study was designed to examine the effects of OWB on gray matter volume (GMV) in patients with SZ. Methods Two hundred fifty subjects were included and stratified into four groups (n = 69, SZ patients with OWB, SZ-OWB; n = 74, SZ patients...

Additional file 1 of CASA: a comprehensive database resource for the COVID-19 Alternative Splicing Atlas

Yaxin Chen, Gang Wang, Jingyi Li, Lei Xia, Lin Zhu, Wenxing Li, Qiang Luo, Yinlu Liao, Yao Lin, Liyun Bi, Hubin Chen, Jiemei Chu, Yueqi Li, Jinming Su, Li Ye, Jun-jun Jiang, Hao Liang, Weimin Li & Sanqi An
Additional file 1: Table S1. Summary of samples in CASA.

Additional file 1 of Speech silence character as a diagnostic biomarker of early cognitive decline and its functional mechanism: a multicenter cross-sectional cohort study

Hua-Long Wang, Ran Tang, Ru-Jing Ren, Eric B. Dammer, Qi-Hao Guo, Guo-Ping Peng, Hai-Lun Cui, You-Min Zhang, Jin-Tao Wang, Xin-Yi Xie, Qiang Huang, Jian-Ping Li, Fu-Hua Yan, Sheng-Di Chen, Na-Ying He & Gang Wang
Additional file 1: Supplemental Figure 1. fMRI task paradigm. Supplemental Figure 2. Group difference in the Semantic Fluency-Fixation contrasts and its behavioral significance. One-way ANOVA, cluster-level P < 0.05, FWE corrected. Supplemental Table 1. The Post-hoc comparisons of the clinical characteristics in the China RSF multi-center cohort (Bonferroni corrected). Supplemental Table 2. Clinical characteristics of NC and AD patients in the Pitt center cohort. Supplemental Table 3. Correlation between PSD and cognition. Supplemental Table 4....

Additional file 3 of Characterization of the primary antibody response to Plasmodium falciparum antigens in infants living in a malaria-endemic area

Samuel Tassi Yunga, Chathura Siriwardhana, Genevieve G. Fouda, Naveen Bobbili, Grace Sama, John J. Chen, Rose F. G. Leke & Diane Wallace Taylor
Additional file 3: Figure S3. Some infants had several IgG responses during the first year of life Note: MFI were similar between the primary and secondary IgG Ab response. Figure A-H show IgG responses of different infants (Baby#). Babies A-E had only 1 to 2 detected infections; whereas, babies F to H had multiple infections.

Additional file 1 of Characterization of the primary antibody response to Plasmodium falciparum antigens in infants living in a malaria-endemic area

Samuel Tassi Yunga, Chathura Siriwardhana, Genevieve G. Fouda, Naveen Bobbili, Grace Sama, John J. Chen, Rose F. G. Leke & Diane Wallace Taylor
Additional file 1: Figure S1. Comparison of antibody levels in babies at 1 week of life whose subsequent primary infections were sub-microscopic (n = 18) or detected by slide-microscopy (n = 39) Horizontal lines = medians. SUB = sub-microscopic infection; Slide = infection detected by microscopy.

Additional file 4 of Characterization of the primary antibody response to Plasmodium falciparum antigens in infants living in a malaria-endemic area

Samuel Tassi Yunga, Chathura Siriwardhana, Genevieve G. Fouda, Naveen Bobbili, Grace Sama, John J. Chen, Rose F. G. Leke & Diane Wallace Taylor
Additional file 4: Figsure S4. No correlation between antibody levels at birth and time to first infection. Ab levels (MFI) in plasma collected at the first visit (mean 9 ± 2 days) of each baby were plotted against time (days) to first infection that was detected by PCR or slide. Simple linear regression was used to determine if Ab levels to any of the antigens was associated with a significant delay in time to infection....

Additional file 5 of Characterization of the primary antibody response to Plasmodium falciparum antigens in infants living in a malaria-endemic area

Samuel Tassi Yunga, Chathura Siriwardhana, Genevieve G. Fouda, Naveen Bobbili, Grace Sama, John J. Chen, Rose F. G. Leke & Diane Wallace Taylor
Additional file 5: Figure S5. No correlation between Ab levels at birth and number of infections detected by PCR. Antibody levels (MFI) for each baby at the first visit (mean 9 ± 2 days) were plotted against the number of times the baby was PCR-positive during the first year of life. No association between Ab levels at birth and number of PCR-detected infections was seen.

Additional file 2 of Systematic characterization of seed overlap microRNA cotargeting associated with lupus pathogenesis

Hiroki Kitai, Noritoshi Kato, Koichi Ogami, Shintaro Komatsu, Yu Watanabe, Seiko Yoshino, Eri Koshi, Shoma Tsubota, Yoshio Funahashi, Takahiro Maeda, Kazuhiro Furuhashi, Takuji Ishimoto, Tomoki Kosugi, Shoichi Maruyama, Kenji Kadomatsu & Hiroshi I. Suzuki
Additional file 2: Table S1. The list of up-regulated and down-regulated miRNAs in pDCs from the IMQ mouse model (miRNA microarray analysis). Table S2. Summary of the number of seed overlap target sites for 50 miRNA pairs and evolutionary trends, as shown in Figure 7A and B. Table S3. Summary of the gene set analysis performed using hallmark gene sets (Figure 7D). Table S4. Primer information for RT-PCR. Table S5. Primer information used for construction...

Additional file 1 of Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson & Abhinav Nellore
Additional file 1. This file includes all supplementary figures and tables referenced in the article.

Additional file 1 of Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson & Abhinav Nellore
Additional file 1. This file includes all supplementary figures and tables referenced in the article.

Additional file 2 of Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson & Abhinav Nellore
Additional file 2. This file includes performance benchmarks applying tool-specific filtering criteria.

Additional file 2 of Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson & Abhinav Nellore
Additional file 2. This file includes performance benchmarks applying tool-specific filtering criteria.

Additional file 1 of Performance of a fully-automated Lumipulse plasma phospho-tau181 assay for Alzheimer’s disease

Edward N. Wilson, Christina B. Young, Javier Ramos Benitez, Michelle S. Swarovski, Igor Feinstein, Manu Vandijck, Yann Le Guen, Nandita M. Kasireddy, Marian Shahid, Nicole K. Corso, Qian Wang, Gabriel Kennedy, Alexandra N. Trelle, Betty Lind, Divya Channappa, Malia Belnap, Veronica Ramirez, Irina Skylar-Scott, Kyan Younes, Maya V. Yutsis, Nathalie Le Bastard, Joseph F. Quinn, Christopher H. van Dyck, Angus Nairn, Carolyn A. Fredericks … & Katrin I. Andreasson
Additional file 1: Table S1. Characteristics of Participants Stratified by Diagnosis and APOE Genotype.

Additional file 4 of Performance of a fully-automated Lumipulse plasma phospho-tau181 assay for Alzheimer’s disease

Edward N. Wilson, Christina B. Young, Javier Ramos Benitez, Michelle S. Swarovski, Igor Feinstein, Manu Vandijck, Yann Le Guen, Nandita M. Kasireddy, Marian Shahid, Nicole K. Corso, Qian Wang, Gabriel Kennedy, Alexandra N. Trelle, Betty Lind, Divya Channappa, Malia Belnap, Veronica Ramirez, Irina Skylar-Scott, Kyan Younes, Maya V. Yutsis, Nathalie Le Bastard, Joseph F. Quinn, Christopher H. van Dyck, Angus Nairn, Carolyn A. Fredericks … & Katrin I. Andreasson
Additional file 4: Table S4. Betas (standard errors) and p values for models examining plasma p-tau181 and cross-sectional cognition and function.

Design method of imaging optical systems using confocal flat phase elements

Tong Yang, Lina Gao, Dewen Cheng & Yongtian Wang
Imaging systems consisting of flat phase element such as diffractive optical element, holographic optical element, and metasurface have important applications in many fields. However, there is still a lack of generalized and efficient design methods of these systems, especially for systems with nonsymmetric configurations. We proposed a design method of imaging system consisting of flat phase elements based on confocal properties. The description of the generalized phase function for realizing point-to-point stigmatic imaging are derived....

SATURN: an inexpensive, freely-available, and fully self-administered cognitive screening test

David Bissig, Deniz Erten-Lyons, Helmi Lutsep & Jeffrey Kaye
Cognitive screening tests improve detection of dementia in the outpatient setting, and are helpful in select inpatient settings. Barriers to widespread screening include provider time investment and variability in test administration and scoring. We therefore developed Self-Administered Tasks Uncovering Risk of Neurodegeneration (SATURN) for inexpensive (<$100) computer tablets. This submission to Dryad accompanies an abstract for the 2020 American Academy of Neurology conference, and is likely to referenced in a later manuscript. This Dryad data...

The Thr92Ala-DIO2 polymorphism affects outcomes in LT4-treated women

Sarah Peterson, Tatiana Fonseca, Kathryn Schuff, Elizabeth McAninch, Antonio Bianco & Mary Samuels
Context: The Thr92Ala-DIO2 polymorphism may affect hypothyroid patients’ responses to levothyroxine (LT4) treatment. Objective: To study whether the Thr92Ala-DIO2 polymorphism affects hypothyroid patients’ responses to levothyroxine (LT4) treatment. Design: Secondary analysis of a randomized intervention study. Setting: Primary care center. Patients or Other Participants: 109 hypothyroid women aged 21-70 years with normal TSH levels grouped in homozygous Thr92-DIO2 (THR; n=39) and homozygous Ala92-DIO2 plus heterozygous (ALA; n=70) groups. Intervention: Change in LT4 dose. Main Outcome...

Characterization of placental and decidual cell development in early pregnancy loss by single-cell RNA sequencing

Yuhua Zheng, Jing Pan, Chenglai Xia, Haiying Chen, Huadong Zhou, Weina Ju, Jerzy Wegiel, Leslie Myatt, James M. Roberts, Xiaoling Guo & Nanbert Zhong
Abstract Background Early pregnancy loss (EPL) presents as sporadic or recurrent miscarriage during the first trimester. In addition to chromosomal defects, EPL may result from impairment of the placental-decidual interface at early gestational age due to gene-environmental interactions. Methods To better understand the pathogenesis associated with this impairment, cell development in chorionic villi and decidua of different forms of EPL (sporadic or recurrent) was investigated with single-cell RNA sequencing and compared to that of normal...

Characterization of placental and decidual cell development in early pregnancy loss by single-cell RNA sequencing

Yuhua Zheng, Jing Pan, Chenglai Xia, Haiying Chen, Huadong Zhou, Weina Ju, Jerzy Wegiel, Leslie Myatt, James M. Roberts, Xiaoling Guo & Nanbert Zhong
Abstract Background Early pregnancy loss (EPL) presents as sporadic or recurrent miscarriage during the first trimester. In addition to chromosomal defects, EPL may result from impairment of the placental-decidual interface at early gestational age due to gene-environmental interactions. Methods To better understand the pathogenesis associated with this impairment, cell development in chorionic villi and decidua of different forms of EPL (sporadic or recurrent) was investigated with single-cell RNA sequencing and compared to that of normal...

Additional file 3 of Dissection of a sensorimotor circuit underlying pathogen aversion in C. elegans

Adam Filipowicz, Jonathan Lalsiamthara & Alejandro Aballay
Additional file 3: Fig. S3. The response to SDS and dodecanoic acid are ASH mediated and can be modeled in the Neural Interactome. (A) Response index to buffer, 0.6 mM SDS, or 1mM dodecanoic acid for animals with no neurons ablated (WT, red) or ASH neurons ablated (ASH(-), purple). Two-way ANOVA with subsequent comparison to the WT groups was performed. Error bars depict standard deviation. N = 15 for buffer, 10 for SDS, and 25...

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